Gene loci information

Transcript annotation

  • This transcript has been annotated as Serum response factor-like protein.

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_2 g8264 g8264.t2 isoform g8264.t2 29379457 29390010
chr_2 g8264 g8264.t2 exon g8264.t2.exon1 29379457 29380447
chr_2 g8264 g8264.t2 TTS g8264.t2 29379459 29379459
chr_2 g8264 g8264.t2 cds g8264.t2.CDS1 29380364 29380447
chr_2 g8264 g8264.t2 exon g8264.t2.exon2 29380510 29380827
chr_2 g8264 g8264.t2 cds g8264.t2.CDS2 29380510 29380827
chr_2 g8264 g8264.t2 exon g8264.t2.exon3 29385749 29386018
chr_2 g8264 g8264.t2 cds g8264.t2.CDS3 29385749 29386018
chr_2 g8264 g8264.t2 exon g8264.t2.exon4 29389474 29390010
chr_2 g8264 g8264.t2 cds g8264.t2.CDS4 29389474 29390010
chr_2 g8264 g8264.t2 TSS g8264.t2 29390415 29390415

Sequences

>g8264.t2 Gene=g8264 Length=2116
ATGGAACCGCCGCGTGAAAATTCACCATCAACACCATCAAGATATCTCAATAGTTATCTT
CAGCAGAATCCAACTGAGCTCTTTCATCAAAACTTTCCTCAACGTCAATTATCGAATCAA
CAGTTTTATGCTGCAGCGGCTGCTGCTGATAATCTCTCAACAAACAATAAAAGCTATTTA
AAACGTCATCATCAAAATTATGAGAAAAATGACGGTGAACGAGATAAGAAATATGAAAAA
TATGATAGCAAAAAACTAGAAGAACAAAGCATTCATCAAACGCAAGGACATCCGTATGAC
GGATTTCATAGTGACGCTTACACGACAAGTGGAGGAAATGGTGCTGGTAGTATAACAACA
TCAACTGGAACGGGATCAACAACCACAGCAACTCAGCAAAAACCTGGAGGAAATACAAAG
AGTCTCTCGAATGGAAAGAAAACCAAAGGACGTGTCAAAATTAAAATGGAATACATAGAC
AATAAATTGCGTCGTTATACGACATTTTCAAAACGAAAAACTGGCATCATGAAAAAGGCC
TACGAGTTATCGACACTGACGGGCACACAAGTTATGCTACTCGTGGCATCCGAAACGGGT
CATGTATACACTTTTGCCACACGCAAGCTTCAACCGATGATCACATCGGAAGCAGGAAAA
ACGCTGATTCAGACTTGTCTTAATTCTCCAGATCTCTCAGCGACTGTTTCGAGTAGTGAT
CAACGCATGTCAGCGACCGGCTTTGAAGAAACTGAACTTAATTATAGCATTTCAGATATT
GGCGACAATCCGGGTGACAAAGAAAAACTTTCTTTTCAGGATGATATCACAAGTACAGAT
GACTCAGAAGAGTCTGAAAATGATGAAAATTTTATTGTACACAGTCAGCAGAATAATCAT
AAATCAATGCCACAACAGCAACAGCAAGCACCTCTTGTTGTCCAACAACCAAGAGTTTTT
GAAGAAGAAAACAAACAATCACTGCATCAACAACAGAACCATAGGATCAATGAAAAAATT
TTAGATAATCAAAAGTTATTACTTGAAAGCCTTTCAAATTTACCACAAAATTTACTTCAA
AATTGGATTCAATCTGGTCAACTACAAGTATCAGTAGATGAAGGTATGGAATGCAATCAA
TATCAATACCTTTTGCAATACAAAAAGAAAATTCAACACAAGAAATTGTCACGAAAAAAA
TTCCAATAAAACTACTAATGGGTAATAAAATAAAATCTGAAGCAGAATGAGAATCACTTA
AAATTATAATTTGACTTAAATCTATCAAATGGTTCATTGATTCATAAGTCATATATTTAA
ATAATTAACTCATATATCGCGAAATAAATTAAATATTGCAATTATTTTTTTTATTATAAA
ATGACTTACAACAGATAAATAGCATCATTTGTTTCATCTGCCCTTTTGAGTGAAATTAAT
TGAGCTTCTTTTTGACAATTTATTTGACTAATCTGTTGTTTTCTATTTTTAATTTTTATA
TGAACAAAAACGTTTGTTTGCTGTTGTCTTTTAGGTTGGAATGTATTTTGAATCATTTCT
ACAGTAATTATGAGATTTGGATCTCAATCAAATCTCAAAATAAGATTTTTTGAAAATCCT
AGTCGTACAAAATTAATTGAATCAATTTATATATCATCTATCTATTTTTCAATTTTATTA
CAAAATCTTTGAATATTCATGAATATTCATAAAAATATTTCAAGCCTATCTCAAATAACC
CCTCTCTTAAATTTAAGTTTTATTTTCTTCTTTTTGTGAGATTTTGTTGAAAACTAAAAT
GATGATTTTGTTTAAAAATAACGTATAAGATTTTCCATACCTTGCCAAAGTAGTGAAAGA
TGATAAAAAAATAATAAAATATCTATGAACGAATGTAGGTAGGCAAACTATTCAAATATT
CAAAGCTTTCTATTAAATCAAGCATGAGAAAAAAAAGATCTATGTTGCTCGAACAATATT
GTGTGATAGCGTAAATACATTATATAAAAATTCATAGCAACTGATTAATTTTTGTATTTT
TGATAAATAAATTCAATACATTTTAATAACAATATGATAATCGAATAAATAAAAGGACAA
AAAAATTGAAGAGTAA

