General information for g2509.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TTS | g2509.t1 | 18337224 | 18337224 |
| chr_3 | g2509 | g2509.t1 | isoform | g2509.t1 | 18337323 | 18340445 |
| chr_3 | g2509 | g2509.t1 | exon | g2509.t1.exon1 | 18337323 | 18337669 |
| chr_3 | g2509 | g2509.t1 | cds | g2509.t1.CDS1 | 18337323 | 18337669 |
| chr_3 | g2509 | g2509.t1 | exon | g2509.t1.exon2 | 18337750 | 18339453 |
| chr_3 | g2509 | g2509.t1 | cds | g2509.t1.CDS2 | 18337750 | 18339453 |
| chr_3 | g2509 | g2509.t1 | exon | g2509.t1.exon3 | 18339507 | 18339677 |
| chr_3 | g2509 | g2509.t1 | cds | g2509.t1.CDS3 | 18339507 | 18339677 |
| chr_3 | g2509 | g2509.t1 | exon | g2509.t1.exon4 | 18339749 | 18340445 |
| chr_3 | g2509 | g2509.t1 | cds | g2509.t1.CDS4 | 18339749 | 18340445 |
| chr_3 | g2509 | g2509.t1 | TSS | g2509.t1 | 18340524 | 18340524 |
Sequences
>g2509.t1 Gene=g2509 Length=2919
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
ATAAAAGCAACAATTGATACAAAAGATTTTGAAAAAGGATTTGCACCAATTGAGAGAACT
AAAATTAATCTTCCACTCACAAACGATGTTAGTCCATTCCTAAAATACGTTCCAGAATTG
ATAATTGAAAATATCGTTGGTTATCTTCAATTCAGCAAGCATTTTGATACCTACATTAAA
CAAAATCACGAAGCTAAAGAAGTCTTTCTTACAACATGCTTGATTTTCATGGGTAATTCC
AAACGTGTCAAAAATCCTCATCTTCGAGCTCATTTATCAGAAGGTTTAGAAAGCTTATTG
CCAAGAGAAAATAGTAATGGTTTTACTATTGACACTCAACTATTTTATCAGCATGAACAT
CGTCGTTTTATAGTTGAAAATTTACTTGATGTGTTTGTGTCGATTGAAATGACTGGACAA
AGTGTGCAATTCGAACAAAAATTTAATTACAGACGTCCGATGTATGCAATTATGAAATAT
TTGTGGGATATTGATGAACAACGTGAATGCTTCAGAAAAATGTCATTATTTGCACAGGAA
CATATCGATGATGTTGAAGTTCCTTTATATCTACGCTTCATAAATGTTCTAATAAATGAT
TCAATTTTTCTGCTTGATGAATCGCTCAATAATTTACAGAAAATTCGAGAGATGGAAGAG
GCAAAATCAAAAGGAGATTGGGACAAGTTACCTCAAAATGAAAGACAACAAAATCATCAG
AATTTGATGCAATTGGGCATGTTAGCAAAGTTCGATAATATTTTGGGAAAAGACACAATT
CACATTCTTAAGTTGCTTACTTCAGAGACAAAGGAGATATTTATTCATCCTACAATGGTT
GAGCGAATTACAAACATGCTGAATTATTTCTTACTTCAATTATGTGGTCCAAATCAAAAA
AGATTCAAAGTTCAGAACAAACAAGAATATGATTTTAATCCAGCTCATACTGTTAAAGAA
ATTTGCCAAATATATTTAAATCTGAAGGATTGCGATGAATTTTGTCTCGCTGTTACTCAA
GATGGTCGCTCTTATTCTTCTGATCTTTTTAAATATGCTGAAAATACTTTGATTAAGATT
GGCGGCGGACAACTTATTACTGACATAACAGAATTTGCTGAAAAAGTAAGACAAGTTGAA
CAACGACAAAAAGAAAATGAAGAAGCGCTTGTCAATCCACCAGATAACTTTTTAGATCCA
ATATTATCGATTTTAATGCGCGATCCTGTAATTTTACCATCATCACGTGTAACTTGTGAT
AAGTCAACAATTTCAAGGCATCTTCTTAGTGATCAAAGTGATCCATTTAATCGTTCTCCA
