Gene loci information

Transcript annotation

  • This transcript has been annotated as Sialin.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_2 g5751 g5751.t2 TTS g5751.t2 11632215 11632215
chr_2 g5751 g5751.t2 isoform g5751.t2 11632268 11633870
chr_2 g5751 g5751.t2 exon g5751.t2.exon1 11632268 11632447
chr_2 g5751 g5751.t2 cds g5751.t2.CDS1 11632268 11632447
chr_2 g5751 g5751.t2 exon g5751.t2.exon2 11632507 11632550
chr_2 g5751 g5751.t2 cds g5751.t2.CDS2 11632507 11632550
chr_2 g5751 g5751.t2 exon g5751.t2.exon3 11632609 11633870
chr_2 g5751 g5751.t2 cds g5751.t2.CDS3 11632609 11633701
chr_2 g5751 g5751.t2 TSS g5751.t2 11633908 11633908

Sequences

>g5751.t2 Gene=g5751 Length=1486
ATGACAGAATTGTAAGTGTTTTTTAAATAGTTTTTTGAAGTTTAAAAAATAATTTTTGAT
TAATAAAAATTATAGAATTGATAATACTCCATTCTTCAAGAAGAAACGCTATCTTGTTGT
GTTAATGGCATTTTTGGGATATATTAATTTATATACATTAAGAGTCAATATGAGTGTAGC
AATTGTAGCTATGACTGATAATAAATCAATCATTCATGACGACAATAGTGAAACTTTTGA
ACCAGAATTTGATTGGAGTTCAAAAGCAAAGGGTTATGTGCTAAGCTCATTTTTTTATGG
ATACATTTGTACGCAAATTCCTGGTGGAATTTTGGCTTCAAAAATTGGTGGTCAATGGGT
TTTTGGCCTCGGAATTTTAGGAACTGCTGTTATGACTTTATTAACACCAATATTATGTTA
TCAAGGAATTGGTTATCTTATTTTGTCAAGAGTTATACAAGGTATTTGCAGTGGTCTTGC
TTATCCATCAATTAATATGGTTTATGCAAATTATATTCCTCCTATTGAACGCTCAAGAAC
TGCTAGTTATGGCACGTCAGGAATATTTGTTGGTACAATTCTCGGTAATTTCTTATCAGG
ACTTATCAGTGAATATTTTGGATGGGAGTATATTTTCTATATTTTTGGAGCTGTTGCAGT
TTTATGGTATGTTCTTTGGTATTTTACTGTCAAAAGTGGACCTGATCATGATAGTTGGAT
GTCACAAGGAGAAAGAGATTTTATTAAAAAAAGTATTGCGAGTCAATCTGGAAATAAAGC
TCAAACAACAAAAACTCCATGGAAAGCAATATTTACTTCTATTCCAGTATATGCTATAGC
AATTTCACATTTTTCATATAACTGGGGTTATTACACTATGTTAACTCAATTGCCTATGTA
TATGCGTGATATTCTTGATTTTGATGTAACAAAAAGTGGTTTCTTGAGTGCACTTCCTTA
TTTAGTACAAACAATTATTGTGTATATTTCTGGATTTTTAGCAGATTTTGTTCAAAAAAA
GAACATTTTAACTACAACTCAAGTGCGAAAATATTTCAATACAACATCATTTGTGTCACA
AACAATTTTTCTTCTTATCGCTGCATTTGTATCAAACACACCAACAATTGTTGCATGCAT
TTCTATGACAGTAGGAATTGGTGCTCTTGCAATGTCTGGATGGCTTGCAAATACACTCGA
TATAGCTCCACAATTTGGAAGTATAATTTTAGGAATATCAAATACTTTGGCAACATTACC
TGGCATAGTATCACCAATATTATCAGGATATATAGCTTCAACACCTAATTCATTTGAATA
TCGAATTATATTCATTATCACATGTGCAATTGGTGTTGCAGGCATGACATTCTATTTATT
CTTTGCAAGTGCAGAATTACAACCATGGGCTGTTGTAGAATCTAATGGTGACATTGAAAA
AAATAAAAATACTGACAAAAAAGCCAAAAATAAATTTAAGGAATAG

>g5751.t2 Gene=g5751 Length=438
MSVAIVAMTDNKSIIHDDNSETFEPEFDWSSKAKGYVLSSFFYGYICTQIPGGILASKIG
GQWVFGLGILGTAVMTLLTPILCYQGIGYLILSRVIQGICSGLAYPSINMVYANYIPPIE
RSRTASYGTSGIFVGTILGNFLSGLISEYFGWEYIFYIFGAVAVLWYVLWYFTVKSGPDH
DSWMSQGERDFIKKSIASQSGNKAQTTKTPWKAIFTSIPVYAIAISHFSYNWGYYTMLTQ
LPMYMRDILDFDVTKSGFLSALPYLVQTIIVYISGFLADFVQKKNILTTTQVRKYFNTTS
FVSQTIFLLIAAFVSNTPTIVACISMTVGIGALAMSGWLANTLDIAPQFGSIILGISNTL
ATLPGIVSPILSGYIASTPNSFEYRIIFIITCAIGVAGMTFYLFFASAELQPWAVVESNG
DIEKNKNTDKKAKNKFKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
30 g5751.t2 CDD cd17318 MFS_SLC17 1 406 1.24671E-135
5 g5751.t2 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains 9 185 1.4E-35
6 g5751.t2 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains 206 411 4.2E-29
2 g5751.t2 PANTHER PTHR11662 SOLUTE CARRIER FAMILY 17 1 423 6.5E-137
3 g5751.t2 PANTHER PTHR11662:SF437 GH23975P 1 423 6.5E-137
1 g5751.t2 Pfam PF07690 Major Facilitator Superfamily 26 289 3.0E-47
17 g5751.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 35 -
27 g5751.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 36 56 -
9 g5751.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 57 62 -
25 g5751.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 63 81 -
15 g5751.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 82 86 -
28 g5751.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 87 112 -
11 g5751.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 113 123 -
26 g5751.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 124 142 -
13 g5751.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 143 153 -
24 g5751.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 154 174 -
12 g5751.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 175 212 -
29 g5751.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 213 235 -
18 g5751.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 236 260 -
21 g5751.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 261 282 -
7 g5751.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 283 293 -
23 g5751.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 294 313 -
16 g5751.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 314 318 -
20 g5751.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 319 340 -
10 g5751.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 341 351 -
22 g5751.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 352 376 -
14 g5751.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 377 381 -
19 g5751.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 382 405 -
8 g5751.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 406 438 -
42 g5751.t2 ProSiteProfiles PS50850 Major facilitator superfamily (MFS) profile. 1 410 26.691
4 g5751.t2 SUPERFAMILY SSF103473 MFS general substrate transporter 23 407 1.27E-69
41 g5751.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 35 57 -
33 g5751.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 62 84 -
34 g5751.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 91 113 -
31 g5751.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 123 145 -
32 g5751.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 152 174 -
39 g5751.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 213 235 -
40 g5751.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 256 278 -
37 g5751.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 298 315 -
38 g5751.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 320 342 -
35 g5751.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 352 374 -
36 g5751.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 386 408 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5751/g5751.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5751.t2.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0055085 transmembrane transport BP
GO:0022857 transmembrane transporter activity MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed