Animal-Genome cDNA 20060611C-000196


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= 20060611C-000196
         (1332 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]    332   3e-91

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

 Score =  332 bits (852), Expect = 3e-91
 Identities = 165/204 (80%), Positives = 177/204 (86%)
 Frame = +1

Query: 274 MEDQRDLISNHEQLPMLGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQG 453
           MEDQRDLISNHEQLPMLGQRPGA ESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQG
Sbjct: 1   MEDQRDLISNHEQLPMLGQRPGAQESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQG 60

Query: 454 RLDKLTVTSQNLQLEXXXXXXXXXXXXXXXXXVSAPMLMQALPMEGPEPMRNATKYGNMT 633
           RLDKLTVTSQNLQLE                 ++ PMLM+ALPM GPEPM+NATKYGNMT
Sbjct: 61  RLDKLTVTSQNLQLENLRMKLPKPAKPMSQMRMATPMLMRALPMAGPEPMKNATKYGNMT 120

Query: 634 QDHVMHLLLKSDPLGVYPKLKGSLPENLKHLKNTMDGVNWKLFENWLRQWLLFEMSKNSL 813
           QDHVMHLLLK+DPL VYP+LKGSLPENLKHLK++MDG++WKLFE+WL QWLLFEMSKNSL
Sbjct: 121 QDHVMHLLLKADPLKVYPQLKGSLPENLKHLKDSMDGLDWKLFESWLHQWLLFEMSKNSL 180

Query: 814 EETPFEVPPKDPLETEDLSSGLGV 885
           EE PFE PPKDP+E E  SSGLGV
Sbjct: 181 EEKPFEGPPKDPMEMEYPSSGLGV 204


  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: 50,669,192
Number of Sequences: 33508
Number of extensions: 1523829
Number of successful extensions: 9836
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 6361
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): 9660
length of database: 16,112,626
effective HSP length: 105
effective length of database: 12,594,286
effective search space used: 4256868668
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 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= 20060611C-000196
         (1332 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]                            394   e-111

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

 Score =  394 bits (1011), Expect = e-111
 Identities = 197/214 (92%), Positives = 197/214 (92%)
 Frame = +1

Query: 274 MEDQRDLISNHEQLPMLGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQG 453
           MEDQRDLISNHEQLPMLGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQG
Sbjct: 1   MEDQRDLISNHEQLPMLGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQG 60

Query: 454 RLDKLTVTSQNLQLEXXXXXXXXXXXXXXXXXVSAPMLMQALPMEGPEPMRNATKYGNMT 633
           RLDKLTVTSQNLQLE                 VSAPMLMQALPMEGPEPMRNATKYGNMT
Sbjct: 61  RLDKLTVTSQNLQLESLRMKLPKPSKPLSKMRVSAPMLMQALPMEGPEPMRNATKYGNMT 120

Query: 634 QDHVMHLLLKSDPLGVYPKLKGSLPENLKHLKNTMDGVNWKLFENWLRQWLLFEMSKNSL 813
           QDHVMHLLLKSDPLGVYPKLKGSLPENLKHLKNTMDGVNWKLFENWLRQWLLFEMSKNSL
Sbjct: 121 QDHVMHLLLKSDPLGVYPKLKGSLPENLKHLKNTMDGVNWKLFENWLRQWLLFEMSKNSL 180

Query: 814 EETPFEVPPKDPLETEDLSSGLGVTKQDLGQVIL 915
           EETPFEVPPKDPLETEDLSSGLGVTKQDLGQVIL
Sbjct: 181 EETPFEVPPKDPLETEDLSSGLGVTKQDLGQVIL 214


  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: 1,312,014
Number of Sequences: 1040
Number of extensions: 36719
Number of successful extensions: 194
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 143
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): 188
length of database: 434,620
effective HSP length: 80
effective length of database: 351,420
effective search space used: 127565460
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= 20060611C-000196
         (1332 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]                306   2e-83
Alignment   gi|NP_001020330.1| CD74 antigen isoform a [Homo sapiens]             276   3e-74
Alignment   gi|NP_001020329.1| CD74 antigen isoform c [Homo sapiens]             186   5e-47

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

 Score =  306 bits (785), Expect = 2e-83
 Identities = 153/214 (71%), Positives = 176/214 (82%), Gaps = 2/214 (0%)
 Frame = +1

