General information for g4732.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein mothers against dpp.
Parent gene
- The parent gene g4732 is located on chr_2: 4462885..4464858 (- 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_2 | g4732 | g4732.t1 | TTS | g4732.t1 | 4462230 | 4462230 |
| chr_2 | g4732 | g4732.t1 | isoform | g4732.t1 | 4462885 | 4464858 |
| chr_2 | g4732 | g4732.t1 | exon | g4732.t1.exon1 | 4462885 | 4464009 |
| chr_2 | g4732 | g4732.t1 | cds | g4732.t1.CDS1 | 4462885 | 4464009 |
| chr_2 | g4732 | g4732.t1 | exon | g4732.t1.exon2 | 4464473 | 4464762 |
| chr_2 | g4732 | g4732.t1 | cds | g4732.t1.CDS2 | 4464473 | 4464762 |
| chr_2 | g4732 | g4732.t1 | exon | g4732.t1.exon3 | 4464843 | 4464858 |
| chr_2 | g4732 | g4732.t1 | cds | g4732.t1.CDS3 | 4464843 | 4464858 |
| chr_2 | g4732 | g4732.t1 | TSS | g4732.t1 | 4464934 | 4464934 |
Sequences
>g4732.t1 Gene=g4732 Length=1431
ATGCAGAATGCACGATTTTATTATAACAAAATTCGTAAAATGGATGATGATGTTGAAACA
TCTACAAGCAGCACAATGTCAAGTCTCAATAGTCTTTTTTCATTTACCAGTCCAGCTGTT
AAAAAGCTCCTTGGATGGAAGCAAGGCGATGAAGAAGAAAAGTGGGCTGAAAAAGCTGTT
GACAGTTTAGTAAAGAAACTTAAGAAAAGAAAAGGCGCAATTGAGGAGCTAGAAAGAGCA
TTATCATGTCCTGGTCAGCCATCTAAATGTGTTACAATTCCACGATCACTTGACGGTCGA
TTGCAAGTTTCACACAGAAAAGGCTTACCGCATGTAATTTACTGCAGAGTTTGGCGATGG
CCAGATTTGCAAAGCCATCATGAACTAAAGCCAATAGAATCATGTCAGTATCCATTCAGT
GCAAAACAGAAGGAAGTTTGCATTAATCCTTATCATTATAAGCGTGTGGAATCGCCAGTT
TTACCACCAGTTCTTGTTCCACGTCATTCAGAATTTGCACCAGGACATTCATTACTTCCT
ATACATCAAATGATTGAACCAACAATGCCACATAATGTTCAATACTCACCATCAGGCTTT
GGCTCACCTCATATGCCACAGAGTCCACTTTCGCCTCATAATATGCAGCCACAATCTCCA
ATGTCTTCAATTTCAAGTCCTGGACCAGTTAATTCCAATCCACAAAGTCCATATTTAGCA
GAAACACCACCACCAGCCTACAGTCCACCAGAAGATAATGGAAATAATAATGGAAATCAA
GATCAACCAATGGATACAAATATGAGTGAAGTTGCACCAGTTAGCTATCAAGAGCCACCA
TATTGGGCCAGTATTGCATATTATGAACTCAATTGTCGTGTTGGTGAAGTTTTTCACTGT
AATTCAACATCAATCATTGTCGATGGCTTCACAAATCCAAGCAACAATTCCGATCGTTTC
TGTTTGGGACAATTGAGTAATGTCAATCGAAATAGTACAATTGAGAATACTCGTCGGCAT
ATAGGCAAAGGTGTGCACTTATATTATGTTGGTGGTGAAGTTTATGCCGAATGTCTATCA
GATTCGGCCATTTTTGTGCAGTCAAGAAATTGCAATCATCATCATGGTTTTCATCCGTCA
ACTGTTTGTAAAATTCCACCTGGCTGCTCGCTCAAAATTTTCAATAATCAAGAATTCGCT
CAGCTACTTTCGCAGTCAGTAAATCACGGATTCGAAGCAGTTTATGAATTGACAAAAATG
TGTACAATTAGAATGAGCTTTGTGAAAGGCTGGGGTGCAGAATATCATCGACAAGATGTG
