Animal-Genome cDNA 20060611S-049573


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-049573
         (1181 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]                            111   4e-37

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

 Score =  111 bits (278), Expect(3) = 4e-37
 Identities = 60/97 (61%), Positives = 69/97 (71%)
 Frame = +2

Query: 239 MDDQRDLISNHEQLPMLVQRPGAPYSKCSRVSLYTGFSVQVVLLLCEHDTNCNIL*QLQG 418
           M+DQRDLISNHEQLPML QRPGAP SKCSR +LYTGFSV V LLL    T    L Q QG
Sbjct: 1   MEDQRDLISNHEQLPMLGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQG 60

Query: 419 RMYKLTITSHN*LIHSLHMKLHNHSNTMSHKRLTAPI 529
           R+ KLT+TS N  + SL MKL   S  +S  R++AP+
Sbjct: 61  RLDKLTVTSQNLQLESLRMKLPKPSKPLSKMRVSAPM 97



 Score = 48.9 bits (115), Expect(3) = 4e-37
 Identities = 25/47 (53%), Positives = 32/47 (68%)
 Frame = +3

Query: 549 IEGP*PMRNFIRYYDMTQDHVIHLLLKNDSQAM*PNI*ERL**YLKH 689
           +EGP PMRN  +Y +MTQDHV+HLLLK+D   + P +   L   LKH
Sbjct: 104 MEGPEPMRNATKYGNMTQDHVMHLLLKSDPLGVYPKLKGSLPENLKH 150



 Score = 28.9 bits (63), Expect(3) = 4e-37
 Identities = 24/58 (41%), Positives = 27/58 (46%)
 Frame = +1

Query: 715 NWKLYQN*LRSVAHRFISS*TQLHETHTRSSVKTPTARLMIISSRLDEIKQDLSQFIL 888
           NWKL++N LR     F  S   L ET      K P      +SS L   KQDL Q IL
Sbjct: 159 NWKLFENWLRQWL-LFEMSKNSLEETPFEVPPKDP-LETEDLSSGLGVTKQDLGQVIL 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: 958,723
Number of Sequences: 1040
Number of extensions: 22264
Number of successful extensions: 62
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 55
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): 62
length of database: 434,620
effective HSP length: 79
effective length of database: 352,460
effective search space used: 110672440
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-049573
         (1181 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]    106   5e-30

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

 Score =  106 bits (264), Expect(2) = 5e-30
 Identities = 57/97 (58%), Positives = 66/97 (68%)
 Frame = +2

Query: 239 MDDQRDLISNHEQLPMLVQRPGAPYSKCSRVSLYTGFSVQVVLLLCEHDTNCNIL*QLQG 418
           M+DQRDLISNHEQLPML QRPGA  SKCSR +LYTGFSV V LLL    T    L Q QG
Sbjct: 1   MEDQRDLISNHEQLPMLGQRPGAQESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQG 60

Query: 419 RMYKLTITSHN*LIHSLHMKLHNHSNTMSHKRLTAPI 529
           R+ KLT+TS N  + +L MKL   +  MS  R+  P+
Sbjct: 61  RLDKLTVTSQNLQLENLRMKLPKPAKPMSQMRMATPM 97



 Score = 43.9 bits (102), Expect(2) = 5e-30
 Identities = 23/45 (51%), Positives = 29/45 (64%)
 Frame = +3

Query: 555 GP*PMRNFIRYYDMTQDHVIHLLLKNDSQAM*PNI*ERL**YLKH 689
           GP PM+N  +Y +MTQDHV+HLLLK D   + P +   L   LKH
Sbjct: 106 GPEPMKNATKYGNMTQDHVMHLLLKADPLKVYPQLKGSLPENLKH 150


  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: 35,786,935
Number of Sequences: 33508
Number of extensions: 867090
Number of successful extensions: 2803
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 2392
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): 2801
length of database: 16,112,626
effective HSP length: 103
effective length of database: 12,661,302
effective search space used: 3671777580
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-049573
         (1181 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...   106   6e-27

