Gene loci information

Transcript annotation

  • This transcript has been annotated as Nucleoporin SEH1.

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_3 g800 g800.t158 TTS g800.t158 6094022 6094022
chr_3 g800 g800.t158 isoform g800.t158 6094101 6095287
chr_3 g800 g800.t158 exon g800.t158.exon1 6094101 6094964
chr_3 g800 g800.t158 cds g800.t158.CDS1 6094101 6094964
chr_3 g800 g800.t158 exon g800.t158.exon2 6095021 6095161
chr_3 g800 g800.t158 cds g800.t158.CDS2 6095021 6095158
chr_3 g800 g800.t158 exon g800.t158.exon3 6095215 6095287
chr_3 g800 g800.t158 TSS g800.t158 6095387 6095387

Sequences

>g800.t158 Gene=g800 Length=1078
ATGAGTTCAATCGTTCATACTGAGCACAGAGATGTTATCCACGATTGCAGTTATGATTAT
TATGGCCAAGTAAAGAATGGCAACATGTTCTTCAGATCAAACAATTAAAATATGGGAGCA
GAATGAGAAAGGTCAGGGACAATGGATTGTTTCAGCAAGTTGGAAAGCACATAGTGGATC
TATTTGGCGTTTAAGTTGGGCTCATCCTGAATTTGGAAGTGTCATTGCGTCAGCGTCATT
TGACAGAACTGCGAGTGTTTGGGAAGAAACAGCAGAACAAAAGCCTACACCAAGCTCTAC
GCCTGCAAAACGATGGATTCGAAGGACTAACCTTGTCGATAGCAGAACTTCAGTAACAGA
TGTCAAATTTTCTCCAAAAAATCTTGGTCTTGTCTTAGCAACTTCATCATCTGATGGAAT
TATCAGAATATATGAGGCACCAGATATATGCAATTTGTCACAATGGACTTTACAACATGA
GATTTTATGCAAGTTACCACTTTCTTCTCTTAGTTGGAATCCATCTCTATTTCGTGCTCA
TGCACCTATGATAGCTGCTGCAAGTGATGTTGCAACTTCAAATGAACCAAAAGTGTTTGT
TTTTGAATATAGTGAACTTAATAGACGTTGGACAAAAACTGAAAGCATAAATGTCACTGA
ACCAGTTCATTCTATCGAATTTGCGCCAAATGTTGGAAGAAGCTATCATATTCTTGCAGT
CGCATCGAAAGACGTTAGCATTTTTAATTTAAAACCCATTGTGGAGCAAACTGGAACTTC
AAGATTCGAAGTGTCACAAGCAGCTCAATTCAATGATAATTTTTGTACTGTTTGGAAAGT
AACTTGGAATGTAACTGGCACAATGTTAGCAACAAGTTCTGATGATGGATATGTAAGAAT
TTGGAGAATGAATTATCAAAAACTTTTCAAATGCATTTGTTCATATAAGCCAGATAGCAG
TAGTGTCAGTCATCCATTAGATTCACAAACAGCAGCCATAATCAATTCCACAACAACTAA
ATTCTTCAAAAAAGGAGTTGGCACTTTTGTAGCATCAAATCAAATACAACAACATTAA

>g800.t158 Gene=g800 Length=333
MATCSSDQTIKIWEQNEKGQGQWIVSASWKAHSGSIWRLSWAHPEFGSVIASASFDRTAS
VWEETAEQKPTPSSTPAKRWIRRTNLVDSRTSVTDVKFSPKNLGLVLATSSSDGIIRIYE
APDICNLSQWTLQHEILCKLPLSSLSWNPSLFRAHAPMIAAASDVATSNEPKVFVFEYSE
LNRRWTKTESINVTEPVHSIEFAPNVGRSYHILAVASKDVSIFNLKPIVEQTGTSRFEVS
QAAQFNDNFCTVWKVTWNVTGTMLATSSDDGYVRIWRMNYQKLFKCICSYKPDSSSVSHP
LDSQTAAIINSTTTKFFKKGVGTFVASNQIQQH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g800.t158 Coils Coil Coil 330 333 -
9 g800.t158 Gene3D G3DSA:2.130.10.10 - 1 293 4.2E-62
3 g800.t158 PANTHER PTHR11024 NUCLEAR PORE COMPLEX PROTEIN SEC13 / SEH1 FAMILY MEMBER 1 293 2.9E-94
4 g800.t158 PANTHER PTHR11024:SF3 NUCLEOPORIN SEH1 1 293 2.9E-94
6 g800.t158 PRINTS PR00320 G protein beta WD-40 repeat signature 1 14 1.1E-5
7 g800.t158 PRINTS PR00320 G protein beta WD-40 repeat signature 50 64 1.1E-5
5 g800.t158 PRINTS PR00320 G protein beta WD-40 repeat signature 264 278 1.1E-5
2 g800.t158 Pfam PF00400 WD domain, G-beta repeat 92 119 0.15
1 g800.t158 Pfam PF00400 WD domain, G-beta repeat 251 276 7.3E-4
15 g800.t158 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 1 129 13.87
19 g800.t158 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 1 14 9.105
18 g800.t158 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 29 63 8.737
16 g800.t158 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 245 286 9.599
17 g800.t158 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 245 279 9.94
14 g800.t158 SMART SM00320 WD40_4 22 63 0.0014
12 g800.t158 SMART SM00320 WD40_4 83 120 0.27
11 g800.t158 SMART SM00320 WD40_4 184 224 160.0
13 g800.t158 SMART SM00320 WD40_4 238 277 0.006
8 g800.t158 SUPERFAMILY SSF50978 WD40 repeat-like 1 297 2.0E-32

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:1904263 positive regulation of TORC1 signaling BP
GO:0005515 protein binding MF
GO:0005198 structural molecule activity MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

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.

Raw TPM values