General information for g12552.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g12552 is located on chr_1: 24372717..24373300 (+ 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 | g12552 | g12552.t2 | isoform | g12552.t2 | 24371870 | 24372717 |
| chr_1 | g12552 | g12552.t2 | exon | g12552.t2.exon1 | 24371870 | 24372717 |
| chr_1 | g12552 | g12552.t2 | cds | g12552.t2.CDS1 | 24371870 | 24372715 |
| chr_1 | g12552 | g12552.t2 | TTS | g12552.t2 | 24373345 | 24373345 |
| chr_1 | g12552 | g12552.t2 | TSS | g12552.t2 | NA | NA |
Sequences
>g12552.t2 Gene=g12552 Length=848
ATGGAACTAAACGAAACAGAAAGAGAACTTAAAGATAATTTAAACAAGTGCAGATGTTGT
TTTCGAATGATAATAAATTTGCGTGGAGCTGTGGAAATAGATGAAAATATTCAAACTCAA
TTTTTTCAACTAACTTCAATTGATGTGAGTATCAAGGTAAAATGTTTTCATTTAAAAATG
CTTAAATTTCAAAATAAATTCCAGCTCATAACATCTGAATGTTTTTCTAATCGAATATGT
CAACTATGTGCTAATGATCTACAAAGTTTTGTTCAACTTCGTGAAGATTTAATAGCAAAA
CAAACTCAACTTTATTCATTAGCTGGATTAGATATAGAAAGTATGCAAGAAACTCATTTA
AATGATGATGCTACTGAAGTAGAAGCAAATGAAGATACCAATTATGATGTAAATTATGAG
TCTGTAGAAGATTATGAAAGTGAAATGCTTGAAGAAGTTATTGAAGAGAATGAATTTGCA
ACAGAAGATGATACTACAGAATCTAATCTAAAAATTCTCAAAATTGAAAAAATTACTAGT
GCAGACGATGTACTGGTTAACGATGATTTACAAGAATCATCTGATTGTTATGGTGAAGAA
AATAGTAAAATAATTTATGGTTCAAATGTAATACTAGTTAATAAACCTGATGTCAAGGAT
GAAGAAGATGTACATTGTGAAATGTGCAAAATTAATGTTCCTCAAAGTTTTTATGATGAA
CATATTGAAACAATGCATTCATATGACTATCTAAGTTGTGAGAAATGTGATCAAAGCTTT
TACAGTAAAATTGCATTAAGAAGGCATGTTTATGATGAGCATGTTCCGCGGAGTAGCAAT
GAGAAAAA
>g12552.t2 Gene=g12552 Length=282
MELNETERELKDNLNKCRCCFRMIINLRGAVEIDENIQTQFFQLTSIDVSIKVKCFHLKM
LKFQNKFQLITSECFSNRICQLCANDLQSFVQLREDLIAKQTQLYSLAGLDIESMQETHL
NDDATEVEANEDTNYDVNYESVEDYESEMLEEVIEENEFATEDDTTESNLKILKIEKITS
ADDVLVNDDLQESSDCYGEENSKIIYGSNVILVNKPDVKDEEDVHCEMCKINVPQSFYDE
HIETMHSYDYLSCEKCDQSFYSKIALRRHVYDEHVPRSSNEK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g12552.t2 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 213 | 275 | 2.0E-5 |
| 4 | g12552.t2 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 253 | 274 | - |
| 6 | g12552.t2 | ProSiteProfiles | PS50157 | Zinc finger C2H2 type domain profile. | 251 | 279 | 9.182 |
| 1 | g12552.t2 | SMART | SM00868 | zf_AD_2 | 16 | 107 | 0.0089 |
| 2 | g12552.t2 | SMART | SM00355 | c2h2final6 | 224 | 246 | 130.0 |
| 3 | g12552.t2 | SMART | SM00355 | c2h2final6 | 251 | 274 | 0.0022 |
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:0005634 | nucleus | CC |
| GO:0008270 | zinc ion 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