General information for g995.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Mothers against decapentaplegic homolog 6.
Parent gene
- The parent gene g995 is located on chr_3: 7344654..7373110 (+ 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_3 | g995 | g995.t1 | TSS | g995.t1 | 7343692 | 7343692 |
| chr_3 | g995 | g995.t1 | isoform | g995.t1 | 7344654 | 7373110 |
| chr_3 | g995 | g995.t1 | exon | g995.t1.exon1 | 7344654 | 7345323 |
| chr_3 | g995 | g995.t1 | cds | g995.t1.CDS1 | 7344654 | 7345323 |
| chr_3 | g995 | g995.t1 | exon | g995.t1.exon2 | 7349206 | 7349244 |
| chr_3 | g995 | g995.t1 | cds | g995.t1.CDS2 | 7349206 | 7349244 |
| chr_3 | g995 | g995.t1 | exon | g995.t1.exon3 | 7356487 | 7356564 |
| chr_3 | g995 | g995.t1 | cds | g995.t1.CDS3 | 7356487 | 7356564 |
| chr_3 | g995 | g995.t1 | exon | g995.t1.exon4 | 7372418 | 7372624 |
| chr_3 | g995 | g995.t1 | cds | g995.t1.CDS4 | 7372418 | 7372624 |
| chr_3 | g995 | g995.t1 | exon | g995.t1.exon5 | 7372696 | 7372861 |
| chr_3 | g995 | g995.t1 | cds | g995.t1.CDS5 | 7372696 | 7372861 |
| chr_3 | g995 | g995.t1 | exon | g995.t1.exon6 | 7372927 | 7373110 |
| chr_3 | g995 | g995.t1 | cds | g995.t1.CDS6 | 7372927 | 7373110 |
| chr_3 | g995 | g995.t1 | TTS | g995.t1 | NA | NA |
Sequences
>g995.t1 Gene=g995 Length=1344
ATGTTCTTCAAAAGATCGAGTCTAAAGAAAAGGCTATGGCGCTCGCATGTGAGGGCAACG
ACCAGTACTACAACAACAACAAGCAACAACTCATCGCGTCAACGTCAAGAGCCAATCAAT
TATTTCCACCAGCAAACACAGCATTCTTCTCTTCCACACTATCAGTGTCTCAGTGGCAGC
GAAGAGATGAGCTGTCAACAAGAGAATGCAAATTATGGCGGTGTCGCAAGAGACGAAGGA
AGTCACTCACTCCTCTCCACTACCACTGCCGTACTAAGAAATTGTTGTACAAACTCAAAT
TCTTCGAGTACAACCGACCTTTACGATCCACCAGCAGCCGAGCATCAAGCATATCAGAGC
TTTCGGCAACTCATGAGACAACTGAAAAAGGAAAATCAACTCGAGACGCTTTGTCAAGCA
ATCGAGTATGGTCTACAAACAGACAGCAATGGAAAAATGTCACCGAATCAATATCAACCG
ACCGATTGCGTGCTCGTACCTCGTGGATCAATCGATGGTGAAGAGCCGCAAGTTGTCGCC
TGTCGTTTATGGCGTTGGAGTGATTTATTATCAAGTCACTCAATTAAAAGGATACCATCT
TGTCCTAATGAAAAAGATCCCGTCTATGTTTGCTGCAATCCAGCACATTGGAGTCGCATT
TATCACTTAGAGACTCCACCTCCTCCTTATGCTGCAATGAAAATTGAAGAAACATCAATG
GATCAAGACTTGTATAGTGGTGCTTATAATAAACAACCGATTGAATCATTAACGACTGAT
GGCGAAGATCTGTCACTAACAGGTTGGTGGTGTCAGCTCGCCTATTGGGAATTAAGTGAA
CGTGTTGGCTCAAAAGTACCTGTAGAAGATTCAGCTGTTGATGTTTTTGGTGAACAGACT
CGTGGCGCTGGACTCTGTATAAAAACCATTGCACAACAGCGATCAACAAAGACACCTGAT
TTAGTATTGAAAACGAGGGAAAAAATTGGACTTGGAGTAACATTAAGTCGTGAGTCAGAT
