General information for g8265.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Serum response factor-like protein.
Parent gene
- The parent gene g8265 is located on chr_2: 29406406..29408261 (+ 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 | g8265 | g8265.t1 | TSS | g8265.t1 | 29400993 | 29400993 |
| chr_2 | g8265 | g8265.t1 | isoform | g8265.t1 | 29401298 | 29408261 |
| chr_2 | g8265 | g8265.t1 | exon | g8265.t1.exon1 | 29401298 | 29401882 |
| chr_2 | g8265 | g8265.t1 | cds | g8265.t1.CDS1 | 29401298 | 29401882 |
| chr_2 | g8265 | g8265.t1 | exon | g8265.t1.exon2 | 29403077 | 29403717 |
| chr_2 | g8265 | g8265.t1 | cds | g8265.t1.CDS2 | 29403077 | 29403717 |
| chr_2 | g8265 | g8265.t1 | exon | g8265.t1.exon3 | 29406660 | 29406689 |
| chr_2 | g8265 | g8265.t1 | cds | g8265.t1.CDS3 | 29406660 | 29406689 |
| chr_2 | g8265 | g8265.t1 | exon | g8265.t1.exon4 | 29408017 | 29408022 |
| chr_2 | g8265 | g8265.t1 | cds | g8265.t1.CDS4 | 29408017 | 29408022 |
| chr_2 | g8265 | g8265.t1 | exon | g8265.t1.exon5 | 29408109 | 29408134 |
| chr_2 | g8265 | g8265.t1 | cds | g8265.t1.CDS5 | 29408109 | 29408134 |
| chr_2 | g8265 | g8265.t1 | exon | g8265.t1.exon6 | 29408194 | 29408261 |
| chr_2 | g8265 | g8265.t1 | cds | g8265.t1.CDS6 | 29408194 | 29408261 |
| chr_2 | g8265 | g8265.t1 | TTS | g8265.t1 | 29408448 | 29408448 |
Sequences
>g8265.t1 Gene=g8265 Length=1356
ATGGAATTAGAGGCAGAAAGAATTTCCCCAACAATTACTTCGCGGTACATGAATAATTAT
ATCACCAATCCTACAACTGATATTTATCATCAGAACTATGATCATTCACCGCGTCAAAAT
ATGCAAAGCTTTTATCCAATGATGGAAAATGATCGAAATTATTTAAAACGTCATTACTAT
ACTAAAGAGGAAGGTGATAGTGATGAACGTGAACGCAAGTACGAAAAATTGGTAGATCAT
GGACAATATGCTCATGCATATAACACAAATGAACAACTTTATGATTCTTACAATAACAAT
ACGCTTTATCCAGACAATAATACTCAAGAAGAGCGTAATGTCATCACAAATACTGAAAGT
AGCATCATTATGACTCCGAATACAAATAGCAATGATAATTATCCTAACAATTCCTCACCC
GTATCTTCCGTTGAAGATGCATCAGATCGTGCTGCTGATAGCCCTAAGAGCATCGTTAGC
GGCAAAAAAACCAAAGGACGTGTTAAAATCAAAATGGAATATATTGAGAACAAGTTGCGG
CGGTATACGACATTTTCAAAACGAAAAACTGGCATCATGAAAAAGGCCTATGAATTATCG
ACACTGACAGGCACACAGATAATGTTACTTGTTGCATCGGAAACGGGTCATGTATACACT
TTTGCCACACGCAAGCTTCAACCGATGATCACATCGGATGCGGGCAAGCAACTTATACAG
ACATGTCTGAATTCTCCAGAAAATGCAGAAGCAGTAACTACAAACAATAACAACACTGGT
ACGATTGTAAATGAACAACGCATGTCAGCGACAGGTTTTGAGGAAACTGAACTAACTTTC
GATGTACAAGAGCTGAATAGTGATATTCCAGAAAAGCAAAAAGTAAGACAACCATTAGCC
