General information for g11287.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Mothers against decapentaplegic homolog 2.
Parent gene
- The parent gene g11287 is located on chr_1: 15422798..15423586 (- 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 | g11287 | g11287.t3 | TTS | g11287.t3 | 15419651 | 15419651 |
| chr_1 | g11287 | g11287.t3 | isoform | g11287.t3 | 15419674 | 15421127 |
| chr_1 | g11287 | g11287.t3 | exon | g11287.t3.exon1 | 15419674 | 15419794 |
| chr_1 | g11287 | g11287.t3 | cds | g11287.t3.CDS1 | 15419674 | 15419794 |
| chr_1 | g11287 | g11287.t3 | exon | g11287.t3.exon2 | 15419855 | 15420383 |
| chr_1 | g11287 | g11287.t3 | cds | g11287.t3.CDS2 | 15419855 | 15420383 |
| chr_1 | g11287 | g11287.t3 | exon | g11287.t3.exon3 | 15420553 | 15420600 |
| chr_1 | g11287 | g11287.t3 | cds | g11287.t3.CDS3 | 15420553 | 15420600 |
| chr_1 | g11287 | g11287.t3 | exon | g11287.t3.exon4 | 15420682 | 15420815 |
| chr_1 | g11287 | g11287.t3 | cds | g11287.t3.CDS4 | 15420682 | 15420781 |
| chr_1 | g11287 | g11287.t3 | exon | g11287.t3.exon5 | 15420869 | 15421127 |
| chr_1 | g11287 | g11287.t3 | TSS | g11287.t3 | 15421902 | 15421902 |
Sequences
>g11287.t3 Gene=g11287 Length=1091
ACAATGATCTGAATTATTTGAGTCATTGCGAATTTGCGTATCACTTAAGAAAGGACGAAG
TCTGTATCAATCCGTATCATTACATTAAAGCTGAAAGAGAATTTCTTCAACCACAATCAC
CTCAAAATCAGCAATTGTCGATTTTAGTACCAAAATATCCGACACCCCCAGCGGAATCAC
CAGACGTTCATCACGTTTCATCATATATAGACGATTTAAGCAATACAGTTCCTTTGAATA
TACAATATAATGCACTAAACCTTCAAAATTCGACACTTGCAAATTATTCAGTGATGGATG
CAACAATGACGCAAATACCAAATAATACTTCGGTGATTGATACTGCCAACATGAGTAGTG
TTGGAATTGCAGCCACAGAAACGCCTCCTCCTGGCTATATGTCAGAAGATGGTGATCCCA
TGGATCAAAACGATAATTTGAATTTTTCACATTTATCGCCATCGCAATCACTCGAAGCAG
CACCTGTTATGTACCAAGATCCAACTTTTTGGTGTTCGATCAGTTACTATGAGCTTAATT
TGCGCGTTGGCGAAACGTTTCATGCATCACAACCTTCAATAACGGTCGATGGATTCACAG
ATCCCTCAAATTCGGAACGTTTCTGTCTCGGTCTGCTCTCGAATGTAAATCGAAATGAGG
TTGTCGAGCAAACACGTCGACACATTGGAAAGGGTGTGAGATTGTATTATATTGGCGGTG
AAGTGTTTGCCGAATGTTTAAGTGATTCAAGCATTTTTGTTCAAAGTCCTAACTGTAATC
AACGCTATGGCTGGCATCCTGCGACAGTTTGCAAAATTCCACCTGGATGTAATCTGAAAA
TATTCAATAATCAGGAATTTGCCGCTCTTTTATCACAGTCAGTGTCGCAGGGTTTTGAAG
CAGTCTATCAATTGACACGAATGTGCACTATACGAATGAGTTTTGTCAAAGGTTGGGGAG
CTGAATATAGACGACAAACGGTAACATCAACGCCGTGTTGGATAGAATTACATTTAAACG
GACCACTTCAATGGCTCGATCGCGTTCTACTTCAAATGCAAGTACCATTACAGTGCAGTT
CTGTATCGTAA
>g11287.t3 Gene=g11287 Length=265
MDATMTQIPNNTSVIDTANMSSVGIAATETPPPGYMSEDGDPMDQNDNLNFSHLSPSQSL
EAAPVMYQDPTFWCSISYYELNLRVGETFHASQPSITVDGFTDPSNSERFCLGLLSNVNR
NEVVEQTRRHIGKGVRLYYIGGEVFAECLSDSSIFVQSPNCNQRYGWHPATVCKIPPGCN
LKIFNNQEFAALLSQSVSQGFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELH
LNGPLQWLDRVLLQMQVPLQCSSVS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11287.t3 | CDD | cd10985 | MH2_SMAD_2_3 | 65 | 255 | 0.000 |
| 6 | g11287.t3 | Gene3D | G3DSA:2.60.200.10 | - | 64 | 265 | 0.000 |
| 2 | g11287.t3 | PANTHER | PTHR13703:SF42 | MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 2 | 4 | 265 | 0.000 |
| 3 | g11287.t3 | PANTHER | PTHR13703 | SMAD | 4 | 265 | 0.000 |
| 1 | g11287.t3 | Pfam | PF03166 | MH2 domain | 72 | 242 | 0.000 |
| 7 | g11287.t3 | ProSiteProfiles | PS51076 | MAD homology domain 2 (MH2) profile. | 73 | 265 | 74.218 |
| 5 | g11287.t3 | SMART | SM00524 | dwBultra2 | 71 | 242 | 0.000 |
| 4 | g11287.t3 | SUPERFAMILY | SSF49879 | SMAD/FHA domain | 38 | 256 | 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:0005515 | protein binding | MF |
| GO:0006355 | regulation of transcription, DNA-templated | BP |
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.
