General information for g12212.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable E3 ubiquitin-protein ligase HERC2.
Parent gene
- The parent gene g12212 is located on chr_1: 21777160..21778160 (+ 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 | g12212 | g12212.t3 | isoform | g12212.t3 | 21776828 | 21778160 |
| chr_1 | g12212 | g12212.t3 | exon | g12212.t3.exon1 | 21776828 | 21776967 |
| chr_1 | g12212 | g12212.t3 | cds | g12212.t3.CDS1 | 21776906 | 21776967 |
| chr_1 | g12212 | g12212.t3 | exon | g12212.t3.exon2 | 21777022 | 21777160 |
| chr_1 | g12212 | g12212.t3 | cds | g12212.t3.CDS2 | 21777022 | 21777160 |
| chr_1 | g12212 | g12212.t3 | exon | g12212.t3.exon3 | 21777272 | 21777403 |
| chr_1 | g12212 | g12212.t3 | cds | g12212.t3.CDS3 | 21777272 | 21777403 |
| chr_1 | g12212 | g12212.t3 | exon | g12212.t3.exon4 | 21777533 | 21777744 |
| chr_1 | g12212 | g12212.t3 | cds | g12212.t3.CDS4 | 21777533 | 21777541 |
| chr_1 | g12212 | g12212.t3 | exon | g12212.t3.exon5 | 21777814 | 21778160 |
| chr_1 | g12212 | g12212.t3 | TTS | g12212.t3 | 21778155 | 21778155 |
| chr_1 | g12212 | g12212.t3 | TSS | g12212.t3 | NA | NA |
Sequences
>g12212.t3 Gene=g12212 Length=970
GGTAAATAAAAATATTTTATTATATGACAATTTTTAATAAATTTAAATATATCTATAAAC
TTCAGGTTCTGGGAAGTAATGGAAGAATTTACAAATCAAGAGCGATCACTTTTTTTAAGA
TTTGTATGGGGAAGAACAAGACTTCCAAGAAGCATCGCTGACTTTAGAGGTCGTGACTTT
GTGTTACAAGTTTTAGATAAATATAATCCAGCAGATCATTTTTTGCCTGAAAGTTATACT
TGCTTCTTTTTGTTGAAAATGCCGAGATATTCATGCAAGGCAGTACTAATGGAAAAACTG
AAATACGCCATTCATTTTTGCAAGTCCATTGACACAGATGACTATGCACGAGTTGCAATG
GGTGATCCGATGAGTCATACTGCTAGCGAAGATAATTCTGATATCGAATCGATCGCCTAA
ATTAATCAGAAAAAAATAGCTTTCATTATATCATTAGTGGATGTTCGTTCCATAGATACT
CTATCACATACATAAATGAATAATTAATCAGGTTTCTCAGCTACTTTTTGTTCGTTCAGT
TTTAGACATGCAGTTACTTTAAAATGATGTTGAAGATTTCAAAGAAAAGAATTGTTAAGA
TTTAGCCATAGACAGAGAATTAGTATGAAAGAAAATCTTTTTGCAATCAGATGTATGCGC
AATAGATGACAAGCAAATGCAAACAAAAAGATGAGTTAAGCAGAGACTAATTAATTATAA
AATTTTGCTATTTAGATACATTCATTTGTTCTCTCTTTTTTTAATTAAAATTAAAGAATA
TTTTATATATTCTAGTCATATATGCAATTAAATTTAATTCTTTCCTTTTCTACCTTTGGA
AAAAAAAATATTGTGTTAAATATAGTATACTTCTTTCTCGAAAAAATTTTCATGTTTTTT
TTGCAAGCAGCCTTGAATTGAACTTTTTAAAAAATTAAAAAATCAAATTTATCAATAAAG
AGCCCTAAAA
>g12212.t3 Gene=g12212 Length=113
MEEFTNQERSLFLRFVWGRTRLPRSIADFRGRDFVLQVLDKYNPADHFLPESYTCFFLLK
MPRYSCKAVLMEKLKYAIHFCKSIDTDDYARVAMGDPMSHTASEDNSDIESIA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g12212.t3 | Gene3D | G3DSA:3.30.2410.10 | Hect | 1 | 84 | 0.000 |
| 2 | g12212.t3 | PANTHER | PTHR22870:SF398 | E3 UBIQUITIN-PROTEIN LIGASE HERC2 | 1 | 108 | 0.000 |
| 3 | g12212.t3 | PANTHER | PTHR22870 | REGULATOR OF CHROMOSOME CONDENSATION | 1 | 108 | 0.000 |
| 1 | g12212.t3 | Pfam | PF00632 | HECT-domain (ubiquitin-transferase) | 1 | 83 | 0.000 |
| 6 | g12212.t3 | ProSiteProfiles | PS50237 | HECT domain profile. | 1 | 92 | 17.165 |
| 4 | g12212.t3 | SUPERFAMILY | SSF56204 | Hect, E3 ligase catalytic domain | 1 | 81 | 0.000 |
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:0004842 | ubiquitin-protein transferase activity | 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.
