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.t2 isoform g11408.t2 16034057 16036039
chr_1 g11408 g11408.t2 exon g11408.t2.exon1 16034057 16034110
chr_1 g11408 g11408.t2 cds g11408.t2.CDS1 16034057 16034110
chr_1 g11408 g11408.t2 exon g11408.t2.exon2 16034187 16034390
chr_1 g11408 g11408.t2 cds g11408.t2.CDS2 16034187 16034390
chr_1 g11408 g11408.t2 exon g11408.t2.exon3 16034465 16034759
chr_1 g11408 g11408.t2 cds g11408.t2.CDS3 16034465 16034759
chr_1 g11408 g11408.t2 exon g11408.t2.exon4 16034838 16034945
chr_1 g11408 g11408.t2 cds g11408.t2.CDS4 16034838 16034945
chr_1 g11408 g11408.t2 exon g11408.t2.exon5 16035140 16035264
chr_1 g11408 g11408.t2 cds g11408.t2.CDS5 16035140 16035264
chr_1 g11408 g11408.t2 exon g11408.t2.exon6 16035330 16035520
chr_1 g11408 g11408.t2 cds g11408.t2.CDS6 16035330 16035520
chr_1 g11408 g11408.t2 exon g11408.t2.exon7 16035586 16035842
chr_1 g11408 g11408.t2 cds g11408.t2.CDS7 16035586 16035842
chr_1 g11408 g11408.t2 exon g11408.t2.exon8 16035915 16036039
chr_1 g11408 g11408.t2 cds g11408.t2.CDS8 16035915 16036039
chr_1 g11408 g11408.t2 TTS g11408.t2 16036423 16036423
chr_1 g11408 g11408.t2 TSS g11408.t2 NA NA

Sequences

>g11408.t2 Gene=g11408 Length=1359
ATGGGTAGAAAAAAAATTCAAATTTCCCGCATCACAGACGAACGGAATAGACAGGTCACA
TTCAACAAACGAAAGTTTGGTGTTATGAAGAAAGCTTATGAGCTTTCGGTGCTGTGCGAT
TGTGAAATTGCACTTATAATCTTCTCAAGCAGTAATAAACTATATCAATATGCGAGCACA
GACATGGATAAAGTTCTTCTCAAATACACAGAATATAATGAACCGCATGAATCGTTGACA
AACAAGAACATAATTGAGAAAGAGAATAAAAATGGCACAATGAGTCCAGAATCACCTGAG
CCAGACGACAACTATACACTTACACCAAGAACAGAAGCAAAGTACAATAAGATTGATGAA
GATTTTCAGATGATGATGCAAAGAAATCAGCAAATATCAGCAAATCGTGCAATGGGAGGA
GCTGCCAATAATTATACTTTGCCTGTTTCTGTACCAGTTGGCGCATATAATGATGCAAAT
TTATTGCAAGCAAGTCCACAGATGGCACATCAGAACATCAGCCCTCGACCATCTAGTTCA
GAAACTGATTCAGTTTATCCCACTGGTAGTATGCTTGAAATGTCAAATGGATACCCTTCT
TCACCACTTGGTGCCTCACCAAGTCCTAGTCCTGGTTTAGGTGGGCATTCTAGTAATAAA
TCACATCATTTAGTTCATAGTAAACAACATTCGCCATCAAACAGAAGTACAAATTTAAGG
GTTGTTATTCCATCAAACCCCTCTTCATCAAATTTAACTTCTGATGATATAAGCTCTTAT
ACAGAGCAAAATCGTCAAACTTCAACACTAAATACTCCTGTTGTTGCTCTTCAGACGCCA
ATCGTATCGGGACTCGGCAATTATCCTGTTAGCACATTCGGTGCTCAAGACTTTTCGATG
ACGTCATCTGATTTAAATATGATAACATCATGGAATTCATCACATCAAAATCTAAGTGCA
ACAATACAACACAACAGTGGAATACCTCATTTGGCTGTGTCGAATAGTACACCGCCACCT
TCCTCATCACCTATACCGGTCAAAATAAAAGCAGAACCAATATCGCCGCCTCGTGATCAA
ATACTAAGTCATCACCAGCAGCAACAACAACAGTCGTTAAGTGCTTCATCTATCATTGGT
GGCATCAGTGGCAATTCGTTAGGTAGCAGTTTAAATCATTCACATATGATGAGCTCACGA
CCGTCATCGACTGGACATTTAACACCAACACCAGGTTCTTCAGTGACACCTAATTCACCG
TCATCTTCATCCCACAATCATAATGTGTCCCATTTACCCGACTACGAGAATGTCTCGCAC
GCCAAGCGACCGAGAATTTCCGAAGGTTGGGCTACATAG

