General information for g800.t1
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.t1 | TTS | g800.t1 | 6094022 | 6094022 |
| chr_3 | g800 | g800.t1 | isoform | g800.t1 | 6094101 | 6095287 |
| chr_3 | g800 | g800.t1 | exon | g800.t1.exon1 | 6094101 | 6094964 |
| chr_3 | g800 | g800.t1 | cds | g800.t1.CDS1 | 6094101 | 6094964 |
| chr_3 | g800 | g800.t1 | exon | g800.t1.exon2 | 6095021 | 6095161 |
| chr_3 | g800 | g800.t1 | cds | g800.t1.CDS2 | 6095021 | 6095161 |
| chr_3 | g800 | g800.t1 | exon | g800.t1.exon3 | 6095219 | 6095287 |
| chr_3 | g800 | g800.t1 | cds | g800.t1.CDS3 | 6095219 | 6095287 |
| chr_3 | g800 | g800.t1 | TSS | g800.t1 | 6095387 | 6095387 |
Sequences
>g800.t1 Gene=g800 Length=1074
ATGAGTTCAATCGTTCATACTGAGCACAGAGATGTTATCCACGATTGCAGTTATGATTAT
TATGGCCAAAGAATGGCAACATGTTCTTCAGATCAAACAATTAAAATATGGGAGCAGAAT
GAGAAAGGTCAGGGACAATGGATTGTTTCAGCAAGTTGGAAAGCACATAGTGGATCTATT
TGGCGTTTAAGTTGGGCTCATCCTGAATTTGGAAGTGTCATTGCGTCAGCGTCATTTGAC
AGAACTGCGAGTGTTTGGGAAGAAACAGCAGAACAAAAGCCTACACCAAGCTCTACGCCT
GCAAAACGATGGATTCGAAGGACTAACCTTGTCGATAGCAGAACTTCAGTAACAGATGTC
AAATTTTCTCCAAAAAATCTTGGTCTTGTCTTAGCAACTTCATCATCTGATGGAATTATC
AGAATATATGAGGCACCAGATATATGCAATTTGTCACAATGGACTTTACAACATGAGATT
TTATGCAAGTTACCACTTTCTTCTCTTAGTTGGAATCCATCTCTATTTCGTGCTCATGCA
CCTATGATAGCTGCTGCAAGTGATGTTGCAACTTCAAATGAACCAAAAGTGTTTGTTTTT
GAATATAGTGAACTTAATAGACGTTGGACAAAAACTGAAAGCATAAATGTCACTGAACCA
GTTCATTCTATCGAATTTGCGCCAAATGTTGGAAGAAGCTATCATATTCTTGCAGTCGCA
TCGAAAGACGTTAGCATTTTTAATTTAAAACCCATTGTGGAGCAAACTGGAACTTCAAGA
TTCGAAGTGTCACAAGCAGCTCAATTCAATGATAATTTTTGTACTGTTTGGAAAGTAACT
TGGAATGTAACTGGCACAATGTTAGCAACAAGTTCTGATGATGGATATGTAAGAATTTGG
AGAATGAATTATCAAAAACTTTTCAAATGCATTTGTTCATATAAGCCAGATAGCAGTAGT
GTCAGTCATCCATTAGATTCACAAACAGCAGCCATAATCAATTCCACAACAACTAAATTC
TTCAAAAAAGGAGTTGGCACTTTTGTAGCATCAAATCAAATACAACAACATTAA
>g800.t1 Gene=g800 Length=357
MSSIVHTEHRDVIHDCSYDYYGQRMATCSSDQTIKIWEQNEKGQGQWIVSASWKAHSGSI
WRLSWAHPEFGSVIASASFDRTASVWEETAEQKPTPSSTPAKRWIRRTNLVDSRTSVTDV
KFSPKNLGLVLATSSSDGIIRIYEAPDICNLSQWTLQHEILCKLPLSSLSWNPSLFRAHA
PMIAAASDVATSNEPKVFVFEYSELNRRWTKTESINVTEPVHSIEFAPNVGRSYHILAVA
SKDVSIFNLKPIVEQTGTSRFEVSQAAQFNDNFCTVWKVTWNVTGTMLATSSDDGYVRIW
RMNYQKLFKCICSYKPDSSSVSHPLDSQTAAIINSTTTKFFKKGVGTFVASNQIQQH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g800.t1 | Gene3D | G3DSA:2.130.10.10 | - | 3 | 317 | 0.000000 |
| 4 | g800.t1 | PANTHER | PTHR11024 | NUCLEAR PORE COMPLEX PROTEIN SEC13 / SEH1 FAMILY MEMBER | 5 | 317 | 0.000000 |
| 5 | g800.t1 | PANTHER | PTHR11024:SF3 | NUCLEOPORIN SEH1 | 5 | 317 | 0.000000 |
| 7 | g800.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 25 | 39 | 0.000026 |
| 6 | g800.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 74 | 88 | 0.000026 |
| 8 | g800.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 288 | 302 | 0.000026 |
| 2 | g800.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 7 | 37 | 0.000830 |
| 3 | g800.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 116 | 143 | 0.160000 |
| 1 | g800.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 275 | 300 | 0.000800 |
| 16 | g800.t1 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 6 | 153 | 14.582000 |
| 19 | g800.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 6 | 38 | 10.007000 |
| 18 | g800.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 53 | 87 | 8.737000 |
| 17 | g800.t1 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 269 | 310 | 9.599000 |
| 20 | g800.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 269 | 303 | 9.940000 |
| 14 | g800.t1 | SMART | SM00320 | WD40_4 | 1 | 38 | 0.002700 |
| 10 | g800.t1 | SMART | SM00320 | WD40_4 | 46 | 87 | 0.001400 |
| 11 | g800.t1 | SMART | SM00320 | WD40_4 | 107 | 144 | 0.270000 |
| 12 | g800.t1 | SMART | SM00320 | WD40_4 | 208 | 248 | 160.000000 |
| 13 | g800.t1 | SMART | SM00320 | WD40_4 | 262 | 301 | 0.006000 |
| 9 | g800.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 7 | 321 | 0.000000 |
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.
