Gene loci information

Transcript annotation

  • This transcript has been annotated as Mothers against decapentaplegic homolog 3.

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 g11287 g11287.t1 TTS g11287.t1 15419651 15419651
chr_1 g11287 g11287.t1 isoform g11287.t1 15419674 15423586
chr_1 g11287 g11287.t1 exon g11287.t1.exon1 15419674 15419794
chr_1 g11287 g11287.t1 cds g11287.t1.CDS1 15419674 15419794
chr_1 g11287 g11287.t1 exon g11287.t1.exon2 15419855 15420383
chr_1 g11287 g11287.t1 cds g11287.t1.CDS2 15419855 15420383
chr_1 g11287 g11287.t1 exon g11287.t1.exon3 15420553 15420600
chr_1 g11287 g11287.t1 cds g11287.t1.CDS3 15420553 15420600
chr_1 g11287 g11287.t1 exon g11287.t1.exon4 15420682 15420815
chr_1 g11287 g11287.t1 cds g11287.t1.CDS4 15420682 15420815
chr_1 g11287 g11287.t1 exon g11287.t1.exon5 15420869 15421131
chr_1 g11287 g11287.t1 cds g11287.t1.CDS5 15420869 15421131
chr_1 g11287 g11287.t1 exon g11287.t1.exon6 15421225 15421303
chr_1 g11287 g11287.t1 cds g11287.t1.CDS6 15421225 15421303
chr_1 g11287 g11287.t1 exon g11287.t1.exon7 15423381 15423586
chr_1 g11287 g11287.t1 cds g11287.t1.CDS7 15423381 15423586
chr_1 g11287 g11287.t1 TSS g11287.t1 15423683 15423683

Sequences

>g11287.t1 Gene=g11287 Length=1380
ATGTTTTCGAACGCGAGTGTAAAGCGCTTACTTCATTATCGTAAGAGCAATGGATCATCG
ATTGAAAATGCTTCTATTGAGAATGCATGGTGTGAAAAGGCTGTTAGATCTTTGGTGAAA
AAATTAAATTCTTCGAAACTGAATATGTTAGAAAATATCTTATCTCAAAAGAACCCGTCA
TCTTCGTGCATAACCATTCCTGCAAGAGCTCGTCCAGACGCAAAAAAGAGTCAAGGCTTG
CCGCATGTTATTTATTGTCGGTTGTGGCGCTGGCCAGATTTATCGTCACACAATGATCTG
AATTATTTGAGTCATTGCGAATTTGCGTATCACTTAAGAAAGGACGAAGTCTGTATCAAT
CCGTATCATTACATTAAAGCTGAAAGAGAATTTCTTCAACCACAATCACCTCAAAATCAG
CAATTGTCGATTTTAGTACCAAAATATCCGACACCCCCAGCGGAATCACCAGACGTTCAT
CACGTTTCATCATATATAGACGATTTAAGCAATACAGTTCCTTTGAATATACAATATAAT
GCACTAAACCTTCAAAATTCGACACTTGCAAATTATTCAGTGATGGATGCAACAATGACG
CAAATACCAAATAATACTTCGGTGATTGATACTGCCAACATGAGTAGTGTTGGAATTGCA
GCCACAGAAACGCCTCCTCCTGGCTATATGTCAGAAGATGGTGATCCCATGGATCAAAAC
GATAATTTGAATTTTTCACATTTATCGCCATCGCAATCACTCGAAGCAGCACCTGTTATG
TACCAAGATCCAACTTTTTGGTGTTCGATCAGTTACTATGAGCTTAATTTGCGCGTTGGC
GAAACGTTTCATGCATCACAACCTTCAATAACGGTCGATGGATTCACAGATCCCTCAAAT
TCGGAACGTTTCTGTCTCGGTCTGCTCTCGAATGTAAATCGAAATGAGGTTGTCGAGCAA
ACACGTCGACACATTGGAAAGGGTGTGAGATTGTATTATATTGGCGGTGAAGTGTTTGCC
GAATGTTTAAGTGATTCAAGCATTTTTGTTCAAAGTCCTAACTGTAATCAACGCTATGGC
TGGCATCCTGCGACAGTTTGCAAAATTCCACCTGGATGTAATCTGAAAATATTCAATAAT
CAGGAATTTGCCGCTCTTTTATCACAGTCAGTGTCGCAGGGTTTTGAAGCAGTCTATCAA
TTGACACGAATGTGCACTATACGAATGAGTTTTGTCAAAGGTTGGGGAGCTGAATATAGA
CGACAAACGGTAACATCAACGCCGTGTTGGATAGAATTACATTTAAACGGACCACTTCAA
TGGCTCGATCGCGTTCTACTTCAAATGCAAGTACCATTACAGTGCAGTTCTGTATCGTAA

>g11287.t1 Gene=g11287 Length=459
MFSNASVKRLLHYRKSNGSSIENASIENAWCEKAVRSLVKKLNSSKLNMLENILSQKNPS
SSCITIPARARPDAKKSQGLPHVIYCRLWRWPDLSSHNDLNYLSHCEFAYHLRKDEVCIN
PYHYIKAEREFLQPQSPQNQQLSILVPKYPTPPAESPDVHHVSSYIDDLSNTVPLNIQYN
ALNLQNSTLANYSVMDATMTQIPNNTSVIDTANMSSVGIAATETPPPGYMSEDGDPMDQN
DNLNFSHLSPSQSLEAAPVMYQDPTFWCSISYYELNLRVGETFHASQPSITVDGFTDPSN
SERFCLGLLSNVNRNEVVEQTRRHIGKGVRLYYIGGEVFAECLSDSSIFVQSPNCNQRYG
WHPATVCKIPPGCNLKIFNNQEFAALLSQSVSQGFEAVYQLTRMCTIRMSFVKGWGAEYR
RQTVTSTPCWIELHLNGPLQWLDRVLLQMQVPLQCSSVS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g11287.t1 CDD cd10985 MH2_SMAD_2_3 259 449 0.000
12 g11287.t1 Gene3D G3DSA:3.90.520.10 Smad3; Chain A 1 140 0.000
11 g11287.t1 Gene3D G3DSA:2.60.200.10 - 258 459 0.000
4 g11287.t1 PANTHER PTHR13703:SF42 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 2 2 71 0.000
6 g11287.t1 PANTHER PTHR13703 SMAD 2 71 0.000
3 g11287.t1 PANTHER PTHR13703:SF42 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 2 76 459 0.000
5 g11287.t1 PANTHER PTHR13703 SMAD 76 459 0.000
2 g11287.t1 Pfam PF03165 MH1 domain 31 125 0.000
1 g11287.t1 Pfam PF03166 MH2 domain 266 436 0.000
14 g11287.t1 ProSiteProfiles PS51075 MAD homology domain 1 (MH1) profile. 5 133 27.545
13 g11287.t1 ProSiteProfiles PS51076 MAD homology domain 2 (MH2) profile. 267 459 74.218
10 g11287.t1 SMART SM00523 dwAneu5 26 131 0.000
9 g11287.t1 SMART SM00524 dwBultra2 265 436 0.000
7 g11287.t1 SUPERFAMILY SSF56366 SMAD MH1 domain 7 126 0.000
8 g11287.t1 SUPERFAMILY SSF49879 SMAD/FHA domain 232 450 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: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

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