General information for g3962.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Protein TIS11.
Parent gene
- The parent gene g3962 is located on chr_3: 29301097..29301897 (+ 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_3 | g3962 | g3962.t1 | TSS | g3962.t1 | 29290127 | 29290127 |
| chr_3 | g3962 | g3962.t1 | isoform | g3962.t1 | 29290391 | 29301515 |
| chr_3 | g3962 | g3962.t1 | exon | g3962.t1.exon1 | 29290391 | 29290453 |
| chr_3 | g3962 | g3962.t1 | cds | g3962.t1.CDS1 | 29290391 | 29290453 |
| chr_3 | g3962 | g3962.t1 | exon | g3962.t1.exon2 | 29300276 | 29300628 |
| chr_3 | g3962 | g3962.t1 | cds | g3962.t1.CDS2 | 29300276 | 29300628 |
| chr_3 | g3962 | g3962.t1 | exon | g3962.t1.exon3 | 29300724 | 29300897 |
| chr_3 | g3962 | g3962.t1 | cds | g3962.t1.CDS3 | 29300724 | 29300897 |
| chr_3 | g3962 | g3962.t1 | exon | g3962.t1.exon4 | 29301026 | 29301515 |
| chr_3 | g3962 | g3962.t1 | cds | g3962.t1.CDS4 | 29301026 | 29301515 |
| chr_3 | g3962 | g3962.t1 | TTS | g3962.t1 | 29301755 | 29301755 |
Sequences
>g3962.t1 Gene=g3962 Length=1080
ATGTCTACTGCAATTTTACATGCTGGAACGTTTATTCACGATTTTAACGATCTAATAATA
AAGAATCAAAATACAAGTTCAAAGGCAATAGGCAATCAGAGCTATAAGGAGAAATTTCAG
CGAAAAGAGGATAACAATATGCATTTTTTGAAGCAACGAAATGACGCTTATATGACAAAT
TTGTTTGCAAGTCAACAAAAAAGAGCATTGCAAGATGTAATTGGGCAACAGCAGCAACAA
CAACATGCTGCATTAGCAAGAACAGTATCAACACCGATAACAGATACAAATCAATCGGTC
GTAAACAATCTTTTTACATCTCTCAATGATATTTTGAATGGAACAACTGCAACAAATGGA
CATCGTAAATTGGAACGTACACAGTCTGAGCCGTTACCACAAACTAATACATCACGCTAC
AAAACGGAACTGTGTCGTCCTTTTGAGGAAGCAGGCGAATGCAAATATGGTGATAAATGT
CAATTTGCTCATGGTTTTCATGAATTGCGTAACTTGCAACGTCATCCAAAATATAAGACG
GAATTGTGTCGCACTTTCCATAGCGTTGGCTTCTGCCCATATGGAGCAAGATGCCATTTC
ATTCACTCCTCTCAAGAAGCACTGACCCATAACAAAAATGTAGCTGCTTATCAAGCTCGT
CTACAACAACAACAGCAATCTCGTATGAAAACTATGAGCTTATCGACAGCATCAGATCGT
GAGACGGCATCTTCGGTTGGTTCACTCTCGCCAACTATGACACACATCCAGAATCAATCG
TCTTCGAATGGCACTTGTTATAGTAGTGATCAAGCAAGTCCAACTAATAACATCTTTACG
TATTCATTTAGTCCATCGGACAGTCCAATACTCAACGGAGGAGATATGCCGGTTATTGCT
TCATCTGTGTCACCACCTCCAATTATTCCTTCAGCCGCCATGTTTATTAAGCCGAAATTC
ATTGAACAGACTGCTGCTGCACATGCAAATGTGATGAAACAAATTCCTGAGGACGCTCGA
TTGCCAGTGTTTAATCAAATTAGCTCAGCGATTGACTCTATGAGTACTTTGACTATTTAA
>g3962.t1 Gene=g3962 Length=359
MSTAILHAGTFIHDFNDLIIKNQNTSSKAIGNQSYKEKFQRKEDNNMHFLKQRNDAYMTN
LFASQQKRALQDVIGQQQQQQHAALARTVSTPITDTNQSVVNNLFTSLNDILNGTTATNG
HRKLERTQSEPLPQTNTSRYKTELCRPFEEAGECKYGDKCQFAHGFHELRNLQRHPKYKT
ELCRTFHSVGFCPYGARCHFIHSSQEALTHNKNVAAYQARLQQQQQSRMKTMSLSTASDR
ETASSVGSLSPTMTHIQNQSSSNGTCYSSDQASPTNNIFTYSFSPSDSPILNGGDMPVIA
SSVSPPPIIPSAAMFIKPKFIEQTAAAHANVMKQIPEDARLPVFNQISSAIDSMSTLTI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g3962.t1 | Gene3D | G3DSA:4.10.1000.10 | CCCH zinc finger | 133 | 171 | 1.2E-18 |
| 11 | g3962.t1 | Gene3D | G3DSA:4.10.1000.10 | CCCH zinc finger | 172 | 209 | 1.5E-14 |
| 9 | g3962.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 226 | 268 | - |
| 3 | g3962.t1 | PANTHER | PTHR12547 | CCCH ZINC FINGER/TIS11-RELATED | 120 | 223 | 2.8E-50 |
| 4 | g3962.t1 | PANTHER | PTHR12547:SF53 | MRNA DECAY ACTIVATOR PROTEIN ZFP36L1 | 120 | 223 | 2.8E-50 |
| 1 | g3962.t1 | Pfam | PF00642 | Zinc finger C-x8-C-x5-C-x3-H type (and similar) | 140 | 166 | 4.8E-11 |
| 2 | g3962.t1 | Pfam | PF00642 | Zinc finger C-x8-C-x5-C-x3-H type (and similar) | 178 | 203 | 1.1E-9 |
| 12 | g3962.t1 | ProSiteProfiles | PS50103 | Zinc finger C3H1-type profile. | 139 | 167 | 16.643 |
| 13 | g3962.t1 | ProSiteProfiles | PS50103 | Zinc finger C3H1-type profile. | 177 | 205 | 15.535 |
| 8 | g3962.t1 | SMART | SM00356 | c3hfinal6 | 139 | 166 | 5.7E-9 |
| 7 | g3962.t1 | SMART | SM00356 | c3hfinal6 | 177 | 204 | 3.9E-8 |
| 6 | g3962.t1 | SUPERFAMILY | SSF90229 | CCCH zinc finger | 136 | 171 | 5.36E-10 |
| 5 | g3962.t1 | SUPERFAMILY | SSF90229 | CCCH zinc finger | 174 | 205 | 8.37E-10 |
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:0046872 | metal ion binding | MF |
KEGG
Orthology
- This transcript has been annotated with K18753 (butyrate 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.
