General information for g11620.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Elongin-C.
Parent gene
- The parent gene g11620 is located on chr_1: 17476781..17477565 (+ 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 | g11620 | g11620.t3 | isoform | g11620.t3 | 17476540 | 17477313 |
| chr_1 | g11620 | g11620.t3 | exon | g11620.t3.exon1 | 17476540 | 17476618 |
| chr_1 | g11620 | g11620.t3 | TSS | g11620.t3 | 17476548 | 17476548 |
| chr_1 | g11620 | g11620.t3 | exon | g11620.t3.exon2 | 17476754 | 17476904 |
| chr_1 | g11620 | g11620.t3 | cds | g11620.t3.CDS1 | 17476781 | 17476904 |
| chr_1 | g11620 | g11620.t3 | exon | g11620.t3.exon3 | 17476968 | 17477034 |
| chr_1 | g11620 | g11620.t3 | cds | g11620.t3.CDS2 | 17476968 | 17477034 |
| chr_1 | g11620 | g11620.t3 | exon | g11620.t3.exon4 | 17477091 | 17477158 |
| chr_1 | g11620 | g11620.t3 | cds | g11620.t3.CDS3 | 17477091 | 17477158 |
| chr_1 | g11620 | g11620.t3 | exon | g11620.t3.exon5 | 17477240 | 17477313 |
| chr_1 | g11620 | g11620.t3 | cds | g11620.t3.CDS4 | 17477240 | 17477313 |
| chr_1 | g11620 | g11620.t3 | TTS | g11620.t3 | 17477379 | 17477379 |
Sequences
>g11620.t3 Gene=g11620 Length=439
TCTCAAATTTAAATTGCAAAAAACAACAACTTTTTTTAGAAAATTACAAAATTGAATTGA
TCAATTTTTTAAAGTGTAGGAAAAATTAAATTTTAATAGCAACAAAATGAATGAAGAAAA
ATATGGAGGATGTGAAGGACCTGATGCGATGTATGTGAAGTTAATTTCATCAGATGGTCA
TGAGTTTATAGTCAAAAGAGAGCATGCATTAACATCAGGTACTATAAAAGCTATGTTATC
TGGTCCTGGACAGTTTGCGGAAAATGAAGCAAATGAAGTCAACTTTAGAGAAATCCCCTC
TCATGTTTTGCAAAAAGTATGCATGTATTTTACTTATAAAGTCCGATACACAAACAGTTC
GACAGAAATTCCTGAGTTTACAATTGCACCAGAGATTGCATTGGAACTTTTGATGGCTGC
AAACTTTCTGGATTGCTAA
>g11620.t3 Gene=g11620 Length=110
MNEEKYGGCEGPDAMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENEANEVNF
REIPSHVLQKVCMYFTYKVRYTNSSTEIPEFTIAPEIALELLMAANFLDC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g11620.t3 | CDD | cd18321 | BTB_POZ_EloC | 16 | 110 | 0 |
| 6 | g11620.t3 | Gene3D | G3DSA:3.30.710.10 | Potassium Channel Kv1.1; Chain A | 14 | 110 | 0 |
| 2 | g11620.t3 | PANTHER | PTHR20648:SF12 | - | 3 | 110 | 0 |
| 3 | g11620.t3 | PANTHER | PTHR20648 | ELONGIN-C | 3 | 110 | 0 |
| 1 | g11620.t3 | Pfam | PF03931 | Skp1 family, tetramerisation domain | 16 | 78 | 0 |
| 5 | g11620.t3 | SMART | SM00512 | skp1_3 | 14 | 110 | 0 |
| 4 | g11620.t3 | SUPERFAMILY | SSF54695 | POZ domain | 12 | 110 | 0 |
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:0006511 | ubiquitin-dependent protein catabolic process | BP |
KEGG
Orthology
- This transcript has been annotated with K03872 (elongin-C)
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.
