Gene: T32N15.9 Putative Identification: similar to glycyl tRNA synthetase Position: before 62687 to beyond 66940, within the putative CDS Strand: + EST match: none Database match: human T-cell mRNA for glycyl tRNA synthetase, D30658
Note: This sequence is partial: both the 5' and 3' ends of T32N15.9 are undefined. Six exons that were predicted by either Grail or MZEF, or selected by similarity to other glycyl tRNA synthetases were assembled into a polypeptide. For example, exon 3 was missed by both Grail and MZEF, yet it encodes sequence that aligns well with other tRNA synthetases (see alignment below, peptide encoded by exon 3 is highlighted). Translation of sequence upstream of exon 1 does not yield any peptide with significant homology to amino-terminal portions of human glycyl tRNA synthetase. In addition, exons predicted by Grail and MZEF which lie downstream of exon 6 cannot be incorporated into an mRNA to maintain an open reading frame. Moreover, T32N15.9 has no matches to the EST database. It is possible, then, that T32N15.9 is not a functional gene.
CDS: exon terminus predicted by Gr=Grail
5' 3' M=MZEF
exon 1 62688 to 62837 Gr Gr
exon 2 62945 to 63056 Gr
exon 3 63138 to 63225
exon 4 63328 to 63541 M,Gr
exon 5 63645 to 63869 M,Gr M,Gr
exon 6 64069 to 64154 Gr Gr
Note: Intron 2 (from position 63057 to 63137) is flanked by the
noncanonical, but previously documented splice junction of /AT~~~AC/.
This maintains an open reading frame in the joining of exon 3, which
exhibits significant similarity to glycyl tRNA synthetases from other
organisms, see above note.
CCATGGAGCTGCTGATTTCGACAAAATGTGGTTAATACTCTCGAGCGGCGTTTGTTCTAT
ATCCCTTCTTTCAAAATCAACCGTGACGTCGCCGGACTATTTGATTAAGGATTGTGCTGT
TAAATCCAATGTTCTTAGCTTCTGGCGTCAACATTTCATTCTTAAGGAGAATATGTATGA
AGTGGATTGTCCATGTGTGACACCAGAGGTTGTTCTCAAGGCATCTGGACATGTAGACCA
GTTCACTGATCTAATGGTTAAGAAAGGCATTTTTGTGAAGGACTTGTATTACTACAATGG
GAGGAAATTTCCCTTTGCTGCTGCTCAAATTGGTCAACCTTTAGAAATGAGTGACGCATA
TTACTTGCAGATATCTCATCGTCAAGGGCTTCTTAGAGTTTGTGAATTCACGCTGGCAGA
AATTGAGCATTTTGTTGATCCTGGGAATAAGTCACATCCGAAATTCTCTGATGTAGCAAA
TTTTGAATTCCTTATGTTTCCAAGAGAGGAACAAATGTCTGGCCAATCTGCGAAAAAACT
TTGCCTTGGCGAAGTTGTTGCCAAGGGAACTGTGAACAAAGAAACTGTAGGCTACTTCAT
TGCGAGAGTGTATCTTTTCCTTGTCCGTCTTGGCACAGACAAGGAACAGTTGCGTTTCCG
CCAGCATTTTGCAAATGAAATGGCCCGCTATGCTGCAGATTGTTTGGATGCTGAATTTGA
GAGTTCATATGGGTGGATTGAATGTGTTGGTATAGCAGATAGGTCTGCATTCGACTTACG
TGCCCACTCGAAACTTGTGATTACTCCTGTGAAGAAAGAACTGGTTCTTGCATTCAAGGG
AAATCAAAAGCATGTCGTTAAATCTTTAGATATAGA
Protein translation:
HGAADFDKMWLILSSGVCSISLLSKSTVTSPDYLIKDCAVKSNVLSFWRQHFILKENMYE
VDCPCVTPEVVLKASGHVDQFTDLMVKKGIFVKDLYYYNGRKFPFAAAQIGQPLEMSDAY
YLQISHRQGLLRVCEFTLAEIEHFVDPGNKSHPKFSDVANFEFLMFPREEQMSGQSAKKL
CLGEVVAKGTVNKETVGYFIARVYLFLVRLGTDKEQLRFRQHFANEMARYAADCLDAEFE
SSYGWIECVGIADRSAFDLRAHSKLVITPVKKELVLAFKGNQKHVVKSLDI