ACAAATACGCCATGCTGGATTGAAATTCATCTGCATGGACCACTGCAATGGCTTGATAAA
GTTTTAATACAAATGGGCTCGCCACATAATGCCATTAGTTCTGTCTCATAA
>g4732.t1 Gene=g4732 Length=476
MQNARFYYNKIRKMDDDVETSTSSTMSSLNSLFSFTSPAVKKLLGWKQGDEEEKWAEKAV
DSLVKKLKKRKGAIEELERALSCPGQPSKCVTIPRSLDGRLQVSHRKGLPHVIYCRVWRW
PDLQSHHELKPIESCQYPFSAKQKEVCINPYHYKRVESPVLPPVLVPRHSEFAPGHSLLP
IHQMIEPTMPHNVQYSPSGFGSPHMPQSPLSPHNMQPQSPMSSISSPGPVNSNPQSPYLA
ETPPPAYSPPEDNGNNNGNQDQPMDTNMSEVAPVSYQEPPYWASIAYYELNCRVGEVFHC
NSTSIIVDGFTNPSNNSDRFCLGQLSNVNRNSTIENTRRHIGKGVHLYYVGGEVYAECLS
DSAIFVQSRNCNHHHGFHPSTVCKIPPGCSLKIFNNQEFAQLLSQSVNHGFEAVYELTKM
CTIRMSFVKGWGAEYHRQDVTNTPCWIEIHLHGPLQWLDKVLIQMGSPHNAISSVS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g4732.t1 | CDD | cd10490 | MH1_SMAD_1_5_9 | 35 | 158 | 9.64692E-93 |
| 10 | g4732.t1 | CDD | cd10497 | MH2_SMAD_1_5_9 | 276 | 476 | 1.04418E-158 |
| 9 | g4732.t1 | Coils | Coil | Coil | 60 | 80 | - |
| 8 | g4732.t1 | Gene3D | G3DSA:3.90.520.10 | Smad3; Chain A | 29 | 170 | 1.2E-64 |
| 7 | g4732.t1 | Gene3D | G3DSA:2.60.200.10 | - | 278 | 476 | 5.1E-94 |
| 14 | g4732.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 200 | 238 | - |
| 15 | g4732.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 200 | 237 | - |
| 3 | g4732.t1 | PANTHER | PTHR13703:SF23 | MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 1 | 29 | 476 | 5.1E-246 |
| 4 | g4732.t1 | PANTHER | PTHR13703 | SMAD | 29 | 476 | 5.1E-246 |
| 2 | g4732.t1 | Pfam | PF03165 | MH1 domain | 57 | 157 | 3.2E-42 |
| 1 | g4732.t1 | Pfam | PF03166 | MH2 domain | 281 | 452 | 3.5E-71 |
| 17 | g4732.t1 | ProSiteProfiles | PS51075 | MAD homology domain 1 (MH1) profile. | 38 | 162 | 37.559 |
| 16 | g4732.t1 | ProSiteProfiles | PS51076 | MAD homology domain 2 (MH2) profile. | 282 | 476 | 73.878 |
| 13 | g4732.t1 | SMART | SM00523 | dwAneu5 | 51 | 160 | 3.8E-68 |
| 12 | g4732.t1 | SMART | SM00524 | dwBultra2 | 280 | 452 | 1.9E-108 |
| 5 | g4732.t1 | SUPERFAMILY | SSF56366 | SMAD MH1 domain | 39 | 157 | 3.92E-45 |
| 6 | g4732.t1 | SUPERFAMILY | SSF49879 | SMAD/FHA domain | 245 | 467 | 6.21E-93 |
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 K04676 (mothers against decapentaplegic homolog 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.
