General information for g800.t156
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Nucleoporin SEH1.
Parent gene
- The parent gene g800 is located on chr_3: 6094101..6095287 (- strand)
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.t156 | TTS | g800.t156 | 6094022 | 6094022 |
| chr_3 | g800 | g800.t156 | isoform | g800.t156 | 6094101 | 6095161 |
| chr_3 | g800 | g800.t156 | exon | g800.t156.exon1 | 6094101 | 6094964 |
| chr_3 | g800 | g800.t156 | cds | g800.t156.CDS1 | 6094101 | 6094964 |
| chr_3 | g800 | g800.t156 | exon | g800.t156.exon2 | 6095021 | 6095161 |
| chr_3 | g800 | g800.t156 | cds | g800.t156.CDS2 | 6095021 | 6095158 |
| chr_3 | g800 | g800.t156 | TSS | g800.t156 | 6095387 | 6095387 |
Sequences
>g800.t156 Gene=g800 Length=1005
AGAATGGCAACATGTTCTTCAGATCAAACAATTAAAATATGGGAGCAGAATGAGAAAGGT
CAGGGACAATGGATTGTTTCAGCAAGTTGGAAAGCACATAGTGGATCTATTTGGCGTTTA
AGTTGGGCTCATCCTGAATTTGGAAGTGTCATTGCGTCAGCGTCATTTGACAGAACTGCG
AGTGTTTGGGAAGAAACAGCAGAACAAAAGCCTACACCAAGCTCTACGCCTGCAAAACGA
TGGATTCGAAGGACTAACCTTGTCGATAGCAGAACTTCAGTAACAGATGTCAAATTTTCT
CCAAAAAATCTTGGTCTTGTCTTAGCAACTTCATCATCTGATGGAATTATCAGAATATAT
GAGGCACCAGATATATGCAATTTGTCACAATGGACTTTACAACATGAGATTTTATGCAAG
TTACCACTTTCTTCTCTTAGTTGGAATCCATCTCTATTTCGTGCTCATGCACCTATGATA
GCTGCTGCAAGTGATGTTGCAACTTCAAATGAACCAAAAGTGTTTGTTTTTGAATATAGT
GAACTTAATAGACGTTGGACAAAAACTGAAAGCATAAATGTCACTGAACCAGTTCATTCT
ATCGAATTTGCGCCAAATGTTGGAAGAAGCTATCATATTCTTGCAGTCGCATCGAAAGAC
GTTAGCATTTTTAATTTAAAACCCATTGTGGAGCAAACTGGAACTTCAAGATTCGAAGTG
TCACAAGCAGCTCAATTCAATGATAATTTTTGTACTGTTTGGAAAGTAACTTGGAATGTA
ACTGGCACAATGTTAGCAACAAGTTCTGATGATGGATATGTAAGAATTTGGAGAATGAAT
TATCAAAAACTTTTCAAATGCATTTGTTCATATAAGCCAGATAGCAGTAGTGTCAGTCAT
CCATTAGATTCACAAACAGCAGCCATAATCAATTCCACAACAACTAAATTCTTCAAAAAA
GGAGTTGGCACTTTTGTAGCATCAAATCAAATACAACAACATTAA
>g800.t156 Gene=g800 Length=333
MATCSSDQTIKIWEQNEKGQGQWIVSASWKAHSGSIWRLSWAHPEFGSVIASASFDRTAS
VWEETAEQKPTPSSTPAKRWIRRTNLVDSRTSVTDVKFSPKNLGLVLATSSSDGIIRIYE
APDICNLSQWTLQHEILCKLPLSSLSWNPSLFRAHAPMIAAASDVATSNEPKVFVFEYSE
LNRRWTKTESINVTEPVHSIEFAPNVGRSYHILAVASKDVSIFNLKPIVEQTGTSRFEVS
QAAQFNDNFCTVWKVTWNVTGTMLATSSDDGYVRIWRMNYQKLFKCICSYKPDSSSVSHP
LDSQTAAIINSTTTKFFKKGVGTFVASNQIQQH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g800.t156 | Gene3D | G3DSA:2.130.10.10 | - | 1 | 293 | 0.000e+00 |
| 3 | g800.t156 | PANTHER | PTHR11024 | NUCLEAR PORE COMPLEX PROTEIN SEC13 / SEH1 FAMILY MEMBER | 1 | 293 | 0.000e+00 |
| 4 | g800.t156 | PANTHER | PTHR11024:SF3 | NUCLEOPORIN SEH1 | 1 | 293 | 0.000e+00 |
| 6 | g800.t156 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 1 | 14 | 1.100e-05 |
| 7 | g800.t156 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 50 | 64 | 1.100e-05 |
| 5 | g800.t156 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 264 | 278 | 1.100e-05 |
| 2 | g800.t156 | Pfam | PF00400 | WD domain, G-beta repeat | 92 | 119 | 1.500e-01 |
| 1 | g800.t156 | Pfam | PF00400 | WD domain, G-beta repeat | 251 | 276 | 7.300e-04 |
| 14 | g800.t156 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 1 | 129 | 1.387e+01 |
| 18 | g800.t156 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 1 | 14 | 9.105e+00 |
| 17 | g800.t156 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 29 | 63 | 8.737e+00 |
| 15 | g800.t156 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 245 | 286 | 9.599e+00 |
| 16 | g800.t156 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 245 | 279 | 9.940e+00 |
| 12 | g800.t156 | SMART | SM00320 | WD40_4 | 22 | 63 | 1.400e-03 |
| 10 | g800.t156 | SMART | SM00320 | WD40_4 | 83 | 120 | 2.700e-01 |
| 9 | g800.t156 | SMART | SM00320 | WD40_4 | 184 | 224 | 1.600e+02 |
| 11 | g800.t156 | SMART | SM00320 | WD40_4 | 238 | 277 | 6.000e-03 |
| 8 | g800.t156 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 1 | 297 | 0.000e+00 |
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
- This transcript has been annotated with K14299 (nucleoporin SEH1)
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.