Query: 274 MEDQRDLISNHEQLPMLGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQG 453
           M+DQRDLISN+EQLPMLG+RPGAPESKCSRGALYTGFS+LV LLLAGQATTAYFLYQQQG
Sbjct: 17  MDDQRDLISNNEQLPMLGRRPGAPESKCSRGALYTGFSILVTLLLAGQATTAYFLYQQQG 76

Query: 454 RLDKLTVTSQNLQLEXXXXXXXXXXXXXXXXXVSAPMLMQALPMEG-PE-PMRNATKYGN 627
           RLDKLTVTSQNLQLE                 ++ P+LMQALPM   P+ PM+NATKYGN
Sbjct: 77  RLDKLTVTSQNLQLENLRMKLPKPPKPVSKMRMATPLLMQALPMGALPQGPMQNATKYGN 136

Query: 628 MTQDHVMHLLLKSDPLGVYPKLKGSLPENLKHLKNTMDGVNWKLFENWLRQWLLFEMSKN 807
           MT+DHVMHLL  +DPL VYP LKGS PENL+HLKNTM+ ++WK+FE+W+  WLLFEMS++
Sbjct: 137 MTEDHVMHLLQNADPLKVYPPLKGSFPENLRHLKNTMETIDWKVFESWMHHWLLFEMSRH 196

Query: 808 SLEETPFEVPPKDPLETEDLSSGLGVTKQDLGQV 909
           SLE+ P + PPK+ LE ED SSGLGVTKQDLG V
Sbjct: 197 SLEQKPTDAPPKESLELEDPSSGLGVTKQDLGPV 230


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

 Score =  276 bits (706), Expect = 3e-74
 Identities = 136/192 (70%), Positives = 158/192 (82%), Gaps = 2/192 (1%)
 Frame = +1

Query: 274 MEDQRDLISNHEQLPMLGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQG 453
           M+DQRDLISN+EQLPMLG+RPGAPESKCSRGALYTGFS+LV LLLAGQATTAYFLYQQQG
Sbjct: 17  MDDQRDLISNNEQLPMLGRRPGAPESKCSRGALYTGFSILVTLLLAGQATTAYFLYQQQG 76

Query: 454 RLDKLTVTSQNLQLEXXXXXXXXXXXXXXXXXVSAPMLMQALPMEG-PE-PMRNATKYGN 627
           RLDKLTVTSQNLQLE                 ++ P+LMQALPM   P+ PM+NATKYGN
Sbjct: 77  RLDKLTVTSQNLQLENLRMKLPKPPKPVSKMRMATPLLMQALPMGALPQGPMQNATKYGN 136

Query: 628 MTQDHVMHLLLKSDPLGVYPKLKGSLPENLKHLKNTMDGVNWKLFENWLRQWLLFEMSKN 807
           MT+DHVMHLL  +DPL VYP LKGS PENL+HLKNTM+ ++WK+FE+W+  WLLFEMS++
Sbjct: 137 MTEDHVMHLLQNADPLKVYPPLKGSFPENLRHLKNTMETIDWKVFESWMHHWLLFEMSRH 196

Query: 808 SLEETPFEVPPK 843
           SLE+ P + PPK
Sbjct: 197 SLEQKPTDAPPK 208


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

 Score =  186 bits (471), Expect = 5e-47
 Identities = 97/130 (74%), Positives = 107/130 (82%), Gaps = 2/130 (1%)
 Frame = +1

Query: 274 MEDQRDLISNHEQLPMLGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQG 453
           M+DQRDLISN+EQLPMLG+RPGAPESKCSRGALYTGFS+LV LLLAGQATTAYFLYQQQG
Sbjct: 17  MDDQRDLISNNEQLPMLGRRPGAPESKCSRGALYTGFSILVTLLLAGQATTAYFLYQQQG 76

Query: 454 RLDKLTVTSQNLQLEXXXXXXXXXXXXXXXXXVSAPMLMQALPMEG-PE-PMRNATKYGN 627
           RLDKLTVTSQNLQLE                 ++ P+LMQALPM   P+ PM+NATKYGN
Sbjct: 77  RLDKLTVTSQNLQLENLRMKLPKPPKPVSKMRMATPLLMQALPMGALPQGPMQNATKYGN 136

