General information for g8264.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Serum response factor-like protein.
Parent gene
- The parent gene g8264 is located on chr_2: 29390010..29395003 (- 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_2 | g8264 | g8264.t1 | TTS | g8264.t1 | 29380313 | 29380313 |
| chr_2 | g8264 | g8264.t1 | isoform | g8264.t1 | 29380323 | 29390010 |
| chr_2 | g8264 | g8264.t1 | exon | g8264.t1.exon1 | 29380323 | 29380447 |
| chr_2 | g8264 | g8264.t1 | cds | g8264.t1.CDS1 | 29380323 | 29380447 |
| chr_2 | g8264 | g8264.t1 | exon | g8264.t1.exon2 | 29380512 | 29380827 |
| chr_2 | g8264 | g8264.t1 | cds | g8264.t1.CDS2 | 29380512 | 29380827 |
| chr_2 | g8264 | g8264.t1 | exon | g8264.t1.exon3 | 29385749 | 29386018 |
| chr_2 | g8264 | g8264.t1 | cds | g8264.t1.CDS3 | 29385749 | 29386018 |
| chr_2 | g8264 | g8264.t1 | exon | g8264.t1.exon4 | 29389474 | 29390010 |
| chr_2 | g8264 | g8264.t1 | cds | g8264.t1.CDS4 | 29389474 | 29390010 |
| chr_2 | g8264 | g8264.t1 | TSS | g8264.t1 | 29390415 | 29390415 |
Sequences
>g8264.t1 Gene=g8264 Length=1248
ATGGAACCGCCGCGTGAAAATTCACCATCAACACCATCAAGATATCTCAATAGTTATCTT
CAGCAGAATCCAACTGAGCTCTTTCATCAAAACTTTCCTCAACGTCAATTATCGAATCAA
CAGTTTTATGCTGCAGCGGCTGCTGCTGATAATCTCTCAACAAACAATAAAAGCTATTTA
AAACGTCATCATCAAAATTATGAGAAAAATGACGGTGAACGAGATAAGAAATATGAAAAA
TATGATAGCAAAAAACTAGAAGAACAAAGCATTCATCAAACGCAAGGACATCCGTATGAC
GGATTTCATAGTGACGCTTACACGACAAGTGGAGGAAATGGTGCTGGTAGTATAACAACA
TCAACTGGAACGGGATCAACAACCACAGCAACTCAGCAAAAACCTGGAGGAAATACAAAG
AGTCTCTCGAATGGAAAGAAAACCAAAGGACGTGTCAAAATTAAAATGGAATACATAGAC
AATAAATTGCGTCGTTATACGACATTTTCAAAACGAAAAACTGGCATCATGAAAAAGGCC
TACGAGTTATCGACACTGACGGGCACACAAGTTATGCTACTCGTGGCATCCGAAACGGGT
CATGTATACACTTTTGCCACACGCAAGCTTCAACCGATGATCACATCGGAAGCAGGAAAA
ACGCTGATTCAGACTTGTCTTAATTCTCCAGATCTCTCAGCGACTGTTTCGAGTAGTGAT
CAACGCATGTCAGCGACCGGCTTTGAAGAAACTGAACTTAATTATAGCATTTCAGATATT
GGCGACAATCCGGGTGACAAAGAAAAACTTTCTTTTCAGGATGATATCACAAGTACAGAT
GACTCAGAAGAGTCTGAAAATGATGAAAATTTTATTGTACACAGTCAGCAGAATAATCAT
AAATCAATGCCACAACAGCAACAGCAAGCACCTCTTGTTGTCCAACAACCAAGAGTTTTT
GAAGAAGAAAACAAACAATCACTGCATCAACAACAGAACCATAGGATCAATGAAAAAATT
TTAGATAATCAAAAGTTATTACTTGAAAGCCTTTCAAATTTACCACAAAATTTACTTCAA
AATTGGATTCAATCTGGTCAACTACAAGTATCAGTAGATGAAGATGGAATGCAATCAATA
TCAATACCTTTTGCAATACAAAAAGAAAATTCAACACAAGAAATTGTCACGAAAAAAATT
CCAATAAAACTACTAATGGGTAATAAAATAAAATCTGAAGCAGAATGA
>g8264.t1 Gene=g8264 Length=415
MEPPRENSPSTPSRYLNSYLQQNPTELFHQNFPQRQLSNQQFYAAAAAADNLSTNNKSYL
KRHHQNYEKNDGERDKKYEKYDSKKLEEQSIHQTQGHPYDGFHSDAYTTSGGNGAGSITT
STGTGSTTTATQQKPGGNTKSLSNGKKTKGRVKIKMEYIDNKLRRYTTFSKRKTGIMKKA
YELSTLTGTQVMLLVASETGHVYTFATRKLQPMITSEAGKTLIQTCLNSPDLSATVSSSD
QRMSATGFEETELNYSISDIGDNPGDKEKLSFQDDITSTDDSEESENDENFIVHSQQNNH
KSMPQQQQQAPLVVQQPRVFEEENKQSLHQQQNHRINEKILDNQKLLLESLSNLPQNLLQ
NWIQSGQLQVSVDEDGMQSISIPFAIQKENSTQEIVTKKIPIKLLMGNKIKSEAE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g8264.t1 | CDD | cd00266 | MADS_SRF_like | 150 | 231 | 6.36014E-29 |
| 8 | g8264.t1 | Gene3D | G3DSA:3.40.1810.10 | - | 161 | 231 | 9.2E-36 |
| 13 | g8264.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 55 | 76 | - |
| 15 | g8264.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 61 | 76 | - |
| 12 | g8264.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 120 | 149 | - |
| 14 | g8264.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 120 | 145 | - |
| 2 | g8264.t1 | PANTHER | PTHR48019 | SERUM RESPONSE FACTOR HOMOLOG | 115 | 266 | 2.1E-73 |
| 3 | g8264.t1 | PANTHER | PTHR48019:SF40 | SERUM RESPONSE FACTOR | 115 | 266 | 2.1E-73 |
| 4 | g8264.t1 | PRINTS | PR00404 | MADS domain signature | 151 | 171 | 1.7E-15 |
| 5 | g8264.t1 | PRINTS | PR00404 | MADS domain signature | 171 | 186 | 1.7E-15 |
| 6 | g8264.t1 | PRINTS | PR00404 | MADS domain signature | 186 | 207 | 1.7E-15 |
| 1 | g8264.t1 | Pfam | PF00319 | SRF-type transcription factor (DNA-binding and dimerisation domain) | 159 | 205 | 1.8E-19 |
| 11 | g8264.t1 | ProSitePatterns | PS00350 | MADS-box domain signature. | 151 | 205 | - |
| 16 | g8264.t1 | ProSiteProfiles | PS50066 | MADS-box domain profile. | 149 | 209 | 23.661 |
| 10 | g8264.t1 | SMART | SM00432 | madsneu2 | 149 | 208 | 1.1E-29 |
| 7 | g8264.t1 | SUPERFAMILY | SSF55455 | SRF-like | 149 | 228 | 1.15E-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
- This transcript has been annotated with K04378 (serum response factor)
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.
