Animal-Genome cDNA 20060611S-012682


Search to RefSeqSP

BLASTX 2.2.10 [Oct-19-2004]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= 20060611S-012682
         (1187 letters)

Database: RefSeqSP 
           1040 sequences; 434,620 total letters

Searching...done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_998939.1| CD74 antigen [Sus scrofa]                            244   5e-90

>ref|NP_998939.1| CD74 antigen [Sus scrofa]
          Length = 214

 Score =  244 bits (624), Expect(2) = 5e-90
 Identities = 120/154 (77%), Positives = 134/154 (87%)
 Frame = +3

Query: 264 RLDELTVPSHNLRLEILRMKLHKPSAPLSRMRVSAPMLMHALPMEGPEPMRYAT*YGDMT 443
           RLD+LTV S NL+LE LRMKL KPS PLS+MRVSAPMLM ALPMEGPEPMR AT YG+MT
Sbjct: 61  RLDKLTVTSQNLQLESLRMKLPKPSKPLSKMRVSAPMLMQALPMEGPEPMRNATKYGNMT 120

Query: 444 HDHVMHLLVNSDPLGVYPNLMGSLPEHLKHLKNTMYGVNWKLFENWLREWLLFDMSNNSL 623
            DHVMHLL+ SDPLGVYP L GSLPE+LKHLKNTM GVNWKLFENWLR+WLLF+MS NSL
Sbjct: 121 QDHVMHLLLKSDPLGVYPKLKGSLPENLKHLKNTMDGVNWKLFENWLRQWLLFEMSKNSL 180

Query: 624 EDTCFVVPHTDPLQTDDLTSRLGVTKHDLGQVLV 725
           E+T F VP  DPL+T+DL+S LGVTK DLGQV++
Sbjct: 181 EETPFEVPPKDPLETEDLSSGLGVTKQDLGQVIL 214



 Score =  100 bits (250), Expect(2) = 5e-90
 Identities = 49/60 (81%), Positives = 52/60 (86%)
 Frame = +2

Query: 83  MEDQRDLISDHEQLPLLGHRPGAPDINCSRGALYPGFSVLVALLLAGHATTTYFLY*LQG 262
           MEDQRDLIS+HEQLP+LG RPGAP+  CSRGALY GFSVLVALLLAG ATT YFLY  QG
Sbjct: 1   MEDQRDLISNHEQLPMLGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQG 60


  Database: RefSeqSP
    Posted date:  Aug 1, 2006  7:14 PM
  Number of letters in database: 434,620
  Number of sequences in database:  1040
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,227,556
Number of Sequences: 1040
Number of extensions: 35491
Number of successful extensions: 107
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 93
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 107
length of database: 434,620
effective HSP length: 79
effective length of database: 352,460
effective search space used: 111377360
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)

Search to RefSeqBP

BLASTX 2.2.10 [Oct-19-2004]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= 20060611S-012682
         (1187 letters)

Database: RefSeqBP 
           33,508 sequences; 16,112,626 total letters

Searching..................................................done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_001029907.1| similar to CD74 antigen isoform b [Bos taurus]    191   2e-71

>ref|NP_001029907.1| similar to CD74 antigen isoform b [Bos taurus]
          Length = 204

 Score =  191 bits (485), Expect(2) = 2e-71
 Identities = 92/144 (63%), Positives = 116/144 (80%)
 Frame = +3

Query: 264 RLDELTVPSHNLRLEILRMKLHKPSAPLSRMRVSAPMLMHALPMEGPEPMRYAT*YGDMT 443
           RLD+LTV S NL+LE LRMKL KP+ P+S+MR++ PMLM ALPM GPEPM+ AT YG+MT
Sbjct: 61  RLDKLTVTSQNLQLENLRMKLPKPAKPMSQMRMATPMLMRALPMAGPEPMKNATKYGNMT 120

Query: 444 HDHVMHLLVNSDPLGVYPNLMGSLPEHLKHLKNTMYGVNWKLFENWLREWLLFDMSNNSL 623
            DHVMHLL+ +DPL VYP L GSLPE+LKHLK++M G++WKLFE+WL +WLLF+MS NSL
Sbjct: 121 QDHVMHLLLKADPLKVYPQLKGSLPENLKHLKDSMDGLDWKLFESWLHQWLLFEMSKNSL 180

Query: 624 EDTCFVVPHTDPLQTDDLTSRLGV 695
           E+  F  P  DP++ +  +S LGV
Sbjct: 181 EEKPFEGPPKDPMEMEYPSSGLGV 204



 Score = 97.8 bits (242), Expect(2) = 2e-71
 Identities = 48/60 (80%), Positives = 51/60 (85%)
 Frame = +2