TATAATCCGTCAACATCGCATCTACAAAATATCTCACAATCATTGCCATCAACTCATAGC
CATCTTTATAGTTTACCTCATCCAACACAGCATTATGCAAATTCTCCTCAAACACATTAC
TCATCTCCACATTATTCACCTCCTTCTCCTTCTCTTAATGTTCAACACTTTCAAGCTCCT
TCATCGACACAATATCCAAGCTATTATGAAAATTCTGGCAATGCATCTGTTCCTCTTAGT
AGCTATCAATCATTAAGATCAACAGTCTCATCGCCTGCCATTCCTATATCACCTCCTACG
AATAGCTCAGCTTCCGAAGCTACTCGTTTTATAAGCGGAATAATTGATCCTTTGTGTGGA
ATTAGTCACGTGTTAATAAAAATTTGGCAAAAAAATAAAAATTTGAACTTACTGAATATG
AAAACGATAAGAGTCATCAAAATAAAAAAAAAATGA
>g8265.t1 Gene=g8265 Length=451
MELEAERISPTITSRYMNNYITNPTTDIYHQNYDHSPRQNMQSFYPMMENDRNYLKRHYY
TKEEGDSDERERKYEKLVDHGQYAHAYNTNEQLYDSYNNNTLYPDNNTQEERNVITNTES
SIIMTPNTNSNDNYPNNSSPVSSVEDASDRAADSPKSIVSGKKTKGRVKIKMEYIENKLR
RYTTFSKRKTGIMKKAYELSTLTGTQIMLLVASETGHVYTFATRKLQPMITSDAGKQLIQ
TCLNSPENAEAVTTNNNNTGTIVNEQRMSATGFEETELTFDVQELNSDIPEKQKVRQPLA
YNPSTSHLQNISQSLPSTHSHLYSLPHPTQHYANSPQTHYSSPHYSPPSPSLNVQHFQAP
SSTQYPSYYENSGNASVPLSSYQSLRSTVSSPAIPISPPTNSSASEATRFISGIIDPLCG
ISHVLIKIWQKNKNLNLLNMKTIRVIKIKKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g8265.t1 | CDD | cd00266 | MADS_SRF_like | 166 | 246 | 6.56974E-29 |
| 8 | g8265.t1 | Gene3D | G3DSA:3.40.1810.10 | - | 177 | 247 | 2.1E-35 |
| 12 | g8265.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 125 | 145 | - |
| 13 | g8265.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 125 | 157 | - |
| 2 | g8265.t1 | PANTHER | PTHR48019 | SERUM RESPONSE FACTOR HOMOLOG | 131 | 404 | 4.7E-69 |
| 3 | g8265.t1 | PANTHER | PTHR48019:SF40 | SERUM RESPONSE FACTOR | 131 | 404 | 4.7E-69 |
| 5 | g8265.t1 | PRINTS | PR00404 | MADS domain signature | 167 | 187 | 1.0E-15 |
| 4 | g8265.t1 | PRINTS | PR00404 | MADS domain signature | 187 | 202 | 1.0E-15 |
| 6 | g8265.t1 | PRINTS | PR00404 | MADS domain signature | 202 | 223 | 1.0E-15 |
| 1 | g8265.t1 | Pfam | PF00319 | SRF-type transcription factor (DNA-binding and dimerisation domain) | 175 | 221 | 8.4E-20 |
| 11 | g8265.t1 | ProSitePatterns | PS00350 | MADS-box domain signature. | 167 | 221 | - |
| 14 | g8265.t1 | ProSiteProfiles | PS50066 | MADS-box domain profile. | 165 | 225 | 23.927 |
| 10 | g8265.t1 | SMART | SM00432 | madsneu2 | 165 | 224 | 4.6E-30 |
| 7 | g8265.t1 | SUPERFAMILY | SSF55455 | SRF-like | 165 | 244 | 1.57E-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. There were no conditions that were differentially expressed