General information for g11408.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Myocyte-specific enhancer factor 2.
Parent gene
- The parent gene g11408 is located on chr_1: 16035838..16037172 (+ 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 | g11408 | g11408.t1 | isoform | g11408.t1 | 16034057 | 16036039 |
| chr_1 | g11408 | g11408.t1 | exon | g11408.t1.exon1 | 16034057 | 16034110 |
| chr_1 | g11408 | g11408.t1 | cds | g11408.t1.CDS1 | 16034057 | 16034110 |
| chr_1 | g11408 | g11408.t1 | exon | g11408.t1.exon2 | 16034187 | 16034390 |
| chr_1 | g11408 | g11408.t1 | cds | g11408.t1.CDS2 | 16034187 | 16034390 |
| chr_1 | g11408 | g11408.t1 | exon | g11408.t1.exon3 | 16034447 | 16034759 |
| chr_1 | g11408 | g11408.t1 | cds | g11408.t1.CDS3 | 16034447 | 16034759 |
| chr_1 | g11408 | g11408.t1 | exon | g11408.t1.exon4 | 16034838 | 16034924 |
| chr_1 | g11408 | g11408.t1 | cds | g11408.t1.CDS4 | 16034838 | 16034924 |
| chr_1 | g11408 | g11408.t1 | exon | g11408.t1.exon5 | 16035140 | 16035264 |
| chr_1 | g11408 | g11408.t1 | cds | g11408.t1.CDS5 | 16035140 | 16035264 |
| chr_1 | g11408 | g11408.t1 | exon | g11408.t1.exon6 | 16035330 | 16035520 |
| chr_1 | g11408 | g11408.t1 | cds | g11408.t1.CDS6 | 16035330 | 16035520 |
| chr_1 | g11408 | g11408.t1 | exon | g11408.t1.exon7 | 16035586 | 16035842 |
| chr_1 | g11408 | g11408.t1 | cds | g11408.t1.CDS7 | 16035586 | 16035842 |
| chr_1 | g11408 | g11408.t1 | exon | g11408.t1.exon8 | 16035915 | 16036039 |
| chr_1 | g11408 | g11408.t1 | cds | g11408.t1.CDS8 | 16035915 | 16036039 |
| chr_1 | g11408 | g11408.t1 | TTS | g11408.t1 | 16036423 | 16036423 |
| chr_1 | g11408 | g11408.t1 | TSS | g11408.t1 | NA | NA |
Sequences
>g11408.t1 Gene=g11408 Length=1356
ATGGGTAGAAAAAAAATTCAAATTTCCCGCATCACAGACGAACGGAATAGACAGGTCACA
TTCAACAAACGAAAGTTTGGTGTTATGAAGAAAGCTTATGAGCTTTCGGTGCTGTGCGAT
TGTGAAATTGCACTTATAATCTTCTCAAGCAGTAATAAACTATATCAATATGCGAGCACA
GACATGGATAAAGTTCTTCTCAAATACACAGAATATAATGAACCGCATGAATCGTTGACA
AACAAGAACATAATTGAGTATCTTGATATGACACAGAAAGAGAATAAAAATGGCACAATG
AGTCCAGAATCACCTGAGCCAGACGACAACTATACACTTACACCAAGAACAGAAGCAAAG
TACAATAAGATTGATGAAGATTTTCAGATGATGATGCAAAGAAATCAGCAAATATCAGCA
AATCGTGCAATGGGAGGAGCTGCCAATAATTATACTTTGCCTGTTTCTGTACCAGTTGGC
GCATATAATGATGCAAATTTATTGCAAGCAAGTCCACAGATGGCACATCAGAACATCAGC
CCTCGACCATCTAGTTCAGAAACTGATTCAGTTTATCCCACTGGTAGTATGCTTGAAATG
TCAAATGGATACCCTTCTTCACCACTTGGTGCCTCACCAAGTCCTAGTCCTGGTTTAGCA
CATCATTTAGTTCATAGTAAACAACATTCGCCATCAAACAGAAGTACAAATTTAAGGGTT
GTTATTCCATCAAACCCCTCTTCATCAAATTTAACTTCTGATGATATAAGCTCTTATACA
GAGCAAAATCGTCAAACTTCAACACTAAATACTCCTGTTGTTGCTCTTCAGACGCCAATC
GTATCGGGACTCGGCAATTATCCTGTTAGCACATTCGGTGCTCAAGACTTTTCGATGACG
TCATCTGATTTAAATATGATAACATCATGGAATTCATCACATCAAAATCTAAGTGCAACA
ATACAACACAACAGTGGAATACCTCATTTGGCTGTGTCGAATAGTACACCGCCACCTTCC
TCATCACCTATACCGGTCAAAATAAAAGCAGAACCAATATCGCCGCCTCGTGATCAAATA
