General information for g3898.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ubiquitin-like modifier-activating enzyme 1.
Parent gene
- The parent gene g3898 is located on chr_3: 28704954..28706269 (+ 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 | g3898 | g3898.t4 | isoform | g3898.t4 | 28703339 | 28704217 |
| chr_3 | g3898 | g3898.t4 | exon | g3898.t4.exon1 | 28703339 | 28704217 |
| chr_3 | g3898 | g3898.t4 | cds | g3898.t4.CDS1 | 28703406 | 28704215 |
| chr_3 | g3898 | g3898.t4 | TSS | g3898.t4 | NA | NA |
| chr_3 | g3898 | g3898.t4 | TTS | g3898.t4 | NA | NA |
Sequences
>g3898.t4 Gene=g3898 Length=879
TTTCAGTATTGGTGACACAACCGGCTTTGATGATTACATTCGTGGTGGTCTTGCAATTCA
AGTGAAGATGCCGAAAACTGTTTCATTTAAACCATTGGAAGAAGCTGAAAAAAGTCCCGA
GTTTATTCTTTCTGATTATGCAAAATTCGATCATCCACAAAATATCAATATTGCATTTAC
CGCCTTGTCACGTTTCAATACTAAATTCAGTCGCAATCCTCGGCCGTGGAACGCTGAAGA
TGCTGCTGAATTCCTCTCATTGTGTAAAGAACGTGCAAAAGAATTGAATGTCGATGAGCT
TAAAGAAGAATTGTTGTTGATCTTTGCTAAAATTTCAAGCGGCGATCTCTGTCCAATTAA
TGCAGTAATTGGTGGTATGAGTGCTCAAGAAGTAATGAAAGCATGCAGTGGAAAGTTTAT
GCCAATAATGCAATTCTTCAGTTTTGATGCAATCGAATGTTTACCAGAAGATCTCAGTGT
CTTGACTGAAAGTGAATGTCAACCAAATGGATCTCGATATGATTCACAAATTGCAATTTT
TGGAAAAACCTTTCAAGAAAAACTGAGTGCATTAAAGTACTTCATTGTTGGTGCAGGAGC
TATCGGTTGTGAGTTGCTCAAAAATTTTGGAATGATGGGTGTTGGTGCTGGACAAAATGG
TGAACTTATTATTACGGATATGGATCTTATTGAAAAATCCAATTTGAATCGTCAATTTTT
GTTCCGGCCTCATGATGTTCAATCACCAAAATCACGTGTTGCTGCAGCCGCTGTTAAACG
AATGAATCCACACATTAACATCACTTATCATGAAAATCGTGTAGGAGCACAGACTGAAAA
CATTTATGATGATGATTTCTTTGAACGATTAAACGGTGT
>g3898.t4 Gene=g3898 Length=270
MPKTVSFKPLEEAEKSPEFILSDYAKFDHPQNINIAFTALSRFNTKFSRNPRPWNAEDAA
EFLSLCKERAKELNVDELKEELLLIFAKISSGDLCPINAVIGGMSAQEVMKACSGKFMPI
MQFFSFDAIECLPEDLSVLTESECQPNGSRYDSQIAIFGKTFQEKLSALKYFIVGAGAIG
CELLKNFGMMGVGAGQNGELIITDMDLIEKSNLNRQFLFRPHDVQSPKSRVAAAAVKRMN
PHINITYHENRVGAQTENIYDDDFFERLNG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g3898.t4 | Gene3D | G3DSA:3.40.50.12550 | - | 1 | 164 | 9.3E-62 |
| 8 | g3898.t4 | Gene3D | G3DSA:3.40.50.720 | - | 165 | 270 | 5.7E-38 |
| 3 | g3898.t4 | PANTHER | PTHR10953:SF195 | UBIQUITIN-LIKE MODIFIER-ACTIVATING ENZYME 1 | 1 | 270 | 2.2E-88 |
| 4 | g3898.t4 | PANTHER | PTHR10953 | UBIQUITIN-ACTIVATING ENZYME E1 | 1 | 270 | 2.2E-88 |
| 1 | g3898.t4 | Pfam | PF16191 | Ubiquitin-activating enzyme E1 four-helix bundle | 2 | 68 | 8.0E-22 |
| 2 | g3898.t4 | Pfam | PF00899 | ThiF family | 151 | 268 | 3.3E-39 |
| 7 | g3898.t4 | ProSitePatterns | PS00536 | Ubiquitin-activating enzyme signature 1. | 111 | 119 | - |
| 6 | g3898.t4 | SUPERFAMILY | SSF69572 | Activating enzymes of the ubiquitin-like proteins | 1 | 134 | 4.45E-26 |
| 5 | g3898.t4 | SUPERFAMILY | SSF69572 | Activating enzymes of the ubiquitin-like proteins | 145 | 268 | 3.66E-45 |
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:0008641 | ubiquitin-like modifier activating enzyme activity | MF |
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.