Query: 83  MEDQRDLISDHEQLPLLGHRPGAPDINCSRGALYPGFSVLVALLLAGHATTTYFLY*LQG 262
           MEDQRDLIS+HEQLP+LG RPGA +  CSRGALY GFSVLVALLLAG ATT YFLY  QG
Sbjct: 1   MEDQRDLISNHEQLPMLGQRPGAQESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQG 60


  Database: RefSeqBP
    Posted date:  Aug 1, 2006  7:14 PM
  Number of letters in database: 16,112,626
  Number of sequences in database:  33,508
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 46,610,291
Number of Sequences: 33508
Number of extensions: 1400804
Number of successful extensions: 5284
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 4357
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 5260
length of database: 16,112,626
effective HSP length: 104
effective length of database: 12,627,794
effective search space used: 3674688054
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)

Search to RefSeqHP

BLASTX 2.2.10 [Oct-19-2004]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= 20060611S-012682
         (1187 letters)

Database: RefSeqHP 
           39,411 sequences; 17,774,539 total letters

Searching..................................................done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_004346.1| CD74 antigen isoform b [Homo sapiens]                178   7e-67
Alignment   gi|NP_001020330.1| CD74 antigen isoform a [Homo sapiens]             158   7e-61
Alignment   gi|NP_001020329.1| CD74 antigen isoform c [Homo sapiens]              96   1e-38

>ref|NP_004346.1| CD74 antigen isoform b [Homo sapiens]
          Length = 232

 Score =  178 bits (451), Expect(2) = 7e-67
 Identities = 91/154 (59%), Positives = 115/154 (74%), Gaps = 2/154 (1%)
 Frame = +3

Query: 264 RLDELTVPSHNLRLEILRMKLHKPSAPLSRMRVSAPMLMHALPMEG-PE-PMRYAT*YGD 437
           RLD+LTV S NL+LE LRMKL KP  P+S+MR++ P+LM ALPM   P+ PM+ AT YG+
Sbjct: 77  RLDKLTVTSQNLQLENLRMKLPKPPKPVSKMRMATPLLMQALPMGALPQGPMQNATKYGN 136

Query: 438 MTHDHVMHLLVNSDPLGVYPNLMGSLPEHLKHLKNTMYGVNWKLFENWLREWLLFDMSNN 617
           MT DHVMHLL N+DPL VYP L GS PE+L+HLKNTM  ++WK+FE+W+  WLLF+MS +
Sbjct: 137 MTEDHVMHLLQNADPLKVYPPLKGSFPENLRHLKNTMETIDWKVFESWMHHWLLFEMSRH 196

Query: 618 SLEDTCFVVPHTDPLQTDDLTSRLGVTKHDLGQV 719
           SLE      P  + L+ +D +S LGVTK DLG V
Sbjct: 197 SLEQKPTDAPPKESLELEDPSSGLGVTKQDLGPV 230



 Score = 95.5 bits (236), Expect(2) = 7e-67
 Identities = 46/64 (71%), Positives = 52/64 (81%)
 Frame = +2

Query: 71  QVRTMEDQRDLISDHEQLPLLGHRPGAPDINCSRGALYPGFSVLVALLLAGHATTTYFLY 250
           Q   M+DQRDLIS++EQLP+LG RPGAP+  CSRGALY GFS+LV LLLAG ATT YFLY
Sbjct: 13  QKPVMDDQRDLISNNEQLPMLGRRPGAPESKCSRGALYTGFSILVTLLLAGQATTAYFLY 72

Query: 251 *LQG 262
             QG
Sbjct: 73  QQQG 76


>ref|NP_001020330.1| CD74 antigen isoform a [Homo sapiens]
          Length = 296

 Score =  158 bits (399), Expect(2) = 7e-61
 Identities = 78/123 (63%), Positives = 98/123 (79%), Gaps = 2/123 (1%)
 Frame = +3

Query: 264 RLDELTVPSHNLRLEILRMKLHKPSAPLSRMRVSAPMLMHALPMEG-PE-PMRYAT*YGD 437
           RLD+LTV S NL+LE LRMKL KP  P+S+MR++ P+LM ALPM   P+ PM+ AT YG+
Sbjct: 77  RLDKLTVTSQNLQLENLRMKLPKPPKPVSKMRMATPLLMQALPMGALPQGPMQNATKYGN 136

