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_1 g9855 g9855.t5 TSS g9855.t5 5632303 5632303
chr_1 g9855 g9855.t5 isoform g9855.t5 5632706 5637183
chr_1 g9855 g9855.t5 exon g9855.t5.exon1 5632706 5632787
chr_1 g9855 g9855.t5 cds g9855.t5.CDS1 5632706 5632787
chr_1 g9855 g9855.t5 exon g9855.t5.exon2 5633427 5633555
chr_1 g9855 g9855.t5 cds g9855.t5.CDS2 5633427 5633555
chr_1 g9855 g9855.t5 exon g9855.t5.exon3 5633625 5633742
chr_1 g9855 g9855.t5 cds g9855.t5.CDS3 5633625 5633742
chr_1 g9855 g9855.t5 exon g9855.t5.exon4 5633863 5634011
chr_1 g9855 g9855.t5 cds g9855.t5.CDS4 5633863 5634011
chr_1 g9855 g9855.t5 exon g9855.t5.exon5 5636262 5636581
chr_1 g9855 g9855.t5 cds g9855.t5.CDS5 5636262 5636581
chr_1 g9855 g9855.t5 exon g9855.t5.exon6 5636659 5637183
chr_1 g9855 g9855.t5 cds g9855.t5.CDS6 5636659 5637183
chr_1 g9855 g9855.t5 TTS g9855.t5 NA NA

Sequences

>g9855.t5 Gene=g9855 Length=1323
ATGAGAGCTATTCATATCAAATCAGAACGTTTCATAGTGGCATTTTTAATATATTCAAGC
TTATCACCATATGCATGCTATGGAAAAACCATTCAAATTCATAGTAAAGATTTGACAGAT
GAAGATTTAGGACTTCAAGATATTAGTCAATCAAATACTGAATCAATGCATACACCTGAT
CCATCAAAAATGCCACGACCAAATAAGAAAAAATTGATAAAATGTCACTGCGACAACTGC
CCAGAAACAAATTATGTGTGTGAAACTGATGGTGTTTGCTTTTACTCGTGGGAAAGAAAT
AATGATAATAAATATGAACACAGACAAAGGGGCTGTCTTGACAGAAAAAATTTCTTTCCG
CCAGAATGGCCGCGATGGTGTAATAATAAAGACACCATAAATTGTTGCAATGAAACTTTT
TGCAATGTATTAAAGTCAGAGATCAATCAGCCTGGTGAGGCTTTAAGAGATGAGTCCGTT
CCCGTTCAAAGTCCTTCTCCATGGATAGAAGGAAACACATCTATATTGTTAATAGCCTTT
ATGGCTTTATTAGCATGTTCTGTTGTAATTGGCGCATTCTCAATGTTCTTCCTTATGCGT
AAACGAAAGCACAACAGTGGAGGTCAACCTCTAATCACTACTGAAGAATCAATGTGTGGA
CAAACAATACAGGATATAATTGAAATGACAACTTCTGGATCAGGTTCTGCAGGCTTACCT
TTACTTGTGCAACGATCAATTGCACGTCAAATTCAACTCGAGAAAATTATCGGAAACGGT
CGATTTGGACAAGTTTGGGTTGGTCGATGGAGAGGTGAAAAGGTGGCGGTAAAAATATTT
TCGAGTCGTGAGGAATGTTCTTGGACACGTGAGGCTGAAATTTATCAGACATCAATGTTA
CGACATGACAACATTCTTGGTTTCATTGCTGCTGATAATAAGGATAATGGAACATGGACA
CAATTGTGGCTTGTAACTGATTATCATGAGAAAGGATCACTTTTTGACTATTTAAACACT
CACACTGTTAGTCCAAAAGAGATGGTTTTAATGGCTTTGACAATCGCAACTGGACTTGCT
CATCTTCATATGGATATTGTGGGAACTTTTGTCTGCAAATCTCACTGCCGTGAATGTAAA
GAATGCACTGGAAAACCTGGCATTGCACATCGTGATTTGAAGAGTAAAAATATTCTCGTA
AAAGCAAACGGTTCATGTGCTATTGGTGATTTGGGTCTTGCTGTTCGTCATAATGCTAAA
ACTGACACTATCGATATTCCATCAACACACAGAGTTGGAACAAAACGTTATATGGCTCCA
GAG

>g9855.t5 Gene=g9855 Length=441
MRAIHIKSERFIVAFLIYSSLSPYACYGKTIQIHSKDLTDEDLGLQDISQSNTESMHTPD
PSKMPRPNKKKLIKCHCDNCPETNYVCETDGVCFYSWERNNDNKYEHRQRGCLDRKNFFP
PEWPRWCNNKDTINCCNETFCNVLKSEINQPGEALRDESVPVQSPSPWIEGNTSILLIAF
MALLACSVVIGAFSMFFLMRKRKHNSGGQPLITTEESMCGQTIQDIIEMTTSGSGSAGLP
LLVQRSIARQIQLEKIIGNGRFGQVWVGRWRGEKVAVKIFSSREECSWTREAEIYQTSML
RHDNILGFIAADNKDNGTWTQLWLVTDYHEKGSLFDYLNTHTVSPKEMVLMALTIATGLA
HLHMDIVGTFVCKSHCRECKECTGKPGIAHRDLKSKNILVKANGSCAIGDLGLAVRHNAK
TDTIDIPSTHRVGTKRYMAPE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g9855.t5 Gene3D G3DSA:2.10.60.10 CD59 72 145 6.7E-16
8 g9855.t5 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 210 330 1.1E-48
9 g9855.t5 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 331 441 2.4E-25
3 g9855.t5 PANTHER PTHR23255:SF71 RECEPTOR PROTEIN SERINE/THREONINE KINASE 71 441 2.0E-135
4 g9855.t5 PANTHER PTHR23255 TRANSFORMING GROWTH FACTOR-BETA RECEPTOR TYPE I AND II 71 441 2.0E-135
1 g9855.t5 Pfam PF08515 Transforming growth factor beta type I GS-motif 222 249 1.1E-11
2 g9855.t5 Pfam PF00069 Protein kinase domain 253 441 2.7E-26
12 g9855.t5 Phobius SIGNAL_PEPTIDE Signal peptide region 1 28 -
13 g9855.t5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 10 -
14 g9855.t5 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 11 21 -
16 g9855.t5 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 22 28 -
11 g9855.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 29 174 -
15 g9855.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 175 198 -
10 g9855.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 199 441 -
19 g9855.t5 ProSitePatterns PS00107 Protein kinases ATP-binding region signature. 257 278 -
18 g9855.t5 ProSitePatterns PS00108 Serine/Threonine protein kinases active-site signature. 388 400 -
22 g9855.t5 ProSiteProfiles PS51256 GS domain profile. 221 250 15.128
23 g9855.t5 ProSiteProfiles PS50011 Protein kinase domain profile. 251 441 31.199
20 g9855.t5 SMART SM00467 GS_4 221 251 1.0E-12
21 g9855.t5 SMART SM00220 serkin_6 251 441 1.3E-7
5 g9855.t5 SUPERFAMILY SSF57302 Snake toxin-like 73 142 7.14E-7
6 g9855.t5 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 230 441 3.78E-50
17 g9855.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 176 198 -

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.

Raw TPM values