CTTTCAATGGATCAACTTATTCCCGATACTAAATTAAAAGCTCAAATCGATGCTTGGATT
AAAGAGCGATTAGAAAAGTATAAAAATGAAAATGAATAA
>g2509.t1 Gene=g2509 Length=972
MNNPFASLVEPQKINEIVENTLLLTLNPEKSNLYYVSNDESKFFTLELLEFVLFERIIAF
DIETDNDKKVILYLYNCFQRVQEEVKKYGSSNELINVLRKIEQLIFQNISTILKEPELIP
NQNLSSQFLDIYKYDQDIDNERDRFLSMSILTALSDCDSDMKKNVTEIFNKCFDTCTRIV
KISSMITLEKWVLSFLMAFSSDKNNPAMANMFIDYITPPENSEGIKYSETLLGQLLSLSI
CPKNNLGPFEYYGDLNNTNLTALNNLSSSLWNYLKIIHDSLGILVKSLLVVGGETRDKML
KWLGNAISSNQKRGQIWNAHSSMILGNFTTAPDSTMIGLSAVLLRLCLPLMKPQLKVMLV
DPTFTVVKNEDIVKKQIHIKDYEKETNLIPFDEDEQRVTAEKYNFITEIFFLTHKCIDLS
YRVCIEKVSRMNREIHRLQQAYQDATRGGGTSDVTENIMNMLTKQSQILLCTQNLILEPK
NDELLLKFYEATAIWLNQLTIKATIDTKDFEKGFAPIERTKINLPLTNDVSPFLKYVPEL
IIENIVGYLQFSKHFDTYIKQNHEAKEVFLTTCLIFMGNSKRVKNPHLRAHLSEGLESLL
PRENSNGFTIDTQLFYQHEHRRFIVENLLDVFVSIEMTGQSVQFEQKFNYRRPMYAIMKY
LWDIDEQRECFRKMSLFAQEHIDDVEVPLYLRFINVLINDSIFLLDESLNNLQKIREMEE
AKSKGDWDKLPQNERQQNHQNLMQLGMLAKFDNILGKDTIHILKLLTSETKEIFIHPTMV
ERITNMLNYFLLQLCGPNQKRFKVQNKQEYDFNPAHTVKEICQIYLNLKDCDEFCLAVTQ
DGRSYSSDLFKYAENTLIKIGGGQLITDITEFAEKVRQVEQRQKENEEALVNPPDNFLDP
ILSILMRDPVILPSSRVTCDKSTISRHLLSDQSDPFNRSPLSMDQLIPDTKLKAQIDAWI
KERLEKYKNENE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g2509.t1 | CDD | cd16657 | RING-Ubox_UBE4A | 895 | 963 | 1.43821E-38 |
| 7 | g2509.t1 | Coils | Coil | Coil | 428 | 448 | - |
| 8 | g2509.t1 | Coils | Coil | Coil | 869 | 889 | - |
| 6 | g2509.t1 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 892 | 971 | 2.5E-24 |
| 3 | g2509.t1 | PANTHER | PTHR13931:SF2 | UBIQUITIN CONJUGATION FACTOR E4 A | 12 | 970 | 6.3E-231 |
| 4 | g2509.t1 | PANTHER | PTHR13931 | UBIQUITINATION FACTOR E4 | 12 | 970 | 6.3E-231 |
| 2 | g2509.t1 | Pfam | PF10408 | Ubiquitin elongating factor core | 232 | 876 | 1.3E-157 |
| 1 | g2509.t1 | Pfam | PF04564 | U-box domain | 894 | 963 | 4.6E-27 |
| 11 | g2509.t1 | ProSiteProfiles | PS51698 | U-box domain profile. | 892 | 966 | 24.84 |
| 10 | g2509.t1 | SMART | SM00504 | Ubox_2 | 896 | 959 | 1.8E-21 |
| 5 | g2509.t1 | SUPERFAMILY | SSF57850 | RING/U-box | 878 | 962 | 2.83E-24 |
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 |
| GO:0004842 | ubiquitin-protein transferase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K10596 (ubiquitin conjugation factor E4 A)
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.
