Gene T13L16.1
Putative Identification component of the nucleus, possibly of the pore complex
Position 371 - 2103, from the initial methionine to the termination codon
Strand +
EST match none
Database match nuclear pore complex proteins, e. g., human Ran/TC4-binding nucleopore protein

 

T13L16.1 exhibits weak similarity to nuclear pore complex (NPC) and RNA-binding (RBP) proteins (the latter may function in RNA transport); T13L16.1 does not show similarity to the RNA-binding domain of the RBPs.

 

CDS:  The table below lists the coordinates of the exons for T13L16.1 and which exon predicting algorithms selected the given termini (GS = GenScan, Gr = Grail, M = MZEF, NPG = NetPlantGene - selects splice sites only, not exons).

Exon

Range

5'

3'

1 371 - 536 Gr GS, NPG
2 967 - 1235 GS, Gr GS, NPG
3 1321 - 1351 GS, NPG GS
4 1459 - 1532 Gr, M, NPG Gr, M, NPG
5 1627 - 1754 Gr, M, NPG M
6 1863 - 1943 Gr, M, NPG Gr, M, NPG
7 2046 - 2103 Gr, NPG Gr

Complete CDS of T13L16.1

ATGGGAGACGGAAGAGAAGGAGACTGGGAATGTTTAGGATGCAGAAACAGGAATTATGCG
TTTAGATCATTCTGTAACAGATGCAAGCAGCCTCGTCTTATCATGGATAATAATACTTCT
CCAAACTCTAAGTGGCTTCCTCGTATCGGCGATTGGATCTGCACTGGTTGTACTAACAAC
AATTATGCATCACGAGAAAAGTGCAAGAAATGTGGGCAATCTAAGGAAGTAGCAGCATTG
TCAGCACTTGCTATCCCTGGAGCTTCTCTTCAAACTCATCTCCATTACTTCACCCGTGGA
CCTGAGTCACATGATCAACCTGGTTCTTTACTCGCATTCTCTAACGCTACAAATCAAGCT
TCGGTTCATAAAGAATGGAGGAGTGGTGACTGGATTTGCAGATGTGGTTTTCACAATTAT
TCCTCTCGTATACAGTGCAAAAAGTGCAATGAAATAGCTCCACTAGCCCTTGGTACAAAG
AGATTAGCATCAGAAGCTTTGGCTCATGAATGGGATAGCAAAAGACTGAATCAAGGATAT
ACAAGCATGCAAACACAGTCAGCGATATATGCATCTTTTCCTGGTATGAGCCTAGGAAGG
GTCTCAAATTGGCAACTTCCTCTCCCGTTTCTACAACAACACTCAACACCTGCTTTACTT
GGAATGGGAGTGAAACAATGGCGTGATGGCGACTGGATGTGTACAAATTGCAAGAATCAC
AATTATGCATCACGAGCAGAGTGCAATAGGTGCAAGACTACACGAGATATCCTTGATCAG
GACATAACTCCAACAGAACAATCTTGA

 

Notes regarding the CDS of T13L16.1:  The start codon (position 371 - 373) is predicted solely by GRAIL. GenScan predicts an internal exon from 325 - 536. Thus, the 5' region of T13L16.1 may not be found on BAC T13L16. GenScan joins T13L16.1 and T13L16.2 as one gene, but the splice-acceptors (AG) of the two GenScan intergenic exons are not predicted by the other algorithms. Lastly, there are two possible splice-donor sites for exon 5: Either at position 1754 (M) or 1814 (Gr). The donor at 1754 was chosen yielding an intron of 109 nt, as opposed to a donor at 1814 resulting in an intron of 49 nt.

 

Protein sequence of T13L16.1

MGDGREGDWECLGCRNRNYAFRSFCNRCKQPRLIMDNNTSPNSKWLPRIGDWICTGCTNN
NYASREKCKKCGQSKEVAALSALAIPGASLQTHLHYFTRGPESHDQPGSLLAFSNATNQA
SVHKEWRSGDWICRCGFHNYSSRIQCKKCNEIAPLALGTKRLASEALAHEWDSKRLNQGY
TSMQTQSAIYASFPGMSLGRVSNWQLPLPFLQQHSTPALLGMGVKQWRDGDWMCTNCKNH
NYASRAECNRCKTTRDILDQDITPTEQS*

 

BLAST output showing similarity to NPC protein

 prf||2115390A Ran/TC4-binding nucleopore protein [Homo sapiens]
            Length = 3224

 Score = 51.2 bits (120), Expect = 6e-06
 Identities = 49/207 (23%), Positives = 77/207 (36%), Gaps = 45/207 (21%)

Query: 5    REGDWECLGCRNRNYAFRSFCNRCKQP-------RLIMDNNTSPNSK---------WLPR 48
            +EG W+C  C  RN A  + C  C+ P         +    +S  SK         +  +
Sbjct: 1665 KEGQWDCSVCLVRNEASATKCIACQNPGKQNQTTSAVSTPASSETSKAPKSGFEGMFTKK 1724

Query: 49   IGDWICTGCTNNNYASREKCKKCGQSKEVAALSALAIPGASLQTHLHYFTRGPESHDQPG 108
             G W C+ C   N AS  KC  C    +    +A++ P +S        ++ P+S  + G
Sbjct: 1725 EGQWDCSVCLVRNEASATKCIACQCPSKQNQTTAISTPASS------EISKAPKSGFE-G 1777

Query: 109  SLLAFSNATNQASVHKEWRSGDWICR-CGFHNYSSRIQCKKCNEIAPL------ALGTKR 161
              +               R G W C  C   N SS ++C  C+   P       A     
Sbjct: 1778 MFI---------------RKGQWDCSVCCVQNESSSLKCVACDASKPTHKPIAEAPSAFT 1822

Query: 162  LASEALAHEWDSKRLNQGYTSMQTQSA 188
            L SE   H+    ++  G+ S  ++ A
Sbjct: 1823 LGSEMKLHDSSGSQVGTGFKSNFSEKA 1849

 

written 16 Dec 97
Larry Parnell