Animal-Genome cDNA 20060611S-027651


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-027651
         (553 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]                            120   2e-29

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

 Score =  120 bits (302), Expect = 2e-29
 Identities = 59/59 (100%), Positives = 59/59 (100%)
 Frame = +1

Query: 61  MEDQRDLISNHEQLPMLGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQ 237
           MEDQRDLISNHEQLPMLGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQ
Sbjct: 1   MEDQRDLISNHEQLPMLGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQ 59


  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: 552,771
Number of Sequences: 1040
Number of extensions: 14106
Number of successful extensions: 55
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 50
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): 54
length of database: 434,620
effective HSP length: 71
effective length of database: 360,780
effective search space used: 40407360
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-027651
         (553 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]    117   4e-27

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

 Score =  117 bits (294), Expect = 4e-27
 Identities = 58/59 (98%), Positives = 58/59 (98%)
 Frame = +1

Query: 61  MEDQRDLISNHEQLPMLGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQ 237
           MEDQRDLISNHEQLPMLGQRPGA ESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQ
Sbjct: 1   MEDQRDLISNHEQLPMLGQRPGAQESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQ 59


  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: 21,265,455
Number of Sequences: 33508
Number of extensions: 585245
Number of successful extensions: 3528
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 2897
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): 3508
length of database: 16,112,626
effective HSP length: 95
effective length of database: 12,929,366
effective search space used: 1137784208
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-027651
         (553 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_001020329.1| CD74 antigen isoform c [Homo sapiens]             114   5e-26
Alignment   gi|NP_001020330.1| CD74 antigen isoform a [Homo sapiens]             114   5e-26
Alignment   gi|NP_004346.1| CD74 antigen isoform b [Homo sapiens]                114   5e-26

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

 Score =  114 bits (285), Expect = 5e-26
 Identities = 55/63 (87%), Positives = 59/63 (93%)
 Frame = +1

Query: 49  QARTMEDQRDLISNHEQLPMLGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLY 228
           Q   M+DQRDLISN+EQLPMLG+RPGAPESKCSRGALYTGFS+LV LLLAGQATTAYFLY
Sbjct: 13  QKPVMDDQRDLISNNEQLPMLGRRPGAPESKCSRGALYTGFSILVTLLLAGQATTAYFLY 72

Query: 229 QQQ 237
           QQQ
Sbjct: 73  QQQ 75


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

 Score =  114 bits (285), Expect = 5e-26
 Identities = 55/63 (87%), Positives = 59/63 (93%)
 Frame = +1

Query: 49  QARTMEDQRDLISNHEQLPMLGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLY 228
           Q   M+DQRDLISN+EQLPMLG+RPGAPESKCSRGALYTGFS+LV LLLAGQATTAYFLY
Sbjct: 13  QKPVMDDQRDLISNNEQLPMLGRRPGAPESKCSRGALYTGFSILVTLLLAGQATTAYFLY 72

Query: 229 QQQ 237
           QQQ
Sbjct: 73  QQQ 75


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

 Score =  114 bits (285), Expect = 5e-26
 Identities = 55/63 (87%), Positives = 59/63 (93%)
 Frame = +1

Query: 49  QARTMEDQRDLISNHEQLPMLGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLY 228
           Q   M+DQRDLISN+EQLPMLG+RPGAPESKCSRGALYTGFS+LV LLLAGQATTAYFLY
Sbjct: 13  QKPVMDDQRDLISNNEQLPMLGRRPGAPESKCSRGALYTGFSILVTLLLAGQATTAYFLY 72

Query: 229 QQQ 237
           QQQ
Sbjct: 73  QQQ 75


  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: 24,658,290
Number of Sequences: 39411
Number of extensions: 725335
Number of successful extensions: 4697
Number of sequences better than 1.0e-05: 3
Number of HSP's better than  0.0 without gapping: 3553
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): 4681
length of database: 17,774,539
effective HSP length: 96
effective length of database: 13,991,083
effective search space used: 1217224221
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-027651
         (553 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]         101   5e-22

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

 Score =  101 bits (251), Expect = 5e-22
 Identities = 51/59 (86%), Positives = 54/59 (91%)
 Frame = +1

Query: 61  MEDQRDLISNHEQLPMLGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQ 237
           M+DQRDLISNHEQLP+LG RP  PE +CSRGALYTG SVLVALLLAGQATTAYFLYQQQ
Sbjct: 1   MDDQRDLISNHEQLPILGNRPREPE-RCSRGALYTGVSVLVALLLAGQATTAYFLYQQQ 58


  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: 28,226,145
Number of Sequences: 45328
Number of extensions: 763751
Number of successful extensions: 4422
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 3660
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): 4410
length of database: 21,768,885
effective HSP length: 97
effective length of database: 17,372,069
effective search space used: 1493997934
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-027651
         (553 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...   119   2e-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 =  119 bits (298), Expect = 2e-27
 Identities = 58/59 (98%), Positives = 59/59 (100%)
 Frame = +1

Query: 61  MEDQRDLISNHEQLPMLGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQ 237
           MEDQRDLISNHEQLP+LGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQ
Sbjct: 1   MEDQRDLISNHEQLPILGQRPGAPESKCSRGALYTGFSVLVALLLAGQATTAYFLYQQQ 59


  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: 24,807,286
Number of Sequences: 33732
Number of extensions: 686973
Number of successful extensions: 4080
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 3316
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): 4071
length of database: 19,266,565
effective HSP length: 97
effective length of database: 15,994,561
effective search space used: 1375532246
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)