CTAAGTCATCACCAGCAGCAACAACAACAGTCGTTAAGTGCTTCATCTATCATTGGTGGC
ATCAGTGGCAATTCGTTAGGTAGCAGTTTAAATCATTCACATATGATGAGCTCACGACCG
TCATCGACTGGACATTTAACACCAACACCAGGTTCTTCAGTGACACCTAATTCACCGTCA
TCTTCATCCCACAATCATAATGTGTCCCATTTACCCGACTACGAGAATGTCTCGCACGCC
AAGCGACCGAGAATTTCCGAAGGTTGGGCTACATAG
>g11408.t1 Gene=g11408 Length=451
MGRKKIQISRITDERNRQVTFNKRKFGVMKKAYELSVLCDCEIALIIFSSSNKLYQYAST
DMDKVLLKYTEYNEPHESLTNKNIIEYLDMTQKENKNGTMSPESPEPDDNYTLTPRTEAK
YNKIDEDFQMMMQRNQQISANRAMGGAANNYTLPVSVPVGAYNDANLLQASPQMAHQNIS
PRPSSSETDSVYPTGSMLEMSNGYPSSPLGASPSPSPGLAHHLVHSKQHSPSNRSTNLRV
VIPSNPSSSNLTSDDISSYTEQNRQTSTLNTPVVALQTPIVSGLGNYPVSTFGAQDFSMT
SSDLNMITSWNSSHQNLSATIQHNSGIPHLAVSNSTPPPSSSPIPVKIKAEPISPPRDQI
LSHHQQQQQQSLSASSIIGGISGNSLGSSLNHSHMMSSRPSSTGHLTPTPGSSVTPNSPS
SSSHNHNVSHLPDYENVSHAKRPRISEGWAT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g11408.t1 | CDD | cd00265 | MADS_MEF2_like | 2 | 78 | 7.30368E-40 |
| 9 | g11408.t1 | Gene3D | G3DSA:3.40.1810.10 | - | 13 | 94 | 1.6E-34 |
| 14 | g11408.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 206 | 264 | - |
| 15 | g11408.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 229 | 264 | - |
| 13 | g11408.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 392 | 432 | - |
| 16 | g11408.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 392 | 451 | - |
| 3 | g11408.t1 | PANTHER | PTHR11945:SF145 | MYOCYTE ENHANCER FACTOR 2AA-RELATED | 1 | 200 | 7.6E-78 |
| 4 | g11408.t1 | PANTHER | PTHR11945 | MADS BOX PROTEIN | 1 | 200 | 7.6E-78 |
| 7 | g11408.t1 | PRINTS | PR00404 | MADS domain signature | 3 | 23 | 7.1E-26 |
| 6 | g11408.t1 | PRINTS | PR00404 | MADS domain signature | 23 | 38 | 7.1E-26 |
| 5 | g11408.t1 | PRINTS | PR00404 | MADS domain signature | 38 | 59 | 7.1E-26 |
| 1 | g11408.t1 | Pfam | PF00319 | SRF-type transcription factor (DNA-binding and dimerisation domain) | 10 | 57 | 3.2E-24 |
| 2 | g11408.t1 | Pfam | PF12347 | Holliday junction regulator protein family C-terminal repeat | 103 | 163 | 1.1E-14 |
| 12 | g11408.t1 | ProSitePatterns | PS00350 | MADS-box domain signature. | 3 | 57 | - |
| 17 | g11408.t1 | ProSiteProfiles | PS50066 | MADS-box domain profile. | 1 | 61 | 29.618 |
| 11 | g11408.t1 | SMART | SM00432 | madsneu2 | 1 | 60 | 2.0E-38 |
| 8 | g11408.t1 | SUPERFAMILY | SSF55455 | SRF-like | 2 | 87 | 4.58E-30 |
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:0003677 | DNA binding | MF |
| GO:0045944 | positive regulation of transcription by RNA polymerase II | BP |
| GO:0000977 | RNA polymerase II transcription regulatory region sequence-specific DNA binding | MF |
| GO:0046983 | protein dimerization activity | MF |
KEGG
Orthology
- This transcript has been annotated with K09260 (MADS-box transcription enhancer factor 2A)
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.