>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 =  106 bits (264), Expect(2) = 6e-27
 Identities = 57/97 (58%), Positives = 66/97 (68%)
 Frame = +2

Query: 239 MDDQRDLISNHEQLPMLVQRPGAPYSKCSRVSLYTGFSVQVVLLLCEHDTNCNIL*QLQG 418
           M+DQRDLISNHEQLP+L QRPGAP SKCSR +LYTGFSV V LLL    T    L Q QG
Sbjct: 1   MEDQRDLISNHEQLPILGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQG 60

Query: 419 RMYKLTITSHN*LIHSLHMKLHNHSNTMSHKRLTAPI 529
           R+ KLT+TS N  + SL MKL      +S  R+  P+
Sbjct: 61  RLDKLTVTSQNLQLESLRMKLPKPPKPLSKMRVATPM 97



 Score = 33.9 bits (76), Expect(2) = 6e-27
 Identities = 15/32 (46%), Positives = 21/32 (65%)
 Frame = +3

Query: 564 PMRNFIRYYDMTQDHVIHLLLKNDSQAM*PNI 659
           P +N   Y +MTQDHV+HLLL+ D   + P +
Sbjct: 111 PTQNATEYGNMTQDHVMHLLLEADPLKVYPKL 142


  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: 41,999,979
Number of Sequences: 33732
Number of extensions: 1015864
Number of successful extensions: 3390
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 2853
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): 3388
length of database: 19,266,565
effective HSP length: 105
effective length of database: 15,724,705
effective search space used: 4528715040
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-049573
         (1181 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_001020330.1| CD74 antigen isoform a [Homo sapiens]             103   8e-26
Alignment   gi|NP_004346.1| CD74 antigen isoform b [Homo sapiens]                103   8e-26
Alignment   gi|NP_001020329.1| CD74 antigen isoform c [Homo sapiens]             103   1e-25

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

 Score =  103 bits (258), Expect(2) = 8e-26
 Identities = 55/97 (56%), Positives = 66/97 (68%)
 Frame = +2

Query: 239 MDDQRDLISNHEQLPMLVQRPGAPYSKCSRVSLYTGFSVQVVLLLCEHDTNCNIL*QLQG 418
           MDDQRDLISN+EQLPML +RPGAP SKCSR +LYTGFS+ V LLL    T    L Q QG
Sbjct: 17  MDDQRDLISNNEQLPMLGRRPGAPESKCSRGALYTGFSILVTLLLAGQATTAYFLYQQQG 76

Query: 419 RMYKLTITSHN*LIHSLHMKLHNHSNTMSHKRLTAPI 529
           R+ KLT+TS N  + +L MKL      +S  R+  P+
Sbjct: 77  RLDKLTVTSQNLQLENLRMKLPKPPKPVSKMRMATPL 113



 Score = 32.3 bits (72), Expect(2) = 8e-26
 Identities = 13/24 (54%), Positives = 18/24 (75%)
 Frame = +3

Query: 564 PMRNFIRYYDMTQDHVIHLLLKND 635
           PM+N  +Y +MT+DHV+HLL   D
Sbjct: 127 PMQNATKYGNMTEDHVMHLLQNAD 150


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

 Score =  103 bits (258), Expect(2) = 8e-26
 Identities = 55/97 (56%), Positives = 66/97 (68%)
 Frame = +2

Query: 239 MDDQRDLISNHEQLPMLVQRPGAPYSKCSRVSLYTGFSVQVVLLLCEHDTNCNIL*QLQG 418
           MDDQRDLISN+EQLPML +RPGAP SKCSR +LYTGFS+ V LLL    T    L Q QG
Sbjct: 17  MDDQRDLISNNEQLPMLGRRPGAPESKCSRGALYTGFSILVTLLLAGQATTAYFLYQQQG 76