Alignment to human glycyl tRNA synthetase, portion of BLAST output
dbj|D30658|HUMGLYCYL Human T-cell mRNA for glycyl tRNA synthetase,
complete cds
Length = 2283
Plus Strand HSPs:
Score = 453 (211.3 bits), Expect = 5.5e-82, Sum P(3) = 4.9e-82
Identities = 81/159 (50%), Positives = 113/159 (71%), Frame = +1
Query: 115 EMSDAYYLQISHRQGLLRVCEFTLAEIEHFVDPGNKSHPKFSDVANFEFLMFPREEQMSG 174
++ +++ +IS R GL+RV EFT+AEIEHFVDP K HPKF +VA+ ++ + Q+SG
Sbjct: 997 QIGNSFRNEISPRSGLIRVREFTMAEIEHFVDPSEKDHPKFQNVADLHLYLYSAKAQVSG 1176
Query: 175 QSAKKLCLGEVVAKGTVNKETVGYFIARVYLFLVRLGTDKEQLRFRQHFANEMARYAADC 234
QSA+K+ LG+ V +G +N +GYFI R+YL+L ++G ++LRFRQH NEMA YA DC
Sbjct: 1177 QSARKMRLGDAVEQGVINNTVLGYFIGRIYLYLTKVGISPDKLRFRQHMENEMAHYACDC 1356
Query: 235 LDAEFESSYGWIECVGIADRSAFDLRAHSKLVITPVKKE 273
DAE ++SYGWIE VG ADRS +DL H++ P+ E
Sbjct: 1357 WDAESKTSYGWIEIVGCADRSCYDLSCHARATKVPLVAE 1473
Score = 177 (82.6 bits), Expect = 5.5e-82, Sum P(3) = 4.9e-82
Identities = 30/50 (60%), Positives = 39/50 (78%), Frame = +1
Query: 38 CAVKSNVLSFWRQHFILKENMYEVDCPCVTPEVVLKASGHVDQFTDLMVK 87
CA+K+N++ WRQHFI +E + E+DC +TPE VLK SGHVD+F D MVK
Sbjct: 487 CALKNNIIQTWRQHFIQEEQILEIDCTMLTPEPVLKTSGHVDKFADFMVK 636
Score = 54 (25.2 bits), Expect = 5.5e-82, Sum P(3) = 4.9e-82
Identities = 12/19 (63%), Positives = 13/19 (68%), Frame = +1
Query: 93 KDLYYYNGRKFPFAAAQIG 111
K L +N K PFAAAQIG
Sbjct: 949 KRLLEFNQGKLPFAAAQIG 1005
Exons predicted by Grail and MZEF:
The following exons reside downstream of the 3'-most exon that is incorporated
into an mRNA molecule coding for the T32N15.9 open reading frame.
Range
Predicting program
DNA sequence of exon followed by its translation Quality
==================================================================================
agAAGTAAGTGGTGTCTTGTCCTTGTCGTTGCTAAAGCGATTAAGCTTTGGGGTTAGGGT 65080 - 65180
TGGTCTTGGTCTCCTCAAGGCGTACGTGAGTCTCCCAAAATATgt Grail
quality = good
VSGVLSLSLLKRLSFGVRVGLGLLKAYVSLPKY
__________________________________________________________________________________
ATGGGTAAGACTTTGGGTCACATTGGTAAACTGCAAGTTGACCACAAAACTTgt 66004 - 66055
Grail
MGKTLGHIGKLQVDHKT quality = excellent
__________________________________________________________________________________
agTGCACCCTCTATCAGAACAAACCAGAAGGAGTGTTGTTTGCTGGAACAAGCTGGAAGC 66297 - 66382
TGTTTCAGAAGACTAAAATGAAGATCAAgt Grail
quality = moderate
__________________________________________________________________________________
agAGGTGCTAAGGTTCTTCTTAGACTCGGTCGTAATAGTGgt 66546 - 66583
Grail
GAKVLLRLGRNS - orf 1 quality = moderate
VLRFFLDSVVIV - orf 2
__________________________________________________________________________________
agGTTGTACAACCGAATGACCACTAAGACCTCATTCTCACCTAGATCTCGGATGGAATGT 66861 - 66940
TATAGTCTGGCCAATCAAAATGgt MZEF
LYNRMTTKTSFSPRSRMECYSLANQN
created 4 Sep 97
updated 5 Sep 97
Larry Parnell