Query: 628 MTQDHVMHLL 657
           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: 58,439,057
Number of Sequences: 39411
Number of extensions: 1861341
Number of successful extensions: 12713
Number of sequences better than 1.0e-05: 3
Number of HSP's better than  0.0 without gapping: 7489
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): 12531
length of database: 17,774,539
effective HSP length: 105
effective length of database: 13,636,384
effective search space used: 4609097792
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= 20060611C-000196
         (1332 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...   288   8e-78

>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 =  288 bits (737), Expect = 8e-78
 Identities = 146/192 (76%), Positives = 162/192 (84%), Gaps = 2/192 (1%)
 Frame = +1

Query: 274 MEDQRDLISNHEQLPMLGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQG 453
           MEDQRDLISNHEQLP+LGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQG
Sbjct: 1   MEDQRDLISNHEQLPILGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQG 60

Query: 454 RLDKLTVTSQNLQLEXXXXXXXXXXXXXXXXXVSAPMLMQALPMEG-PE-PMRNATKYGN 627
           RLDKLTVTSQNLQLE                 V+ PM+MQALP++  P+ P +NAT+YGN
Sbjct: 61  RLDKLTVTSQNLQLESLRMKLPKPPKPLSKMRVATPMMMQALPIQSLPQGPTQNATEYGN 120

Query: 628 MTQDHVMHLLLKSDPLGVYPKLKGSLPENLKHLKNTMDGVNWKLFENWLRQWLLFEMSKN 807
           MTQDHVMHLLL++DPL VYPKLKGS PENLKHLKNTM+ ++WK+FENW+ QWLLFEMSKN
Sbjct: 121 MTQDHVMHLLLEADPLKVYPKLKGSFPENLKHLKNTMETLDWKVFENWMYQWLLFEMSKN 180

Query: 808 SLEETPFEVPPK 843
           SLE+   EVP K
Sbjct: 181 SLEKKSTEVPLK 192


  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: 59,327,029
Number of Sequences: 33732
Number of extensions: 1792646
Number of successful extensions: 11515
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 7080
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): 11352
length of database: 19,266,565
effective HSP length: 106
effective length of database: 15,690,973
effective search space used: 5287857901
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= 20060611C-000196
         (1332 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]         296   3e-80

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

 Score =  296 bits (759), Expect = 3e-80
 Identities = 151/217 (69%), Positives = 175/217 (80%), Gaps = 3/217 (1%)
 Frame = +1

Query: 274 MEDQRDLISNHEQLPMLGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQG 453
           M+DQRDLISNHEQLP+LG RP  PE +CSRGALYTG SVLVALLLAGQATTAYFLYQQQG
Sbjct: 1   MDDQRDLISNHEQLPILGNRPREPE-RCSRGALYTGVSVLVALLLAGQATTAYFLYQQQG 59

Query: 454 RLDKLTVTSQNLQLEXXXXXXXXXXXXXXXXXVSAPMLMQALPMEGP--EPMRNATKYGN 627
           RLDKLT+TSQNLQLE                 ++ P+LM+ + M+     P++N TKYGN
Sbjct: 60  RLDKLTITSQNLQLESLRMKLPKSAKPVSQMRMATPLLMRPMSMDNMLLGPVKNVTKYGN 119

Query: 628 MTQDHVMHLLLKSDPLGVYPKLKGSLPENLKHLKNTMDGVNWKLFENWLRQWLLFEMSKN 807
           MTQDHVMHLL +S PL  YP+LKG+ PENLKHLKN+MDGVNWK+FE+W++QWLLFEMSKN
Sbjct: 120 MTQDHVMHLLTRSGPL-EYPQLKGTFPENLKHLKNSMDGVNWKIFESWMKQWLLFEMSKN 178

Query: 808 SLEE-TPFEVPPKDPLETEDLSSGLGVTKQDLGQVIL 915
           SLEE  P E PPK+PL+ EDLSSGLGVT+Q+LGQV L
Sbjct: 179 SLEEKKPTEAPPKEPLDMEDLSSGLGVTRQELGQVTL 215


  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: 67,058,496
Number of Sequences: 45328
Number of extensions: 1974374
Number of successful extensions: 12069
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 7607
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): 11811
length of database: 21,768,885
effective HSP length: 107
effective length of database: 16,918,789
effective search space used: 5684713104
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)