General information for g2416.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Biotin–protein ligase.
Parent gene
- The parent gene g2416 is located on chr_3: 17859983..17861143 (- 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 | g2416 | g2416.t1 | TTS | g2416.t1 | 17859657 | 17859657 |
| chr_3 | g2416 | g2416.t1 | isoform | g2416.t1 | 17859983 | 17861143 |
| chr_3 | g2416 | g2416.t1 | exon | g2416.t1.exon1 | 17859983 | 17860160 |
| chr_3 | g2416 | g2416.t1 | cds | g2416.t1.CDS1 | 17859983 | 17860160 |
| chr_3 | g2416 | g2416.t1 | exon | g2416.t1.exon2 | 17860227 | 17860440 |
| chr_3 | g2416 | g2416.t1 | cds | g2416.t1.CDS2 | 17860227 | 17860440 |
| chr_3 | g2416 | g2416.t1 | exon | g2416.t1.exon3 | 17860511 | 17860625 |
| chr_3 | g2416 | g2416.t1 | cds | g2416.t1.CDS3 | 17860511 | 17860625 |
| chr_3 | g2416 | g2416.t1 | exon | g2416.t1.exon4 | 17861120 | 17861143 |
| chr_3 | g2416 | g2416.t1 | cds | g2416.t1.CDS4 | 17861120 | 17861143 |
| chr_3 | g2416 | g2416.t1 | TSS | g2416.t1 | NA | NA |
Sequences
>g2416.t1 Gene=g2416 Length=531
ATGCATATATATGTGTACAGACAAGCATTGGATTTAAATGTTAAATGGCCGAATGACATT
TATGTAAATGGTGAAATTAAAATTGGTGGATTGATTGTTAATTCTATAATAGAAGCGGAT
TCTGCAATTTGCAATATTGGTCTCGGTGTAAATTTATCAAATTCAATTCCAACGACATGT
ATTAATGACTTAATCAAAGAATATAATAAAAAACATTCAGGAAATTTAAAGGAACTTTCC
TATGAGAAAACACTAGCGATCATTTTCAACGAAATAGAAAGTATTTTGAACCGCATACAA
GATGGAGATATAAATCACCTTTATGAGCTTTATTACGCTTGCTGGTTGCACACGGACACA
TCTGTCAAAGTGCTCTCACAAAACGGACAAGAGAAAAATGGAAAGATCCTGGGAATTGAT
GAATATGGGTTCCTAAAGATTCGTCTCGACAACAACACCATCGAGTCAGTGCAACCAGAT
GGAAATTCTTTCGACATGTTGCGAGGATTAATCATTCCAAAAGCAAACTAA
>g2416.t1 Gene=g2416 Length=176
MHIYVYRQALDLNVKWPNDIYVNGEIKIGGLIVNSIIEADSAICNIGLGVNLSNSIPTTC
INDLIKEYNKKHSGNLKELSYEKTLAIIFNEIESILNRIQDGDINHLYELYYACWLHTDT
SVKVLSQNGQEKNGKILGIDEYGFLKIRLDNNTIESVQPDGNSFDMLRGLIIPKAN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g2416.t1 | Gene3D | G3DSA:3.30.930.10 | Bira Bifunctional Protein; Domain 2 | 3 | 111 | 0.000000 |
| 3 | g2416.t1 | PANTHER | PTHR12835 | BIOTIN PROTEIN LIGASE | 8 | 175 | 0.000000 |
| 4 | g2416.t1 | PANTHER | PTHR12835:SF9 | BIOTIN–PROTEIN LIGASE | 8 | 175 | 0.000000 |
| 2 | g2416.t1 | Pfam | PF03099 | Biotin/lipoate A/B protein ligase family | 12 | 51 | 0.000039 |
| 1 | g2416.t1 | Pfam | PF02237 | Biotin protein ligase C terminal domain | 122 | 166 | 0.000000 |
| 7 | g2416.t1 | ProSiteProfiles | PS51733 | Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile. | 1 | 100 | 13.160000 |
| 5 | g2416.t1 | SUPERFAMILY | SSF55681 | Class II aaRS and biotin synthetases | 9 | 115 | 0.000000 |
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:0006464 | cellular protein modification process | BP |
KEGG
Orthology
- This transcript has been annotated with K01942 (biotin—protein ligase)
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.
