Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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 g8265 g8265.t5 TSS g8265.t5 29400993 29400993
chr_2 g8265 g8265.t5 isoform g8265.t5 29401298 29408261
chr_2 g8265 g8265.t5 exon g8265.t5.exon1 29401298 29401882
chr_2 g8265 g8265.t5 cds g8265.t5.CDS1 29401298 29401882
chr_2 g8265 g8265.t5 exon g8265.t5.exon2 29403077 29403373
chr_2 g8265 g8265.t5 cds g8265.t5.CDS2 29403077 29403373
chr_2 g8265 g8265.t5 exon g8265.t5.exon3 29406402 29406686
chr_2 g8265 g8265.t5 cds g8265.t5.CDS3 29406402 29406443
chr_2 g8265 g8265.t5 exon g8265.t5.exon4 29408017 29408134
chr_2 g8265 g8265.t5 exon g8265.t5.exon5 29408194 29408261
chr_2 g8265 g8265.t5 TTS g8265.t5 29408448 29408448

Sequences

>g8265.t5 Gene=g8265 Length=1353
ATGGAATTAGAGGCAGAAAGAATTTCCCCAACAATTACTTCGCGGTACATGAATAATTAT
ATCACCAATCCTACAACTGATATTTATCATCAGAACTATGATCATTCACCGCGTCAAAAT
ATGCAAAGCTTTTATCCAATGATGGAAAATGATCGAAATTATTTAAAACGTCATTACTAT
ACTAAAGAGGAAGGTGATAGTGATGAACGTGAACGCAAGTACGAAAAATTGGTAGATCAT
GGACAATATGCTCATGCATATAACACAAATGAACAACTTTATGATTCTTACAATAACAAT
ACGCTTTATCCAGACAATAATACTCAAGAAGAGCGTAATGTCATCACAAATACTGAAAGT
AGCATCATTATGACTCCGAATACAAATAGCAATGATAATTATCCTAACAATTCCTCACCC
GTATCTTCCGTTGAAGATGCATCAGATCGTGCTGCTGATAGCCCTAAGAGCATCGTTAGC
GGCAAAAAAACCAAAGGACGTGTTAAAATCAAAATGGAATATATTGAGAACAAGTTGCGG
CGGTATACGACATTTTCAAAACGAAAAACTGGCATCATGAAAAAGGCCTATGAATTATCG
ACACTGACAGGCACACAGATAATGTTACTTGTTGCATCGGAAACGGGTCATGTATACACT
TTTGCCACACGCAAGCTTCAACCGATGATCACATCGGATGCGGGCAAGCAACTTATACAG
ACATGTCTGAATTCTCCAGAAAATGCAGAAGCAGTAACTACAAACAATAACAACACTGGT
ACGATTGTAAATGAACAACGCATGTCAGCGACAGGTTTTGAGGAAACTGAACTAACTTTC
GATGTACAAGAGCTGAATAGTGATATTCCAGAAAAGCAAAAATTCCTTTTCCCAATCGAT
TTTGACTTGAGCGATTTCCTATGAATAAGGAATGATAGAAAAATTCTTTGCTGGAATTTG
AAAAAATTACAAAATAACTTCAATTTATCATGTAGATTTAGTGCGTTTAGTTATTCACAT
TATGGTATTCAATTCGACACTGATAGAACATATATATCCAAAGGATAGAACGCACTAAAA
TCTAAGCCAAAAGTTTTAATTCAAAAAGGGTCTCAATTTATATATATTTAATTTTTTAAG
TTTTATAAGCGGAATAATTGATCCTTTTGGAATGTAAGCGATTATTTGTTGAAAGGACTA
ATCAGAATGAGCAGCTGTAATGCAAAATTTTGGCTTATAGATATAATCAAACATTTTAGT
AGTCACGTGTTAATAAAAATTTGGCAAAAAAATAAAAATTTGAACTTACTGAATATGAAA
ACGATAAGAGTCATCAAAATAAAAAAAAAATGA

>g8265.t5 Gene=g8265 Length=307
MELEAERISPTITSRYMNNYITNPTTDIYHQNYDHSPRQNMQSFYPMMENDRNYLKRHYY
TKEEGDSDERERKYEKLVDHGQYAHAYNTNEQLYDSYNNNTLYPDNNTQEERNVITNTES
SIIMTPNTNSNDNYPNNSSPVSSVEDASDRAADSPKSIVSGKKTKGRVKIKMEYIENKLR
RYTTFSKRKTGIMKKAYELSTLTGTQIMLLVASETGHVYTFATRKLQPMITSDAGKQLIQ
TCLNSPENAEAVTTNNNNTGTIVNEQRMSATGFEETELTFDVQELNSDIPEKQKFLFPID
FDLSDFL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g8265.t5 CDD cd00266 MADS_SRF_like 166 246 1.09459E-29
8 g8265.t5 Gene3D G3DSA:3.40.1810.10 - 177 247 1.1E-35
12 g8265.t5 MobiDBLite mobidb-lite consensus disorder prediction 125 145 -
13 g8265.t5 MobiDBLite mobidb-lite consensus disorder prediction 125 157 -
2 g8265.t5 PANTHER PTHR48019 SERUM RESPONSE FACTOR HOMOLOG 130 294 6.8E-69
3 g8265.t5 PANTHER PTHR48019:SF40 SERUM RESPONSE FACTOR 130 294 6.8E-69
5 g8265.t5 PRINTS PR00404 MADS domain signature 167 187 3.9E-16
4 g8265.t5 PRINTS PR00404 MADS domain signature 187 202 3.9E-16
6 g8265.t5 PRINTS PR00404 MADS domain signature 202 223 3.9E-16
1 g8265.t5 Pfam PF00319 SRF-type transcription factor (DNA-binding and dimerisation domain) 175 221 4.8E-20
11 g8265.t5 ProSitePatterns PS00350 MADS-box domain signature. 167 221 -
14 g8265.t5 ProSiteProfiles PS50066 MADS-box domain profile. 165 225 23.927
10 g8265.t5 SMART SM00432 madsneu2 165 224 4.6E-30
7 g8265.t5 SUPERFAMILY SSF55455 SRF-like 166 249 7.85E-22

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. There were no conditions that were differentially expressed