Gene loci information

Transcript annotation

  • This transcript has been annotated as Myocyte-specific enhancer factor 2.

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 g11408 g11408.t6 TSS g11408.t6 16022867 16022867
chr_1 g11408 g11408.t6 isoform g11408.t6 16023777 16034924
chr_1 g11408 g11408.t6 exon g11408.t6.exon1 16023777 16023781
chr_1 g11408 g11408.t6 exon g11408.t6.exon2 16024481 16024542
chr_1 g11408 g11408.t6 exon g11408.t6.exon3 16033742 16034110
chr_1 g11408 g11408.t6 cds g11408.t6.CDS1 16034057 16034110
chr_1 g11408 g11408.t6 exon g11408.t6.exon4 16034187 16034390
chr_1 g11408 g11408.t6 cds g11408.t6.CDS2 16034187 16034390
chr_1 g11408 g11408.t6 exon g11408.t6.exon5 16034447 16034759
chr_1 g11408 g11408.t6 cds g11408.t6.CDS3 16034447 16034759
chr_1 g11408 g11408.t6 exon g11408.t6.exon6 16034838 16034924
chr_1 g11408 g11408.t6 cds g11408.t6.CDS4 16034838 16034923
chr_1 g11408 g11408.t6 TTS g11408.t6 NA NA

Sequences

>g11408.t6 Gene=g11408 Length=1040
AAAAGATGCAAAGTTTAATTTGGTATAATATTGATGGTAACTTAAAAAAAGAAAAGGTAT
GTTATCAGATTTACATAAAGTAGTAATCGTATTAAATTGTCTTACATGGAAAGAAAAATA
TAAGAGATATAAAAATTAGCATAACGAATCTGCTGCATACGTAACTTGAGAACAATAAAC
ACAATACATAGAGAGAGAGAGAGACATATAGAAAAATTGTCAAACAGTTGTTGCACAAAA
AACAGTGTGTTTTTTTTTAAATTTAATCGCTCAAAGCGAAAGTTTGATAAAAATAAAATA
TAAATTTGGTGAAAATTCGTAGTAGCAACAAACAATTAACAACTAATTGTTATTCTTGAA
ACATTCATTTTGTGCCATCATCATGGGTAGAAAAAAAATTCAAATTTCCCGCATCACAGA
CGAACGGAATAGACAGGTCACATTCAACAAACGAAAGTTTGGTGTTATGAAGAAAGCTTA
TGAGCTTTCGGTGCTGTGCGATTGTGAAATTGCACTTATAATCTTCTCAAGCAGTAATAA
ACTATATCAATATGCGAGCACAGACATGGATAAAGTTCTTCTCAAATACACAGAATATAA
TGAACCGCATGAATCGTTGACAAACAAGAACATAATTGAGTATCTTGATATGACACAGAA
AGAGAATAAAAATGGCACAATGAGTCCAGAATCACCTGAGCCAGACGACAACTATACACT
TACACCAAGAACAGAAGCAAAGTACAATAAGATTGATGAAGATTTTCAGATGATGATGCA
AAGAAATCAGCAAATATCAGCAAATCGTGCAATGGGAGGAGCTGCCAATAATTATACTTT
GCCTGTTTCTGTACCAGTTGGCGCATATAATGATGCAAATTTATTGCAAGCAAGTCCACA
GATGGCACATCAGAACATCAGCCCTCGACCATCTAGTTCAGAAACTGATTCAGTTTATCC
CACTGGTAGTATGCTTGAAATGTCAAATGGATACCCTTCTTCACCACTTGGTGCCTCACC
AAGTCCTAGTCCTGGTTTAG

>g11408.t6 Gene=g11408 Length=219
MGRKKIQISRITDERNRQVTFNKRKFGVMKKAYELSVLCDCEIALIIFSSSNKLYQYAST
DMDKVLLKYTEYNEPHESLTNKNIIEYLDMTQKENKNGTMSPESPEPDDNYTLTPRTEAK
YNKIDEDFQMMMQRNQQISANRAMGGAANNYTLPVSVPVGAYNDANLLQASPQMAHQNIS
PRPSSSETDSVYPTGSMLEMSNGYPSSPLGASPSPSPGL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g11408.t6 CDD cd00265 MADS_MEF2_like 2 78 5.88272E-42
9 g11408.t6 Gene3D G3DSA:3.40.1810.10 - 13 94 4.3E-35
13 g11408.t6 MobiDBLite mobidb-lite consensus disorder prediction 175 219 -
14 g11408.t6 MobiDBLite mobidb-lite consensus disorder prediction 175 209 -
3 g11408.t6 PANTHER PTHR11945:SF145 MYOCYTE ENHANCER FACTOR 2AA-RELATED 1 185 7.2E-77
4 g11408.t6 PANTHER PTHR11945 MADS BOX PROTEIN 1 185 7.2E-77
7 g11408.t6 PRINTS PR00404 MADS domain signature 3 23 1.2E-26
6 g11408.t6 PRINTS PR00404 MADS domain signature 23 38 1.2E-26
5 g11408.t6 PRINTS PR00404 MADS domain signature 38 59 1.2E-26
1 g11408.t6 Pfam PF00319 SRF-type transcription factor (DNA-binding and dimerisation domain) 10 57 1.1E-24
2 g11408.t6 Pfam PF12347 Holliday junction regulator protein family C-terminal repeat 103 163 3.0E-15
12 g11408.t6 ProSitePatterns PS00350 MADS-box domain signature. 3 57 -
15 g11408.t6 ProSiteProfiles PS50066 MADS-box domain profile. 1 61 29.618
11 g11408.t6 SMART SM00432 madsneu2 1 60 2.0E-38
8 g11408.t6 SUPERFAMILY SSF55455 SRF-like 2 88 1.14E-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

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