GGTGTTTGGCTCTATAATCGATCATCACAACCAGTATTTGTACATTCACCGACATTATGT
GACATGGATTCGAGAGCAACGATTCCTTGTCCTTACAAAATTCCGCCTGGCCATTGCATT
CGTGCATTTGATCCCTTAAAAGTAAACGAATCTATAATTTGGCCATCGACGATAAGTGGC
ATTCAACTTGGTCCAGTTGACACGCATAGCGTAAGAATAAGCTTTGCAAAAGGCTGGGGT
CAAAACTATTCCCGGCAAGATGTCACAAGTTGTCCCTGCTGGCTTGAGGTACTGCTCAGT
CGAAGTCATTTACCGTGCCGGTGA
>g995.t1 Gene=g995 Length=447
MFFKRSSLKKRLWRSHVRATTSTTTTTSNNSSRQRQEPINYFHQQTQHSSLPHYQCLSGS
EEMSCQQENANYGGVARDEGSHSLLSTTTAVLRNCCTNSNSSSTTDLYDPPAAEHQAYQS
FRQLMRQLKKENQLETLCQAIEYGLQTDSNGKMSPNQYQPTDCVLVPRGSIDGEEPQVVA
CRLWRWSDLLSSHSIKRIPSCPNEKDPVYVCCNPAHWSRIYHLETPPPPYAAMKIEETSM
DQDLYSGAYNKQPIESLTTDGEDLSLTGWWCQLAYWELSERVGSKVPVEDSAVDVFGEQT
RGAGLCIKTIAQQRSTKTPDLVLKTREKIGLGVTLSRESDGVWLYNRSSQPVFVHSPTLC
DMDSRATIPCPYKIPPGHCIRAFDPLKVNESIIWPSTISGIQLGPVDTHSVRISFAKGWG
QNYSRQDVTSCPCWLEVLLSRSHLPCR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g995.t1 | CDD | cd10489 | MH1_SMAD_6_7 | 110 | 224 | 7.15613E-28 |
| 9 | g995.t1 | Gene3D | G3DSA:3.90.520.10 | Smad3; Chain A | 92 | 223 | 5.2E-19 |
| 8 | g995.t1 | Gene3D | G3DSA:2.60.200.10 | - | 268 | 444 | 5.0E-51 |
| 13 | g995.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 14 | 36 | - |
| 14 | g995.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 17 | 36 | - |
| 3 | g995.t1 | PANTHER | PTHR13703:SF54 | MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG | 111 | 440 | 3.2E-77 |
| 4 | g995.t1 | PANTHER | PTHR13703 | SMAD | 111 | 440 | 3.2E-77 |
| 2 | g995.t1 | Pfam | PF03165 | MH1 domain | 119 | 220 | 1.2E-19 |
| 1 | g995.t1 | Pfam | PF03166 | MH2 domain | 270 | 439 | 3.7E-41 |
| 16 | g995.t1 | ProSiteProfiles | PS51075 | MAD homology domain 1 (MH1) profile. | 90 | 226 | 16.769 |
| 15 | g995.t1 | ProSiteProfiles | PS51076 | MAD homology domain 2 (MH2) profile. | 270 | 447 | 35.586 |
| 12 | g995.t1 | SMART | SM00523 | dwAneu5 | 112 | 224 | 5.7E-19 |
| 11 | g995.t1 | SMART | SM00524 | dwBultra2 | 268 | 440 | 3.0E-38 |
| 5 | g995.t1 | SUPERFAMILY | SSF56366 | SMAD MH1 domain | 112 | 221 | 8.76E-22 |
| 6 | g995.t1 | SUPERFAMILY | SSF49879 | SMAD/FHA domain | 202 | 440 | 1.06E-46 |
| 7 | g995.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 19 | - |
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 K04677 (mothers against decapentaplegic homolog 6)
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.
