General information for g2047.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Elongin-B.
Parent gene
- The parent gene g2047 is located on chr_3: 14822873..14823811 (+ 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 | g2047 | g2047.t3 | TSS | g2047.t3 | 14822159 | 14822159 |
| chr_3 | g2047 | g2047.t3 | isoform | g2047.t3 | 14822287 | 14823811 |
| chr_3 | g2047 | g2047.t3 | exon | g2047.t3.exon1 | 14822287 | 14822289 |
| chr_3 | g2047 | g2047.t3 | cds | g2047.t3.CDS1 | 14822287 | 14822289 |
| chr_3 | g2047 | g2047.t3 | exon | g2047.t3.exon2 | 14822977 | 14823593 |
| chr_3 | g2047 | g2047.t3 | cds | g2047.t3.CDS2 | 14822977 | 14823315 |
| chr_3 | g2047 | g2047.t3 | exon | g2047.t3.exon3 | 14823751 | 14823811 |
| chr_3 | g2047 | g2047.t3 | TTS | g2047.t3 | 14823818 | 14823818 |
Sequences
>g2047.t3 Gene=g2047 Length=681
ATGGATGTTTTTATGATGATTAGACGTAAAAAGACAACAATATTCACAGATGCTAAAGAT
ACTACAACTGTTCACGAGTTGAAAAAAATGATTGAAGGAATTTTAAAAGTTCCACCTAAA
GATCAAAGATTGTTTAGCAAAGATAGCACAGTAATGGAAGATGATAAGCAGCTGCAAGAT
TATGGTATCACAGTGATGACGGCAAAAGCTCAACAACCAGCTGTTCTTGGACTCGCACTT
CGTATTGATCATGATTTTGAACCTCTAGAAATGATTCCATATTCACAACCACCTGATTTG
CCTGAAGTGATGAAACAAGAAGCAAACGGACAGGAGGCTTAACTTTAATTACACATTAAT
TAAAATAAACATTAAACTCAAATGAATTTTCACATCCTTTTATTGTTAAAAAAAGAGGAA
GAATTAACAAAAAAGAAACGTAATTGTAAACCATACACAAGACTAACAAAAACATACATG
TATCTCTTAAGAAGTGTAGACAGACAAACGCATTATAGAACAAGCAAAAGTCAAAAAAGG
AGACAGCTACACACACACATACACACAATCGTCATCAATGCTTTATAATTTATTATATAA
ATTGTCTTAAAAAACATTAGCATCATAATGTTTTTTTGTGTAAAAAAGAATTTTCTTATA
AGAAATAAAAGCAAGCAAATT
>g2047.t3 Gene=g2047 Length=113
MDVFMMIRRKKTTIFTDAKDTTTVHELKKMIEGILKVPPKDQRLFSKDSTVMEDDKQLQD
YGITVMTAKAQQPAVLGLALRIDHDFEPLEMIPYSQPPDLPEVMKQEANGQEA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g2047.t3 | CDD | cd01788 | Ubl_ElonginB | 2 | 103 | 0.0000000 |
| 5 | g2047.t3 | Gene3D | G3DSA:3.10.20.90 | - | 1 | 99 | 0.0000000 |
| 2 | g2047.t3 | PANTHER | PTHR13248:SF4 | ELONGIN B | 1 | 112 | 0.0000000 |
| 3 | g2047.t3 | PANTHER | PTHR13248 | TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 | 1 | 112 | 0.0000000 |
| 1 | g2047.t3 | Pfam | PF00240 | Ubiquitin family | 10 | 64 | 0.0000001 |
| 6 | g2047.t3 | ProSiteProfiles | PS50053 | Ubiquitin domain profile. | 1 | 63 | 13.7940000 |
| 4 | g2047.t3 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 1 | 105 | 0.0000000 |
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:0006368 | transcription elongation from RNA polymerase II promoter | BP |
| GO:0005515 | protein binding | MF |
| GO:0030891 | VCB complex | CC |
| GO:0070449 | elongin complex | CC |
KEGG
Orthology
- This transcript has been annotated with K03873 (elongin-B)
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.
