Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Elongin-B.

Parent gene

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.t5 TSS g2047.t5 14822159 14822159
chr_3 g2047 g2047.t5 isoform g2047.t5 14822287 14823811
chr_3 g2047 g2047.t5 exon g2047.t5.exon1 14822287 14822873
chr_3 g2047 g2047.t5 exon g2047.t5.exon2 14822977 14823811
chr_3 g2047 g2047.t5 cds g2047.t5.CDS1 14822986 14823315
chr_3 g2047 g2047.t5 TTS g2047.t5 14823818 14823818

Sequences

>g2047.t5 Gene=g2047 Length=1422
ATGGTGAGTAAATAGTAATCAAAATGACTCAGCGAAAAATCACAGAACAATTTTATATGC
AGTAAAATAGTGACATTGTGTACAATTTTTTCTGAGAAAAGCTTATTCGTGAATTTTCTC
TTGCAAAAAATATAGTTTAACTAAAAACTCTAAGCAAAACTTAAATTTAATGTCGAGCAA
ATAGAGAATGAGGATAAATAAGTTTATTAAAATTTTCTTATAAACGTGACCTAAAAAGTA
ACATTTACTCTAGGTAATCTAAATAATTGAATTTATTAAATGACCGGTTATTAGACTATC
ATTTCAACAACACCTTCATTCATCTTTTAAATGATAATTTATTAATTAAAGTATTCAATA
AAATATTCAATTATATTGAGAGTTATAAGGAAGCACATTAAAGAAATATATGCAGAGAAT
TAACATTAATTTCTATCTATATGACATTTAGGAAAACAAAACTATTAAATTTCTCATGTA
AAAATAATGATTCTATTCATAATTAAAATGTTCTTTTTTGAAATTTCTAATTGCATATAT
ACATACGTGAATGTTTTACTGTCACCTACGGACTTTGACCTTTATAAGATGTTTTTATGA
TGATTAGACGTAAAAAGACAACAATATTCACAGATGCTAAAGATACTACAACTGTTCACG
AGTTGAAAAAAATGATTGAAGGAATTTTAAAAGTTCCACCTAAAGATCAAAGATTGTTTA
GCAAAGATAGCACAGTAATGGAAGATGATAAGCAGCTGCAAGATTATGGTATCACAGTGA
TGACGGCAAAAGCTCAACAACCAGCTGTTCTTGGACTCGCACTTCGTATTGATCATGATT
TTGAACCTCTAGAAATGATTCCATATTCACAACCACCTGATTTGCCTGAAGTGATGAAAC
AAGAAGCAAACGGACAGGAGGCTTAACTTTAATTACACATTAATTAAAATAAACATTAAA
CTCAAATGAATTTTCACATCCTTTTATTGTTAAAAAAAGAGGAAGAATTAACAAAAAAGA
AACGTAATTGTAAACCATACACAAGACTAACAAAAACATACATGTATCTCTTAAGAAGTG
TAGACAGACAAACGCATTATAGAACAAGCAAAAGTCAAAAAAGGAGACAGCTACACACAC
ACATACACACAATCGTCATCAATGCTTTATAATTTATTATATAAATTGTCTTAAAAAACA
TTAGGTATGAAGCGATGTGAGCAAGCACGAGTGAGAGAGAATGGAGTTAATTGCCTTAAT
TTTAAAATGAATGGTTCACTGTGAAAATGTACTTTTAAGTTCTTTCTTCAAATTTCCTTC
TGTCCTTCTCAGATTTTATTATATTTTTGTTTTTTTCCAAGCATCATAATGTTTTTTTGT
GTAAAAAAGAATTTTCTTATAAGAAATAAAAGCAAGCAAATT

>g2047.t5 Gene=g2047 Length=109
MMIRRKKTTIFTDAKDTTTVHELKKMIEGILKVPPKDQRLFSKDSTVMEDDKQLQDYGIT
VMTAKAQQPAVLGLALRIDHDFEPLEMIPYSQPPDLPEVMKQEANGQEA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g2047.t5 CDD cd01788 Ubl_ElonginB 1 99 1.86382E-53
6 g2047.t5 Gene3D G3DSA:3.10.20.90 - 1 95 2.7E-27
5 g2047.t5 MobiDBLite mobidb-lite consensus disorder prediction 90 109 -
2 g2047.t5 PANTHER PTHR13248:SF4 ELONGIN B 1 108 2.4E-43
3 g2047.t5 PANTHER PTHR13248 TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 1 108 2.4E-43
1 g2047.t5 Pfam PF00240 Ubiquitin family 6 60 9.3E-8
7 g2047.t5 ProSiteProfiles PS50053 Ubiquitin domain profile. 1 59 12.662
4 g2047.t5 SUPERFAMILY SSF54236 Ubiquitin-like 3 101 2.3E-23

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 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.

Raw TPM values