Query: 438 MTHDHVMHLLVNSDPLGVYPNLMGSLPEHLKHLKNTMYGVNWKLFENWLREWLLFDMSNN 617
           MT DHVMHLL N+DPL VYP L GS PE+L+HLKNTM  ++WK+FE+W+  WLLF+MS +
Sbjct: 137 MTEDHVMHLLQNADPLKVYPPLKGSFPENLRHLKNTMETIDWKVFESWMHHWLLFEMSRH 196

Query: 618 SLE 626
           SLE
Sbjct: 197 SLE 199



 Score = 95.5 bits (236), Expect(2) = 7e-61
 Identities = 46/64 (71%), Positives = 52/64 (81%)
 Frame = +2

Query: 71  QVRTMEDQRDLISDHEQLPLLGHRPGAPDINCSRGALYPGFSVLVALLLAGHATTTYFLY 250
           Q   M+DQRDLIS++EQLP+LG RPGAP+  CSRGALY GFS+LV LLLAG ATT YFLY
Sbjct: 13  QKPVMDDQRDLISNNEQLPMLGRRPGAPESKCSRGALYTGFSILVTLLLAGQATTAYFLY 72

Query: 251 *LQG 262
             QG
Sbjct: 73  QQQG 76


>ref|NP_001020329.1| CD74 antigen isoform c [Homo sapiens]
          Length = 160

 Score = 95.5 bits (236), Expect(2) = 1e-38
 Identities = 46/64 (71%), Positives = 52/64 (81%)
 Frame = +2

Query: 71  QVRTMEDQRDLISDHEQLPLLGHRPGAPDINCSRGALYPGFSVLVALLLAGHATTTYFLY 250
           Q   M+DQRDLIS++EQLP+LG RPGAP+  CSRGALY GFS+LV LLLAG ATT YFLY
Sbjct: 13  QKPVMDDQRDLISNNEQLPMLGRRPGAPESKCSRGALYTGFSILVTLLLAGQATTAYFLY 72

Query: 251 *LQG 262
             QG
Sbjct: 73  QQQG 76



 Score = 84.0 bits (206), Expect(2) = 1e-38
 Identities = 45/70 (64%), Positives = 55/70 (78%), Gaps = 2/70 (2%)
 Frame = +3

Query: 264 RLDELTVPSHNLRLEILRMKLHKPSAPLSRMRVSAPMLMHALPMEG-PE-PMRYAT*YGD 437
           RLD+LTV S NL+LE LRMKL KP  P+S+MR++ P+LM ALPM   P+ PM+ AT YG+
Sbjct: 77  RLDKLTVTSQNLQLENLRMKLPKPPKPVSKMRMATPLLMQALPMGALPQGPMQNATKYGN 136

Query: 438 MTHDHVMHLL 467
           MT DHVMHLL
Sbjct: 137 MTEDHVMHLL 146


  Database: RefSeqHP
    Posted date:  Aug 2, 2006 12:57 AM
  Number of letters in database: 17,774,539
  Number of sequences in database:  39,411
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 53,151,381
Number of Sequences: 39411
Number of extensions: 1662076
Number of successful extensions: 6614
Number of sequences better than 1.0e-05: 3
Number of HSP's better than  0.0 without gapping: 4967
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 6599
length of database: 17,774,539
effective HSP length: 104
effective length of database: 13,675,795
effective search space used: 3979656345
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)

Search to RefSeqCP

BLASTX 2.2.10 [Oct-19-2004]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= 20060611S-012682
         (1187 letters)

Database: RefSeqCP 
           33,732 sequences; 19,266,565 total letters

Searching..................................................done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|XP_536468.2| PREDICTED: similar to HLA class II histocompati...   164   3e-64

>ref|XP_536468.2| PREDICTED: similar to HLA class II histocompatibility antigen,
           gamma chain (HLA-DR antigens associated invariant chain)
           (Ia antigen-associated invariant chain) (Ii) (p33) (CD74
           antigen) [Canis familiaris]
          Length = 272

 Score =  164 bits (415), Expect(2) = 3e-64
 Identities = 82/130 (63%), Positives = 101/130 (77%), Gaps = 2/130 (1%)
 Frame = +3

Query: 264 RLDELTVPSHNLRLEILRMKLHKPSAPLSRMRVSAPMLMHALPMEG-PE-PMRYAT*YGD 437
           RLD+LTV S NL+LE LRMKL KP  PLS+MRV+ PM+M ALP++  P+ P + AT YG+
Sbjct: 61  RLDKLTVTSQNLQLESLRMKLPKPPKPLSKMRVATPMMMQALPIQSLPQGPTQNATEYGN 120

