General information for g11408.t7
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.t7 | isoform | g11408.t7 | 16034057 | 16035520 |
| chr_1 | g11408 | g11408.t7 | exon | g11408.t7.exon1 | 16034057 | 16034390 |
| chr_1 | g11408 | g11408.t7 | cds | g11408.t7.CDS1 | 16034217 | 16034390 |
| chr_1 | g11408 | g11408.t7 | exon | g11408.t7.exon2 | 16034465 | 16034759 |
| chr_1 | g11408 | g11408.t7 | cds | g11408.t7.CDS2 | 16034465 | 16034759 |
| chr_1 | g11408 | g11408.t7 | exon | g11408.t7.exon3 | 16034838 | 16034924 |
| chr_1 | g11408 | g11408.t7 | cds | g11408.t7.CDS3 | 16034838 | 16034924 |
| chr_1 | g11408 | g11408.t7 | exon | g11408.t7.exon4 | 16035140 | 16035264 |
| chr_1 | g11408 | g11408.t7 | cds | g11408.t7.CDS4 | 16035140 | 16035264 |
| chr_1 | g11408 | g11408.t7 | exon | g11408.t7.exon5 | 16035378 | 16035520 |
| chr_1 | g11408 | g11408.t7 | cds | g11408.t7.CDS5 | 16035378 | 16035518 |
| chr_1 | g11408 | g11408.t7 | TTS | g11408.t7 | 16036423 | 16036423 |
| chr_1 | g11408 | g11408.t7 | TSS | g11408.t7 | NA | NA |
Sequences
>g11408.t7 Gene=g11408 Length=984
ATGGGTAGAAAAAAAATTCAAATTTCCCGCATCACAGACGAACGGAATAGACAGGTGACA
CCGAAAATACATTACTTATTATGACAAACATTTGCATTGAAGAATTTTTTTTCAATTTAT
GCAATTTTAGGTCACATTCAACAAACGAAAGTTTGGTGTTATGAAGAAAGCTTATGAGCT
TTCGGTGCTGTGCGATTGTGAAATTGCACTTATAATCTTCTCAAGCAGTAATAAACTATA
TCAATATGCGAGCACAGACATGGATAAAGTTCTTCTCAAATACACAGAATATAATGAACC
GCATGAATCGTTGACAAACAAGAACATAATTGAGAAAGAGAATAAAAATGGCACAATGAG
TCCAGAATCACCTGAGCCAGACGACAACTATACACTTACACCAAGAACAGAAGCAAAGTA
CAATAAGATTGATGAAGATTTTCAGATGATGATGCAAAGAAATCAGCAAATATCAGCAAA
TCGTGCAATGGGAGGAGCTGCCAATAATTATACTTTGCCTGTTTCTGTACCAGTTGGCGC
ATATAATGATGCAAATTTATTGCAAGCAAGTCCACAGATGGCACATCAGAACATCAGCCC
TCGACCATCTAGTTCAGAAACTGATTCAGTTTATCCCACTGGTAGTATGCTTGAAATGTC
AAATGGATACCCTTCTTCACCACTTGGTGCCTCACCAAGTCCTAGTCCTGGTTTAGCACA
TCATTTAGTTCATAGTAAACAACATTCGCCATCAAACAGAAGTACAAATTTAAGGGTTGT
TATTCCATCAAACCCCTCTTCATCAAATTTAACTTCTGATGATATAAGCTCTTATACAGA
GACGCCAATCGTATCGGGACTCGGCAATTATCCTGTTAGCACATTCGGTGCTCAAGACTT
TTCGATGACGTCATCTGATTTAAATATGATAACATCATGGAATTCATCACATCAAAATCT
AAGTGCAACAATACAACACAACAG
>g11408.t7 Gene=g11408 Length=274
MKKAYELSVLCDCEIALIIFSSSNKLYQYASTDMDKVLLKYTEYNEPHESLTNKNIIEKE
NKNGTMSPESPEPDDNYTLTPRTEAKYNKIDEDFQMMMQRNQQISANRAMGGAANNYTLP
VSVPVGAYNDANLLQASPQMAHQNISPRPSSSETDSVYPTGSMLEMSNGYPSSPLGASPS
PSPGLAHHLVHSKQHSPSNRSTNLRVVIPSNPSSSNLTSDDISSYTETPIVSGLGNYPVS
TFGAQDFSMTSSDLNMITSWNSSHQNLSATIQHN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g11408.t7 | Gene3D | G3DSA:3.40.1810.10 | - | 1 | 66 | 2.5E-26 |
| 7 | g11408.t7 | MobiDBLite | mobidb-lite | consensus disorder prediction | 53 | 75 | - |
| 8 | g11408.t7 | MobiDBLite | mobidb-lite | consensus disorder prediction | 172 | 202 | - |
| 3 | g11408.t7 | PANTHER | PTHR11945:SF145 | MYOCYTE ENHANCER FACTOR 2AA-RELATED | 1 | 168 | 4.3E-55 |
| 4 | g11408.t7 | PANTHER | PTHR11945 | MADS BOX PROTEIN | 1 | 168 | 4.3E-55 |
| 1 | g11408.t7 | Pfam | PF00319 | SRF-type transcription factor (DNA-binding and dimerisation domain) | 1 | 29 | 3.3E-12 |
| 2 | g11408.t7 | Pfam | PF12347 | Holliday junction regulator protein family C-terminal repeat | 69 | 129 | 4.6E-15 |
| 10 | g11408.t7 | ProSiteProfiles | PS50066 | MADS-box domain profile. | 1 | 33 | 16.035 |
| 6 | g11408.t7 | SMART | SM00432 | madsneu2 | 1 | 32 | 5.4E-5 |
| 5 | g11408.t7 | SUPERFAMILY | SSF55455 | SRF-like | 1 | 59 | 1.23E-16 |
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:0046983 | protein dimerization activity | MF |
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.