>g11408.t2 Gene=g11408 Length=452
MGRKKIQISRITDERNRQVTFNKRKFGVMKKAYELSVLCDCEIALIIFSSSNKLYQYAST
DMDKVLLKYTEYNEPHESLTNKNIIEKENKNGTMSPESPEPDDNYTLTPRTEAKYNKIDE
DFQMMMQRNQQISANRAMGGAANNYTLPVSVPVGAYNDANLLQASPQMAHQNISPRPSSS
ETDSVYPTGSMLEMSNGYPSSPLGASPSPSPGLGGHSSNKSHHLVHSKQHSPSNRSTNLR
VVIPSNPSSSNLTSDDISSYTEQNRQTSTLNTPVVALQTPIVSGLGNYPVSTFGAQDFSM
TSSDLNMITSWNSSHQNLSATIQHNSGIPHLAVSNSTPPPSSSPIPVKIKAEPISPPRDQ
ILSHHQQQQQQSLSASSIIGGISGNSLGSSLNHSHMMSSRPSSTGHLTPTPGSSVTPNSP
SSSSHNHNVSHLPDYENVSHAKRPRISEGWAT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g11408.t2 CDD cd00265 MADS_MEF2_like 2 78 1.52851E-39
9 g11408.t2 Gene3D G3DSA:3.40.1810.10 - 13 94 6.1E-35
15 g11408.t2 MobiDBLite mobidb-lite consensus disorder prediction 83 104 -
14 g11408.t2 MobiDBLite mobidb-lite consensus disorder prediction 199 267 -
16 g11408.t2 MobiDBLite mobidb-lite consensus disorder prediction 230 267 -
13 g11408.t2 MobiDBLite mobidb-lite consensus disorder prediction 393 433 -
17 g11408.t2 MobiDBLite mobidb-lite consensus disorder prediction 393 452 -
3 g11408.t2 PANTHER PTHR11945:SF145 MYOCYTE ENHANCER FACTOR 2AA-RELATED 1 409 1.3E-78
4 g11408.t2 PANTHER PTHR11945 MADS BOX PROTEIN 1 409 1.3E-78
7 g11408.t2 PRINTS PR00404 MADS domain signature 3 23 7.1E-26
6 g11408.t2 PRINTS PR00404 MADS domain signature 23 38 7.1E-26
5 g11408.t2 PRINTS PR00404 MADS domain signature 38 59 7.1E-26
1 g11408.t2 Pfam PF00319 SRF-type transcription factor (DNA-binding and dimerisation domain) 10 57 3.3E-24
2 g11408.t2 Pfam PF12347 Holliday junction regulator protein family C-terminal repeat 97 157 1.0E-14
12 g11408.t2 ProSitePatterns PS00350 MADS-box domain signature. 3 57 -
18 g11408.t2 ProSiteProfiles PS50066 MADS-box domain profile. 1 61 29.618
11 g11408.t2 SMART SM00432 madsneu2 1 60 2.0E-38
8 g11408.t2 SUPERFAMILY SSF55455 SRF-like 2 87 5.89E-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