General information for g10598.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Mothers against decapentaplegic homolog 4.
Parent gene
- The parent gene g10598 is located on chr_1: 10600476..10601537 (+ 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 | g10598 | g10598.t1 | TSS | g10598.t1 | 10597641 | 10597641 |
| chr_1 | g10598 | g10598.t1 | isoform | g10598.t1 | 10597781 | 10600476 |
| chr_1 | g10598 | g10598.t1 | exon | g10598.t1.exon1 | 10597781 | 10597820 |
| chr_1 | g10598 | g10598.t1 | cds | g10598.t1.CDS1 | 10597781 | 10597820 |
| chr_1 | g10598 | g10598.t1 | exon | g10598.t1.exon2 | 10597957 | 10598036 |
| chr_1 | g10598 | g10598.t1 | cds | g10598.t1.CDS2 | 10597957 | 10598036 |
| chr_1 | g10598 | g10598.t1 | exon | g10598.t1.exon3 | 10598139 | 10598670 |
| chr_1 | g10598 | g10598.t1 | cds | g10598.t1.CDS3 | 10598139 | 10598670 |
| chr_1 | g10598 | g10598.t1 | exon | g10598.t1.exon4 | 10598830 | 10598991 |
| chr_1 | g10598 | g10598.t1 | cds | g10598.t1.CDS4 | 10598830 | 10598991 |
| chr_1 | g10598 | g10598.t1 | exon | g10598.t1.exon5 | 10599111 | 10599394 |
| chr_1 | g10598 | g10598.t1 | cds | g10598.t1.CDS5 | 10599111 | 10599394 |
| chr_1 | g10598 | g10598.t1 | exon | g10598.t1.exon6 | 10599461 | 10599560 |
| chr_1 | g10598 | g10598.t1 | cds | g10598.t1.CDS6 | 10599461 | 10599560 |
| chr_1 | g10598 | g10598.t1 | exon | g10598.t1.exon7 | 10599627 | 10599864 |
| chr_1 | g10598 | g10598.t1 | cds | g10598.t1.CDS7 | 10599627 | 10599864 |
| chr_1 | g10598 | g10598.t1 | exon | g10598.t1.exon8 | 10599924 | 10600216 |
| chr_1 | g10598 | g10598.t1 | cds | g10598.t1.CDS8 | 10599924 | 10600216 |
| chr_1 | g10598 | g10598.t1 | exon | g10598.t1.exon9 | 10600274 | 10600476 |
| chr_1 | g10598 | g10598.t1 | cds | g10598.t1.CDS9 | 10600274 | 10600476 |
| chr_1 | g10598 | g10598.t1 | TTS | g10598.t1 | 10601442 | 10601442 |
Sequences
>g10598.t1 Gene=g10598 Length=1932
ATGGTTTCCGGACTTTATTCGACAGGATCACAAGAAAAAAAAATGAACACTATGCCGTCA
ACTGCACCGACTAGTGCGGATGCTTGTTTAAGCATTGTGCACAGTTTAATGTGTCATCGT
CAAGGAGGCGAATCAGAAGGCTTTGCAAAACGAGCGATTGAGTCGCTTGTAAAGAAGCTA
AAAGAAAAACGTGATGAACTAGATTCACTTATAACAGCAATTACTACGAATGGTGCACAT
CCAAGCAAATGTGTTACCATTCAGAGGACGCTTGATGGTCGTTTGCAAGTAGCTGGTCGC
AAAGGCTTTCCACATGTGATTTATGCACGCATATGGCGTTGGCCTGATTTACATAAAAAC
GAATTGAAGCATGTAAAATACTGCCAATTTGCATTCGACCTCAAATGTGATTCCGTTTGC
GTCAATCCTTACCATTATGAGCGTGTTGTGTCACCAGGCATTGATTTATCAGGACTTACG
CTTCAAGCTGGACCACGAAATATAGTTAAAGATGAATATAGTGCTGGTTCTTCTATGGTA
GGAACATCAAATATTGAAATGGACGGCAATGAAATTGGTACAATTCAACATCATCCAATT
CATATTAGTATGGGCTATTCTACTATGACTATGCATCAAACACCTGGCTCTGGCGATACA
AAAAATCCATCAATAATTTATCCACCTCGTGTGGTGCCAAAGGTTGAACCCAATAGTGAT
GTGCAAGTTGTGAGAAATCAAATTTGGGGACAACCACCAACTAATCAGATACCACCGCAA
CAACAAGCTCAGCAGCCACAACGTTTAGCACATCCTACTACACACATTTTACCAGTGAGC
AGTCCTGAAAATGCTCTCTTACAGCAGCAAAAACCAACTTCATCGACACAAACATCACAA
CAGCAAACGCCACAACAGTCATCACAAATACCCGGAACGAGTTTAATCAATCAGCAGGCA
GCGGGTAGCTCACAAGCATCAGCAAACAATCAGCAGTCGCAAGATCAAAGTTATTTTACC
ACTTCGACCGATACTCAAATCACTGATTCCCAAACAGCTACATCTCCCATTCAAATGCCA
CAAAATAATGGTTATGCGGCAGCAGCATGGACAGCACGTGGTTCCAACACATTGACCTAT
ACACAATCAATGCAACCGCCTGATCATCCCAGTTCACGACCTATTAATCAACCTTATTGG
CCACAAATGCAAACTGAAATGACAGGACAACAACGTTTATCACGACAACCAGCACCCGAA
TATTGGTGTTCAATTGCATATTTTGAGCTCGATACGCAAGTTGGTGAGACATTCAAAGTG
CCATCAAGTAAACCTCATGTCACAGTCGATGGCTATGTCGATCCAAGTGGTGGTAATCGA