>g8264.t2 Gene=g8264 Length=402
MEPPRENSPSTPSRYLNSYLQQNPTELFHQNFPQRQLSNQQFYAAAAAADNLSTNNKSYL
KRHHQNYEKNDGERDKKYEKYDSKKLEEQSIHQTQGHPYDGFHSDAYTTSGGNGAGSITT
STGTGSTTTATQQKPGGNTKSLSNGKKTKGRVKIKMEYIDNKLRRYTTFSKRKTGIMKKA
YELSTLTGTQVMLLVASETGHVYTFATRKLQPMITSEAGKTLIQTCLNSPDLSATVSSSD
QRMSATGFEETELNYSISDIGDNPGDKEKLSFQDDITSTDDSEESENDENFIVHSQQNNH
KSMPQQQQQAPLVVQQPRVFEEENKQSLHQQQNHRINEKILDNQKLLLESLSNLPQNLLQ
NWIQSGQLQVSVDEGMECNQYQYLLQYKKKIQHKKLSRKKFQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g8264.t2 CDD cd00266 MADS_SRF_like 150 231 5.20457E-29
8 g8264.t2 Gene3D G3DSA:3.40.1810.10 - 161 231 8.8E-36
13 g8264.t2 MobiDBLite mobidb-lite consensus disorder prediction 55 76 -
15 g8264.t2 MobiDBLite mobidb-lite consensus disorder prediction 61 76 -
12 g8264.t2 MobiDBLite mobidb-lite consensus disorder prediction 120 149 -
14 g8264.t2 MobiDBLite mobidb-lite consensus disorder prediction 120 145 -
2 g8264.t2 PANTHER PTHR48019 SERUM RESPONSE FACTOR HOMOLOG 115 266 7.8E-73
3 g8264.t2 PANTHER PTHR48019:SF40 SERUM RESPONSE FACTOR 115 266 7.8E-73
4 g8264.t2 PRINTS PR00404 MADS domain signature 151 171 1.6E-15
5 g8264.t2 PRINTS PR00404 MADS domain signature 171 186 1.6E-15
6 g8264.t2 PRINTS PR00404 MADS domain signature 186 207 1.6E-15
1 g8264.t2 Pfam PF00319 SRF-type transcription factor (DNA-binding and dimerisation domain) 159 205 1.7E-19
11 g8264.t2 ProSitePatterns PS00350 MADS-box domain signature. 151 205 -
16 g8264.t2 ProSiteProfiles PS50066 MADS-box domain profile. 149 209 23.661
10 g8264.t2 SMART SM00432 madsneu2 149 208 1.1E-29
7 g8264.t2 SUPERFAMILY SSF55455 SRF-like 149 228 1.1E-21

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:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific MF
GO:0045944 positive regulation of transcription by RNA polymerase II BP
GO:0000987 cis-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