Gene loci information

Transcript annotation

  • This transcript has been annotated as Toll-interacting protein.

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_1 g13364 g13364.t1 TSS g13364.t1 29524246 29524246
chr_1 g13364 g13364.t1 isoform g13364.t1 29524357 29525705
chr_1 g13364 g13364.t1 exon g13364.t1.exon1 29524357 29524398
chr_1 g13364 g13364.t1 cds g13364.t1.CDS1 29524357 29524398
chr_1 g13364 g13364.t1 exon g13364.t1.exon2 29524495 29524617
chr_1 g13364 g13364.t1 cds g13364.t1.CDS2 29524495 29524617
chr_1 g13364 g13364.t1 exon g13364.t1.exon3 29524932 29525177
chr_1 g13364 g13364.t1 cds g13364.t1.CDS3 29524932 29525177
chr_1 g13364 g13364.t1 exon g13364.t1.exon4 29525256 29525705
chr_1 g13364 g13364.t1 cds g13364.t1.CDS4 29525256 29525705
chr_1 g13364 g13364.t1 TTS g13364.t1 29526017 29526017

Sequences

>g13364.t1 Gene=g13364 Length=861
ATGGCATCAGAAGGAAGAGTATCAAAAGAAGAGTGGACAAGAGCTGTAACAACCATTCCA
CCAAACTTTTTACGATTAAACTCACAGCAAGAAGTGTTAGACAGAGAAGCAGCTTTAGCT
CTTCATCAACAACAAATTGGTCACTACAATCACATCGGTCTAGCTGCAAATACTGTTGGA
CGATTATCGATTACAGTTGCGCAAGCAAAATTAACAAAAAATTATGGACTTACACGAATG
GATCCTTATGTCAGAATTAGAGTGGGTCATTACATTTATGAAACGCAAACTGATACAAAT
GGAGGAAAAACACCACATTGGAATAGAGTGTTTCATTGTCAACTTCCAAGTGGAGTAAAT
AAAATATTTCTAGAAATTTACGATGAATGTAACTTCACTATGGATGAATTGATTGCATGG
GCAGAAATCAGAATTCCAGAAGCTGTTATTGAAAAATGTGAGACACATGAGGACTGGTAT
GCACTATCTGGAAAAACAGGAGACAATAAGGAAGGCATGATTGATCTTGTTCTTAGTTTT
ACACCAGCTTCATGTTTATATCAAAGACCAGCAATTGGTCAGCAACAAGTTGTACTTGTA
CCAAATGTTTCGAACCGTGCCCTTCCTGTTTATGTATCTCCAACACCAGTACAACAAATT
GCTCAACAACCACAATTGCCACAACAACAGCAGCAGCCAATAGAAATGCCAGCAGTACCA
CAAACTTTGACTGATGAAGATATAGCAAACCTTATGGAAATGTTTCCAAGTGTTGACAAA
GATGTCATTAAATCAATTGGAGAGGCTAATAGAGGAGACAAAAACGCTACAATTAATTCT
TTACTACAATTAACCAACTAA

>g13364.t1 Gene=g13364 Length=286
MASEGRVSKEEWTRAVTTIPPNFLRLNSQQEVLDREAALALHQQQIGHYNHIGLAANTVG
RLSITVAQAKLTKNYGLTRMDPYVRIRVGHYIYETQTDTNGGKTPHWNRVFHCQLPSGVN
KIFLEIYDECNFTMDELIAWAEIRIPEAVIEKCETHEDWYALSGKTGDNKEGMIDLVLSF
TPASCLYQRPAIGQQQVVLVPNVSNRALPVYVSPTPVQQIAQQPQLPQQQQQPIEMPAVP
QTLTDEDIANLMEMFPSVDKDVIKSIGEANRGDKNATINSLLQLTN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g13364.t1 CDD cd04016 C2_Tollip 59 180 0.000e+00
9 g13364.t1 Gene3D G3DSA:2.60.40.150 - 58 183 0.000e+00
8 g13364.t1 Gene3D G3DSA:1.10.8.10 DNA helicase RuvA subunit 239 286 0.000e+00
3 g13364.t1 PANTHER PTHR16461 TOLL-INTERACTING PROTEIN 16 285 0.000e+00
1 g13364.t1 Pfam PF00168 C2 domain 60 162 0.000e+00
2 g13364.t1 Pfam PF02845 CUE domain 245 284 0.000e+00
10 g13364.t1 ProSiteProfiles PS50004 C2 domain profile. 47 142 9.154e+00
11 g13364.t1 ProSiteProfiles PS51140 CUE domain profile. 243 286 1.557e+01
6 g13364.t1 SMART SM00239 C2_3c 61 157 3.700e-03
7 g13364.t1 SMART SM00546 cue_7 243 285 7.000e-07
4 g13364.t1 SUPERFAMILY SSF49562 C2 domain (Calcium/lipid-binding domain, CaLB) 58 183 0.000e+00
5 g13364.t1 SUPERFAMILY SSF46934 UBA-like 237 285 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:0043130 ubiquitin binding MF
GO:0005515 protein binding 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