General information for g11472.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g11472 is located on chr_1: 16433414..16434361 (+ 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_1 | g11472 | g11472.t4 | TSS | g11472.t4 | 16432803 | 16432803 |
| chr_1 | g11472 | g11472.t4 | isoform | g11472.t4 | 16433197 | 16434361 |
| chr_1 | g11472 | g11472.t4 | exon | g11472.t4.exon1 | 16433197 | 16433349 |
| chr_1 | g11472 | g11472.t4 | exon | g11472.t4.exon2 | 16433414 | 16433563 |
| chr_1 | g11472 | g11472.t4 | exon | g11472.t4.exon3 | 16433640 | 16433797 |
| chr_1 | g11472 | g11472.t4 | exon | g11472.t4.exon4 | 16433856 | 16434361 |
| chr_1 | g11472 | g11472.t4 | cds | g11472.t4.CDS1 | 16433891 | 16434361 |
| chr_1 | g11472 | g11472.t4 | TTS | g11472.t4 | 16434402 | 16434402 |
Sequences
>g11472.t4 Gene=g11472 Length=967
ATGGATTACATTATAGCCAACGTTGATGGAGCTTTTTTAAAAATAGAGACAGAGTTAAAT
GAACAGATTGGATGGAATGAATTGCCTTTTACAGGAATGGACAAATCAACTTCCGCTGTT
TGTAATTTCTTTAATCAAGGAAAATGTGAAAAAGAATTTTGTCCTTTTCGACATATTAAA
GCAGAACAAAAGACAATAGTATGTAAACATTGGCTACGAGCTCTTTGTAAAAAAGGAGAT
AGCTGTGAATTTTTGCATGAATATGATATGAGCAAGATGCCTGAATGTTACTTTTTTAGG
TAATAAATATCACGCTTGTCACAAAAAGGAGTGTACATTTCTTCATATTGATCCTGAGAG
TAAAATAAAAGATTGTGCGTGGTATGATCGAGGTTTTTGTCGACATGGTCCTATTTGCCG
TCATCGACATGTCCGTAGAGTTCTTTGTAAAAATTACTTAGCTGGTTTCTGTCCAGATGG
TCAGTCTTGTAAATTTATGCATCCACGTTTTGAACTTCCACCTGCATCTGATCCTAAAGA
TAGTCATAAGCGACCACCACAATGTCACTTTTGTAGTGAATTGGGACACAAAATGCAAAA
TTGTCCAAAAATATCACAAGAACAACGTGAAATTGAGCGTCTCAATAATATCAAAAACTC
TCCTTATAGTGCACATCATAATTTACAAAAAATGCAAAAACCAAACACAGGAGGAGTAGA
AGGAAATTCAGATCAACAGCAACAACAACAACAGCAAATACCACCTCAACAACAGCAGCA
TCATAATAATCCACCTCCCACTCATCGTGGTCATTTCAATCACCATCATAATCAAAATGG
TCCGAGAGCACCATATGTGCCAAGAAAATTAGAAGACATTACCTGCTTTAAATGTGGCAT
GAAGGGACATTACGCAAATAGATGTTATAGTTTCTTAAATAATTCAGTAGATAATAACAG
TAAATAA
>g11472.t4 Gene=g11472 Length=156
MHPRFELPPASDPKDSHKRPPQCHFCSELGHKMQNCPKISQEQREIERLNNIKNSPYSAH
HNLQKMQKPNTGGVEGNSDQQQQQQQQIPPQQQQHHNNPPPTHRGHFNHHHNQNGPRAPY
VPRKLEDITCFKCGMKGHYANRCYSFLNNSVDNNSK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11472.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 101 | - |
| 8 | g11472.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 25 | - |
| 7 | g11472.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 50 | 101 | - |
| 1 | g11472.t4 | Pfam | PF00098 | Zinc knuckle | 128 | 143 | 0.004 |
| 9 | g11472.t4 | ProSiteProfiles | PS50158 | Zinc finger CCHC-type profile. | 130 | 143 | 9.653 |
| 5 | g11472.t4 | SMART | SM00343 | c2hcfinal6 | 22 | 38 | 0.11 |
| 4 | g11472.t4 | SMART | SM00343 | c2hcfinal6 | 129 | 145 | 0.023 |
| 2 | g11472.t4 | SUPERFAMILY | SSF57756 | Retrovirus zinc finger-like domains | 12 | 43 | 1.92E-6 |
| 3 | g11472.t4 | SUPERFAMILY | SSF57756 | Retrovirus zinc finger-like domains | 110 | 147 | 7.33E-6 |
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:0008270 | zinc ion binding | MF |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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