General information for g2509.t28
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Ubiquitin conjugation factor E4 A.
Parent gene
- The parent gene g2509 is located on chr_3: 18339764..18340445 (- 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 | g2509 | g2509.t28 | isoform | g2509.t28 | 18338806 | 18340445 |
| chr_3 | g2509 | g2509.t28 | exon | g2509.t28.exon1 | 18338806 | 18339453 |
| chr_3 | g2509 | g2509.t28 | cds | g2509.t28.CDS1 | 18338807 | 18339453 |
| chr_3 | g2509 | g2509.t28 | exon | g2509.t28.exon2 | 18339507 | 18339677 |
| chr_3 | g2509 | g2509.t28 | cds | g2509.t28.CDS2 | 18339507 | 18339677 |
| chr_3 | g2509 | g2509.t28 | exon | g2509.t28.exon3 | 18339749 | 18340445 |
| chr_3 | g2509 | g2509.t28 | cds | g2509.t28.CDS3 | 18339749 | 18340445 |
| chr_3 | g2509 | g2509.t28 | TSS | g2509.t28 | 18340524 | 18340524 |
| chr_3 | g2509 | g2509.t28 | TTS | g2509.t28 | NA | NA |
Sequences
>g2509.t28 Gene=g2509 Length=1516
ATGAATAATCCATTTGCATCATTAGTAGAGCCACAGAAAATCAATGAAATTGTTGAGAAC
ACACTATTGTTAACGTTAAATCCAGAAAAAAGTAATTTGTATTATGTGTCGAATGACGAG
TCAAAATTTTTCACTCTAGAGCTTCTTGAATTCGTGCTATTTGAGCGAATTATTGCCTTT
GATATTGAAACAGACAACGATAAAAAGGTAATTCTTTATCTATACAACTGTTTTCAACGA
GTCCAAGAGGAAGTAAAAAAGTATGGCAGTTCAAACGAGTTAATCAATGTTTTGAGAAAA
ATAGAGCAGCTAATTTTTCAAAATATATCGACAATTCTAAAAGAACCAGAGCTCATACCA
AATCAAAATTTGAGTTCTCAGTTTTTGGATATTTATAAATATGATCAAGATATTGATAAT
GAGAGAGATAGATTTCTTTCGATGTCAATTCTAACAGCACTTTCGGATTGTGATTCTGAT
ATGAAAAAGAATGTTACAGAAATTTTTAACAAATGTTTCGATACTTGTACACGAATCGTT
AAAATATCGTCTATGATCACATTAGAAAAATGGGTATTGAGTTTCTTAATGGCTTTTTCA
AGTGACAAAAATAATCCAGCTATGGCAAATATGTTCATTGATTACATTACACCACCAGAA
AACAGCGAAGGAATCAAATACTCTGAAACATTATTAGGTCAACTTTTGAGTTTGAGCATT
TGCCCAAAAAATAATTTGGGACCATTTGAGTACTATGGAGATTTAAATAACACAAATTTA
ACAGCTTTAAATAATCTATCATCGTCTCTATGGAATTATTTAAAAATTATACATGACTCT
TTAGGAATTCTTGTAAAATCGCTATTAGTTGTTGGAGGAGAAACAAGAGATAAAATGTTG
AAATGGCTCGGTAATGCAATAAGTTCAAATCAAAAGAGAGGACAAATTTGGAATGCTCAT
TCTTCAATGATTCTCGGAAATTTTACAACAGCTCCAGATTCAACAATGATTGGTCTTAGT
GCTGTACTTCTTCGACTTTGTTTGCCACTTATGAAACCACAATTAAAAGTAATGCTTGTT
GATCCAACATTTACTGTCGTTAAAAATGAAGATATTGTTAAAAAACAAATTCATATTAAA
GACTATGAAAAAGAGACTAATTTGATTCCATTTGATGAAGACGAGCAACGAGTGACTGCT
GAAAAATATAATTTTATTACCGAGATTTTCTTTTTGACTCACAAATGTATCGACCTTTCA
TACCGCGTATGTATCGAAAAAGTATCAAGAATGAATAGAGAAATTCATCGATTGCAACAA
GCTTATCAAGATGCTACTAGAGGTGGTGGGACTTCTGATGTGACTGAAAATATAATGAAT
ATGTTAACGAAGCAATCACAAATTTTGTTATGCACACAGAATTTAATTTTAGAACCAAAA
AATGATGAACTTCTTTTAAAATTTTACGAAGCAACTGCAATTTGGTTAAATCAACTTACC
ATAAAAGCAACAATTG
>g2509.t28 Gene=g2509 Length=505
MNNPFASLVEPQKINEIVENTLLLTLNPEKSNLYYVSNDESKFFTLELLEFVLFERIIAF
DIETDNDKKVILYLYNCFQRVQEEVKKYGSSNELINVLRKIEQLIFQNISTILKEPELIP
NQNLSSQFLDIYKYDQDIDNERDRFLSMSILTALSDCDSDMKKNVTEIFNKCFDTCTRIV
KISSMITLEKWVLSFLMAFSSDKNNPAMANMFIDYITPPENSEGIKYSETLLGQLLSLSI
CPKNNLGPFEYYGDLNNTNLTALNNLSSSLWNYLKIIHDSLGILVKSLLVVGGETRDKML
KWLGNAISSNQKRGQIWNAHSSMILGNFTTAPDSTMIGLSAVLLRLCLPLMKPQLKVMLV
DPTFTVVKNEDIVKKQIHIKDYEKETNLIPFDEDEQRVTAEKYNFITEIFFLTHKCIDLS
YRVCIEKVSRMNREIHRLQQAYQDATRGGGTSDVTENIMNMLTKQSQILLCTQNLILEPK
NDELLLKFYEATAIWLNQLTIKATI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g2509.t28 | Coils | Coil | Coil | 428 | 448 | - |
| 2 | g2509.t28 | PANTHER | PTHR13931:SF2 | UBIQUITIN CONJUGATION FACTOR E4 A | 12 | 501 | 3.2E-65 |
| 3 | g2509.t28 | PANTHER | PTHR13931 | UBIQUITINATION FACTOR E4 | 12 | 501 | 3.2E-65 |
| 1 | g2509.t28 | Pfam | PF10408 | Ubiquitin elongating factor core | 232 | 499 | 4.9E-49 |
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:0034450 | ubiquitin-ubiquitin ligase activity | MF |
| GO:0006511 | ubiquitin-dependent protein catabolic process | BP |
| GO:0000151 | ubiquitin ligase complex | CC |
| GO:0016567 | protein ubiquitination | BP |
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