General information for g9855.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as TGF-beta receptor type-1.
Parent gene
- The parent gene g9855 is located on chr_1: 5637672..5639149 (+ 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_1 | g9855 | g9855.t1 | TSS | g9855.t1 | 5632303 | 5632303 |
| chr_1 | g9855 | g9855.t1 | isoform | g9855.t1 | 5632706 | 5637672 |
| chr_1 | g9855 | g9855.t1 | exon | g9855.t1.exon1 | 5632706 | 5632787 |
| chr_1 | g9855 | g9855.t1 | cds | g9855.t1.CDS1 | 5632706 | 5632787 |
| chr_1 | g9855 | g9855.t1 | exon | g9855.t1.exon2 | 5633427 | 5633555 |
| chr_1 | g9855 | g9855.t1 | cds | g9855.t1.CDS2 | 5633427 | 5633555 |
| chr_1 | g9855 | g9855.t1 | exon | g9855.t1.exon3 | 5633625 | 5633742 |
| chr_1 | g9855 | g9855.t1 | cds | g9855.t1.CDS3 | 5633625 | 5633742 |
| chr_1 | g9855 | g9855.t1 | exon | g9855.t1.exon4 | 5634656 | 5634789 |
| chr_1 | g9855 | g9855.t1 | cds | g9855.t1.CDS4 | 5634656 | 5634789 |
| chr_1 | g9855 | g9855.t1 | exon | g9855.t1.exon5 | 5636262 | 5636581 |
| chr_1 | g9855 | g9855.t1 | cds | g9855.t1.CDS5 | 5636262 | 5636581 |
| chr_1 | g9855 | g9855.t1 | exon | g9855.t1.exon6 | 5636659 | 5637183 |
| chr_1 | g9855 | g9855.t1 | cds | g9855.t1.CDS6 | 5636659 | 5637183 |
| chr_1 | g9855 | g9855.t1 | exon | g9855.t1.exon7 | 5637242 | 5637424 |
| chr_1 | g9855 | g9855.t1 | cds | g9855.t1.CDS7 | 5637242 | 5637424 |
| chr_1 | g9855 | g9855.t1 | exon | g9855.t1.exon8 | 5637496 | 5637672 |
| chr_1 | g9855 | g9855.t1 | cds | g9855.t1.CDS8 | 5637496 | 5637672 |
| chr_1 | g9855 | g9855.t1 | TTS | g9855.t1 | NA | NA |
Sequences
>g9855.t1 Gene=g9855 Length=1668
ATGAGAGCTATTCATATCAAATCAGAACGTTTCATAGTGGCATTTTTAATATATTCAAGC
TTATCACCATATGCATGCTATGGAAAAACCATTCAAATTCATAGTAAAGATTTGACAGAT
GAAGATTTAGGACTTCAAGATATTAGTCAATCAAATACTGAATCAATGCATACACCTGAT
CCATCAAAAATGCCACGACCAAATAAGAAAAAATTGATAAAATGTCACTGCGACAACTGC
CCAGAAACAAATTATGTGTGTGAAACTGATGGTGTTTGCTTTTACTCGTGGGAAAGAAAT
AATGATAATAAATATGAACACAGACAAAGTTGTTTAGACTCAGGACTCATCATTGAAGGT
CGATTTCCTATACAATGTTATTCGACAAAACAAAAAAAGGAGTTTTATAATTCAGATTGC
TGCAAAACAGATTTTTGCAATGCCAACGTTTTGCCACAGCCAGTTCCCGTTCAAAGTCCT
TCTCCATGGATAGAAGGAAACACATCTATATTGTTAATAGCCTTTATGGCTTTATTAGCA
TGTTCTGTTGTAATTGGCGCATTCTCAATGTTCTTCCTTATGCGTAAACGAAAGCACAAC
AGTGGAGGTCAACCTCTAATCACTACTGAAGAATCAATGTGTGGACAAACAATACAGGAT
ATAATTGAAATGACAACTTCTGGATCAGGTTCTGCAGGCTTACCTTTACTTGTGCAACGA
TCAATTGCACGTCAAATTCAACTCGAGAAAATTATCGGAAACGGTCGATTTGGACAAGTT
TGGGTTGGTCGATGGAGAGGTGAAAAGGTGGCGGTAAAAATATTTTCGAGTCGTGAGGAA
TGTTCTTGGACACGTGAGGCTGAAATTTATCAGACATCAATGTTACGACATGACAACATT
CTTGGTTTCATTGCTGCTGATAATAAGGATAATGGAACATGGACACAATTGTGGCTTGTA
ACTGATTATCATGAGAAAGGATCACTTTTTGACTATTTAAACACTCACACTGTTAGTCCA
AAAGAGATGGTTTTAATGGCTTTGACAATCGCAACTGGACTTGCTCATCTTCATATGGAT
ATTGTGGGAACTTTTGTCTGCAAATCTCACTGCCGTGAATGTAAAGAATGCACTGGAAAA
CCTGGCATTGCACATCGTGATTTGAAGAGTAAAAATATTCTCGTAAAAGCAAACGGTTCA
TGTGCTATTGGTGATTTGGGTCTTGCTGTTCGTCATAATGCTAAAACTGACACTATCGAT
ATTCCATCAACACACAGAGTTGGAACAAAACGTTATATGGCTCCAGAGGTTCTTGATGAT
ACAATCAATATTCATCATTTTGACTCCTTTAAACGTGCTGACATTTATGCATATGGTTTA
ATACTATGGGAAATTGCGAGAAGATGTAATATCAATAACATGTATGAAGATTATCAACTG
CCGTTCTTTGATGTTGTTCAACCAGATCCGAGTATAGAGGAAATGAAAAAAGTGGTTTGT
ACTGATAATCAACGTCCAGTGATTCCAAATAAATGGCAGTCGTCTGATTTGCTGCTCGGA
ATGTCAAAGATCATGAAAGATTGCTGGTATCAAAACCCAGCTGCACGTTTAACAGCCTTG
AGAATAAAGAAGACATTATCAACGTTAAGTGTGAATGAGAAACTCTAA
>g9855.t1 Gene=g9855 Length=555
MRAIHIKSERFIVAFLIYSSLSPYACYGKTIQIHSKDLTDEDLGLQDISQSNTESMHTPD
PSKMPRPNKKKLIKCHCDNCPETNYVCETDGVCFYSWERNNDNKYEHRQSCLDSGLIIEG
RFPIQCYSTKQKKEFYNSDCCKTDFCNANVLPQPVPVQSPSPWIEGNTSILLIAFMALLA