Query: 419 RMYKLTITSHN*LIHSLHMKLHNHSNTMSHKRLTAPI 529
           R+ KLT+TS N  + +L MKL      +S  R+  P+
Sbjct: 77  RLDKLTVTSQNLQLENLRMKLPKPPKPVSKMRMATPL 113



 Score = 32.3 bits (72), Expect(2) = 8e-26
 Identities = 13/24 (54%), Positives = 18/24 (75%)
 Frame = +3

Query: 564 PMRNFIRYYDMTQDHVIHLLLKND 635
           PM+N  +Y +MT+DHV+HLL   D
Sbjct: 127 PMQNATKYGNMTEDHVMHLLQNAD 150


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

 Score =  103 bits (258), Expect(2) = 1e-25
 Identities = 55/97 (56%), Positives = 66/97 (68%)
 Frame = +2

Query: 239 MDDQRDLISNHEQLPMLVQRPGAPYSKCSRVSLYTGFSVQVVLLLCEHDTNCNIL*QLQG 418
           MDDQRDLISN+EQLPML +RPGAP SKCSR +LYTGFS+ V LLL    T    L Q QG
Sbjct: 17  MDDQRDLISNNEQLPMLGRRPGAPESKCSRGALYTGFSILVTLLLAGQATTAYFLYQQQG 76

Query: 419 RMYKLTITSHN*LIHSLHMKLHNHSNTMSHKRLTAPI 529
           R+ KLT+TS N  + +L MKL      +S  R+  P+
Sbjct: 77  RLDKLTVTSQNLQLENLRMKLPKPPKPVSKMRMATPL 113



 Score = 31.6 bits (70), Expect(2) = 1e-25
 Identities = 12/20 (60%), Positives = 17/20 (85%)
 Frame = +3

Query: 564 PMRNFIRYYDMTQDHVIHLL 623
           PM+N  +Y +MT+DHV+HLL
Sbjct: 127 PMQNATKYGNMTEDHVMHLL 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: 40,565,468
Number of Sequences: 39411
Number of extensions: 1014331
Number of successful extensions: 3200
Number of sequences better than 1.0e-05: 3
Number of HSP's better than  0.0 without gapping: 2703
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): 3196
length of database: 17,774,539
effective HSP length: 104
effective length of database: 13,675,795
effective search space used: 3952304755
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-049573
         (1181 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]          94   7e-23

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

 Score = 94.0 bits (232), Expect(2) = 7e-23
 Identities = 53/97 (54%), Positives = 62/97 (63%)
 Frame = +2

Query: 239 MDDQRDLISNHEQLPMLVQRPGAPYSKCSRVSLYTGFSVQVVLLLCEHDTNCNIL*QLQG 418
           MDDQRDLISNHEQLP+L  RP  P  +CSR +LYTG SV V LLL    T    L Q QG
Sbjct: 1   MDDQRDLISNHEQLPILGNRPREP-ERCSRGALYTGVSVLVALLLAGQATTAYFLYQQQG 59

Query: 419 RMYKLTITSHN*LIHSLHMKLHNHSNTMSHKRLTAPI 529
           R+ KLTITS N  + SL MKL   +  +S  R+  P+
Sbjct: 60  RLDKLTITSQNLQLESLRMKLPKSAKPVSQMRMATPL 96



 Score = 32.7 bits (73), Expect(2) = 7e-23
 Identities = 12/23 (52%), Positives = 19/23 (82%)
 Frame = +3

Query: 564 PMRNFIRYYDMTQDHVIHLLLKN 632
           P++N  +Y +MTQDHV+HLL ++
Sbjct: 110 PVKNVTKYGNMTQDHVMHLLTRS 132


  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: 48,010,624
Number of Sequences: 45328
Number of extensions: 1158124
Number of successful extensions: 3584
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 3052
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): 3560
length of database: 21,768,885
effective HSP length: 106
effective length of database: 16,964,117
effective search space used: 4868701579
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)