Query: 438 MTHDHVMHLLVNSDPLGVYPNLMGSLPEHLKHLKNTMYGVNWKLFENWLREWLLFDMSNN 617
           MT DHVMHLL+ +DPL VYP L GS PE+LKHLKNTM  ++WK+FENW+ +WLLF+MS N
Sbjct: 121 MTQDHVMHLLLEADPLKVYPKLKGSFPENLKHLKNTMETLDWKVFENWMYQWLLFEMSKN 180

Query: 618 SLEDTCFVVP 647
           SLE     VP
Sbjct: 181 SLEKKSTEVP 190



 Score =  100 bits (250), Expect(2) = 3e-64
 Identities = 49/60 (81%), Positives = 52/60 (86%)
 Frame = +2

Query: 83  MEDQRDLISDHEQLPLLGHRPGAPDINCSRGALYPGFSVLVALLLAGHATTTYFLY*LQG 262
           MEDQRDLIS+HEQLP+LG RPGAP+  CSRGALY GFSVLVALLLAG ATT YFLY  QG
Sbjct: 1   MEDQRDLISNHEQLPILGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQG 60


  Database: RefSeqCP
    Posted date:  Aug 1, 2006  9:25 PM
  Number of letters in database: 19,266,565
  Number of sequences in database:  33,732
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 54,545,613
Number of Sequences: 33732
Number of extensions: 1639874
Number of successful extensions: 6199
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 4875
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 6186
length of database: 19,266,565
effective HSP length: 105
effective length of database: 15,724,705
effective search space used: 4560164450
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)

Search to RefSeqMP

BLASTX 2.2.10 [Oct-19-2004]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= 20060611S-012682
         (1187 letters)

Database: RefSeqMP 
           45,328 sequences; 21,768,885 total letters

Searching..................................................done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_034675.1| Ia-associated invariant chain [Mus musculus]         167   1e-61

>ref|NP_034675.1| Ia-associated invariant chain [Mus musculus]
          Length = 215

 Score =  167 bits (424), Expect(2) = 1e-61
 Identities = 85/155 (54%), Positives = 114/155 (73%), Gaps = 3/155 (1%)
 Frame = +3

Query: 264 RLDELTVPSHNLRLEILRMKLHKPSAPLSRMRVSAPMLMHALPMEGP--EPMRYAT*YGD 437
           RLD+LT+ S NL+LE LRMKL K + P+S+MR++ P+LM  + M+     P++  T YG+
Sbjct: 60  RLDKLTITSQNLQLESLRMKLPKSAKPVSQMRMATPLLMRPMSMDNMLLGPVKNVTKYGN 119

Query: 438 MTHDHVMHLLVNSDPLGVYPNLMGSLPEHLKHLKNTMYGVNWKLFENWLREWLLFDMSNN 617
           MT DHVMHLL  S PL  YP L G+ PE+LKHLKN+M GVNWK+FE+W+++WLLF+MS N
Sbjct: 120 MTQDHVMHLLTRSGPLE-YPQLKGTFPENLKHLKNSMDGVNWKIFESWMKQWLLFEMSKN 178

Query: 618 SLED-TCFVVPHTDPLQTDDLTSRLGVTKHDLGQV 719
           SLE+      P  +PL  +DL+S LGVT+ +LGQV
Sbjct: 179 SLEEKKPTEAPPKEPLDMEDLSSGLGVTRQELGQV 213



 Score = 88.6 bits (218), Expect(2) = 1e-61
 Identities = 45/60 (75%), Positives = 50/60 (83%)
 Frame = +2

Query: 83  MEDQRDLISDHEQLPLLGHRPGAPDINCSRGALYPGFSVLVALLLAGHATTTYFLY*LQG 262
           M+DQRDLIS+HEQLP+LG+RP  P+  CSRGALY G SVLVALLLAG ATT YFLY  QG
Sbjct: 1   MDDQRDLISNHEQLPILGNRPREPE-RCSRGALYTGVSVLVALLLAGQATTAYFLYQQQG 59


  Database: RefSeqMP
    Posted date:  Aug 2, 2006 12:58 AM
  Number of letters in database: 21,768,885
  Number of sequences in database:  45,328
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 61,907,781
Number of Sequences: 45328
Number of extensions: 1821953
Number of successful extensions: 6627
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 5397
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 6613
length of database: 21,768,885
effective HSP length: 106
effective length of database: 16,964,117
effective search space used: 4902629813
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)