TTTTGTTTGGGTGCACTTAGTAATGTACATCGAACTGAACAAAGTGAAAGAGCTCGTTTA
CATATTGGAAAAGGTGTTCAATTAGATTTGCGAGGTGAAGGTGATGTTTGGTTGAGATGT
TTAAGTGATCATTCGGTATTTGTGCAAAGTTATTATCTTGATCGTGAAGCTGGTCGTACG
CCTGGTGATGCTGTTCATAAAATATATCCTTCAGCGTGTATAAAAGTCTTTGATTTGCGT
CAGTGTCATCAACAAATGCAATCACTTGCAGCTAATGCTCAAGCTGCTGCTGCTGCACAG
GCTGCTGCTGTCGCTGGAATACCAGGACATAATGTTGTTCCATCTAGAAATATATCAGCA
GCTGCTGGCATAGGTGTTGATGATTTGAGGCGTCTTTGTATTTTACGTCTTAGTTTTGTG
AAAGGATGGGGACCCGATTATCCACGTCAATCAATCAAAGATACACCATGCTGGGTTGAA
GTTCACTTACATCGTGCACTTCAGCTTCTTGACGAGGTATTACATAACATGCCTATCGAT
GGTCGTGATTAA
>g10598.t1 Gene=g10598 Length=643
MVSGLYSTGSQEKKMNTMPSTAPTSADACLSIVHSLMCHRQGGESEGFAKRAIESLVKKL
KEKRDELDSLITAITTNGAHPSKCVTIQRTLDGRLQVAGRKGFPHVIYARIWRWPDLHKN
ELKHVKYCQFAFDLKCDSVCVNPYHYERVVSPGIDLSGLTLQAGPRNIVKDEYSAGSSMV
GTSNIEMDGNEIGTIQHHPIHISMGYSTMTMHQTPGSGDTKNPSIIYPPRVVPKVEPNSD
VQVVRNQIWGQPPTNQIPPQQQAQQPQRLAHPTTHILPVSSPENALLQQQKPTSSTQTSQ
QQTPQQSSQIPGTSLINQQAAGSSQASANNQQSQDQSYFTTSTDTQITDSQTATSPIQMP
QNNGYAAAAWTARGSNTLTYTQSMQPPDHPSSRPINQPYWPQMQTEMTGQQRLSRQPAPE
YWCSIAYFELDTQVGETFKVPSSKPHVTVDGYVDPSGGNRFCLGALSNVHRTEQSERARL
HIGKGVQLDLRGEGDVWLRCLSDHSVFVQSYYLDREAGRTPGDAVHKIYPSACIKVFDLR
QCHQQMQSLAANAQAAAAAQAAAVAGIPGHNVVPSRNISAAAGIGVDDLRRLCILRLSFV
KGWGPDYPRQSIKDTPCWVEVHLHRALQLLDEVLHNMPIDGRD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g10598.t1 | CDD | cd10492 | MH1_SMAD_4 | 27 | 151 | 3.41179E-96 |
| 13 | g10598.t1 | CDD | cd10498 | MH2_SMAD_4 | 419 | 635 | 2.61708E-148 |
| 11 | g10598.t1 | Coils | Coil | Coil | 50 | 77 | - |
| 10 | g10598.t1 | Gene3D | G3DSA:3.90.520.10 | Smad3; Chain A | 22 | 153 | 1.4E-62 |
| 9 | g10598.t1 | Gene3D | G3DSA:2.60.200.10 | - | 413 | 642 | 1.3E-111 |
| 16 | g10598.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 20 | - |
| 17 | g10598.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 285 | 360 | - |
| 4 | g10598.t1 | PANTHER | PTHR13703:SF50 | EXPRESSED SEQUENCE CR929477-RELATED | 21 | 175 | 2.6E-237 |
| 6 | g10598.t1 | PANTHER | PTHR13703 | SMAD | 21 | 175 | 2.6E-237 |
| 3 | g10598.t1 | PANTHER | PTHR13703:SF50 | EXPRESSED SEQUENCE CR929477-RELATED | 288 | 640 | 2.6E-237 |
| 5 | g10598.t1 | PANTHER | PTHR13703 | SMAD | 288 | 640 | 2.6E-237 |
| 2 | g10598.t1 | Pfam | PF03165 | MH1 domain | 50 | 150 | 5.3E-39 |
| 1 | g10598.t1 | Pfam | PF03166 | MH2 domain | 420 | 624 | 1.7E-72 |
| 19 | g10598.t1 | ProSiteProfiles | PS51075 | MAD homology domain 1 (MH1) profile. | 31 | 155 | 35.517 |
| 18 | g10598.t1 | ProSiteProfiles | PS51076 | MAD homology domain 2 (MH2) profile. | 422 | 643 | 67.18 |
| 15 | g10598.t1 | SMART | SM00523 | dwAneu5 | 44 | 153 | 2.7E-63 |
| 14 | g10598.t1 | SMART | SM00524 | dwBultra2 | 420 | 624 | 6.8E-115 |
| 7 | g10598.t1 | SUPERFAMILY | SSF56366 | SMAD MH1 domain | 32 | 150 | 1.14E-40 |
| 8 | g10598.t1 | SUPERFAMILY | SSF49879 | SMAD/FHA domain | 389 | 638 | 4.97E-92 |
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:0007179 | transforming growth factor beta receptor signaling pathway | BP |
| GO:0005515 | protein binding | MF |
| GO:0006355 | regulation of transcription, DNA-templated | BP |
| GO:0005667 | transcription regulator complex | CC |
KEGG
Orthology
- This transcript has been annotated with K04501 (mothers against decapentaplegic homolog 4)
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.