CSVVIGAFSMFFLMRKRKHNSGGQPLITTEESMCGQTIQDIIEMTTSGSGSAGLPLLVQR
SIARQIQLEKIIGNGRFGQVWVGRWRGEKVAVKIFSSREECSWTREAEIYQTSMLRHDNI
LGFIAADNKDNGTWTQLWLVTDYHEKGSLFDYLNTHTVSPKEMVLMALTIATGLAHLHMD
IVGTFVCKSHCRECKECTGKPGIAHRDLKSKNILVKANGSCAIGDLGLAVRHNAKTDTID
IPSTHRVGTKRYMAPEVLDDTINIHHFDSFKRADIYAYGLILWEIARRCNINNMYEDYQL
PFFDVVQPDPSIEEMKKVVCTDNQRPVIPNKWQSSDLLLGMSKIMKDCWYQNPAARLTAL
RIKKTLSTLSVNEKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g9855.t1 | CDD | cd14143 | STKc_TGFbR1_ACVR1b_ACVR1c | 251 | 550 | 0.0 |
| 8 | g9855.t1 | Gene3D | G3DSA:2.10.60.10 | CD59 | 72 | 150 | 1.1E-17 |
| 9 | g9855.t1 | Gene3D | G3DSA:3.30.200.20 | Phosphorylase Kinase; domain 1 | 205 | 325 | 1.6E-48 |
| 10 | g9855.t1 | Gene3D | G3DSA:1.10.510.10 | Transferase(Phosphotransferase) domain 1 | 326 | 554 | 4.4E-58 |
| 4 | g9855.t1 | PANTHER | PTHR23255:SF71 | RECEPTOR PROTEIN SERINE/THREONINE KINASE | 71 | 553 | 1.6E-197 |
| 5 | g9855.t1 | PANTHER | PTHR23255 | TRANSFORMING GROWTH FACTOR-BETA RECEPTOR TYPE I AND II | 71 | 553 | 1.6E-197 |
| 18 | g9855.t1 | PIRSF | PIRSF037393 | TGFRII | 41 | 555 | 8.6E-76 |
| 3 | g9855.t1 | Pfam | PF01064 | Activin types I and II receptor domain | 74 | 149 | 2.0E-6 |
| 1 | g9855.t1 | Pfam | PF08515 | Transforming growth factor beta type I GS-motif | 217 | 244 | 1.5E-11 |
| 2 | g9855.t1 | Pfam | PF00069 | Protein kinase domain | 248 | 544 | 6.1E-35 |
| 13 | g9855.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 28 | - |
| 14 | g9855.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 10 | - |
| 15 | g9855.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 11 | 21 | - |
| 17 | g9855.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 22 | 28 | - |
| 12 | g9855.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 29 | 169 | - |
| 16 | g9855.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 170 | 193 | - |
| 11 | g9855.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 194 | 555 | - |
| 24 | g9855.t1 | ProSitePatterns | PS00107 | Protein kinases ATP-binding region signature. | 252 | 273 | - |
| 23 | g9855.t1 | ProSitePatterns | PS00108 | Serine/Threonine protein kinases active-site signature. | 383 | 395 | - |
| 25 | g9855.t1 | ProSiteProfiles | PS51256 | GS domain profile. | 216 | 245 | 15.128 |
| 26 | g9855.t1 | ProSiteProfiles | PS50011 | Protein kinase domain profile. | 246 | 549 | 37.573 |
| 21 | g9855.t1 | SMART | SM00467 | GS_4 | 216 | 246 | 1.0E-12 |
| 22 | g9855.t1 | SMART | SM00220 | serkin_6 | 246 | 549 | 1.0E-25 |
| 6 | g9855.t1 | SUPERFAMILY | SSF57302 | Snake toxin-like | 73 | 154 | 4.81E-11 |
| 7 | g9855.t1 | SUPERFAMILY | SSF56112 | Protein kinase-like (PK-like) | 225 | 546 | 1.48E-69 |
| 20 | g9855.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 171 | 193 | - |
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:0038023 | signaling receptor activity | MF |
| GO:0016020 | membrane | CC |
| GO:0005524 | ATP binding | MF |
| GO:0006468 | protein phosphorylation | BP |
| GO:0007178 | transmembrane receptor protein serine/threonine kinase signaling pathway | BP |
| GO:0043235 | receptor complex | CC |
| GO:0046872 | metal ion binding | MF |
| GO:0004674 | protein serine/threonine kinase activity | MF |
| GO:0004672 | protein kinase activity | MF |
| GO:0016021 | integral component of membrane | CC |
| GO:0004675 | transmembrane receptor protein serine/threonine kinase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K04674 (TGF-beta receptor type-1)
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.
