Gene loci information

Transcript annotation

  • This transcript has been annotated as TGF-beta receptor type-1.

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_4 g16045 g16045.t1 TTS g16045.t1 7920685 7920685
chr_4 g16045 g16045.t1 isoform g16045.t1 7920793 7922106
chr_4 g16045 g16045.t1 exon g16045.t1.exon1 7920793 7920966
chr_4 g16045 g16045.t1 cds g16045.t1.CDS1 7920793 7920966
chr_4 g16045 g16045.t1 exon g16045.t1.exon2 7921038 7921220
chr_4 g16045 g16045.t1 cds g16045.t1.CDS2 7921038 7921220
chr_4 g16045 g16045.t1 exon g16045.t1.exon3 7921579 7922106
chr_4 g16045 g16045.t1 cds g16045.t1.CDS3 7921579 7922106
chr_4 g16045 g16045.t1 TSS g16045.t1 7922496 7922496

Sequences

>g16045.t1 Gene=g16045 Length=885
ATGCATTTTAAGGTTGGAAACTGGAGACATGAAAAAGTAGCCATTAAAATTTTTTCAACA
AGTGATAAAAATTCTTGGATGAATGAAATAGAAATTTATCGAATTCCAATGTTCAATCAT
AAAAATATTCTTGGGTTTATTGCAGCAGATATGAAACTCTTTAAAAATAATTTTCAATTT
TGGCTTATCACCGACTACCATGAAAATGGTTCACTTTATGATTTTTTAAACCTTAACAGT
GTTAGTCCACAAACTGCAATTCTTATGGCTTTATCAATTGCATCTGGTTTATGTCATCTT
CATATGGAAATTATCACAAATTATTTCTCAAAATCACATTGTGAAACTTACAAAAATTTT
AAAAACAAACCCAAAATTTCTCATTGTGATTTAAACAGCAAAAATATTTTTATTAAATCA
AATTTAACATGTGCAATTGGTGGTTTGAGTTCTGCAATTTACCAAAATGATGAAAATAAT
TACAAACTTCCTGAGAAAATTGAAAATCTTCGCTATTTATCACCAGAAATTGTAAATGGA
ACAATAAATTTGACAAATTTCGATTCATTTTGTTATGCTGATATTTATTCATATGGTCTA
ATTCTTTGGGAAATAACAAGACGATGTAAAATTAATGACAAAACTGAAAATTATCAATTA
CCATACTTTGATGTCATACAAACGAATACAAATATTGACGAAATAAGAGAAGTGATATGC
ATAAAAAAGATTCGTCCAATAATTTCCAATGAATGGCTTAAATCTGACTTACTACGCTCG
ATGTCAAAGATCATGTGTGATTGTTGGTATGAAAATGCATCAGCACGTGTCTCTGCCTTG
AGAATTAAAAAATCATTATCAGGACTCAATGTCAATACACCTTGA

>g16045.t1 Gene=g16045 Length=294
MHFKVGNWRHEKVAIKIFSTSDKNSWMNEIEIYRIPMFNHKNILGFIAADMKLFKNNFQF
WLITDYHENGSLYDFLNLNSVSPQTAILMALSIASGLCHLHMEIITNYFSKSHCETYKNF
KNKPKISHCDLNSKNIFIKSNLTCAIGGLSSAIYQNDENNYKLPEKIENLRYLSPEIVNG
TINLTNFDSFCYADIYSYGLILWEITRRCKINDKTENYQLPYFDVIQTNTNIDEIREVIC
IKKIRPIISNEWLKSDLLRSMSKIMCDCWYENASARVSALRIKKSLSGLNVNTP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g16045.t1 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 3 68 0.000
6 g16045.t1 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 69 292 0.000
2 g16045.t1 PANTHER PTHR23255:SF71 RECEPTOR PROTEIN SERINE/THREONINE KINASE 6 290 0.000
3 g16045.t1 PANTHER PTHR23255 TRANSFORMING GROWTH FACTOR-BETA RECEPTOR TYPE I AND II 6 290 0.000
8 g16045.t1 PIRSF PIRSF000654 ILK 1 293 0.000
1 g16045.t1 Pfam PF07714 Protein tyrosine and serine/threonine kinase 9 285 0.000
7 g16045.t1 ProSiteProfiles PS50011 Protein kinase domain profile. 1 294 22.888
4 g16045.t1 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 7 287 0.000

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:0016020 membrane CC
GO:0005524 ATP binding MF
GO:0004672 protein kinase activity MF
GO:0006468 protein phosphorylation BP
GO:0007178 transmembrane receptor protein serine/threonine kinase signaling pathway BP
GO:0004675 transmembrane receptor protein serine/threonine kinase 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