General information for g3996.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Phosphopantothenate–cysteine ligase.
Parent gene
- The parent gene g3996 is located on chr_3: 29409869..29410662 (+ 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 | g3996 | g3996.t2 | TSS | g3996.t2 | 29409557 | 29409557 |
| chr_3 | g3996 | g3996.t2 | isoform | g3996.t2 | 29409869 | 29410662 |
| chr_3 | g3996 | g3996.t2 | exon | g3996.t2.exon1 | 29409869 | 29410662 |
| chr_3 | g3996 | g3996.t2 | cds | g3996.t2.CDS1 | 29410036 | 29410662 |
| chr_3 | g3996 | g3996.t2 | TTS | g3996.t2 | NA | NA |
Sequences
>g3996.t2 Gene=g3996 Length=794
CACTTGAGCACAACACTGTAAGATTTGTCGATAATTTTAGCGCTGGTAATCGTGGTAGTG
CATCAGCTGAATTTTTCTTAGATCGAGGATATGCGGTTATTTTCCTCTTTCGCACAAAAT
CACTAGAGCCATTTACAAGACATTTTAGTGGACAACAATTTTTAGATATGCTCGAAATTA
ATGACAGAGAGCATACAGAAAATCCAAGCATAAATGTAAAGCCTGATTCTGTGGATATTT
TATTACCAATTTTAAGAAAGTATAAAGAAGCTCAAGAGAGTAATCGACTGCTCTATATTA
ACTTTACAAGTGTAAGCGATTATTTATGGCTGTTGAGAGCTGCTTGTGAGGCACTTGCCT
CATTCGAAAAAAGGGCATTGCTTTTTCTTGCTGCAGCCGTAAGTGATTTTTATGTTCCTC
AAGATGACATGCCAAAACACAAAATTCAATCGAGCGGTGCACCAAAAATATCATTGCAAT
TAGTTCCAAAAATTTTGAAACCTTTAGTTGGCAATTGGGTACCACAGGCATTTGTCGTAT
CATTTAAACTAGAAACGGATGACTCCTTACTCATTGCAAAATCTAGAGAAAGTTTGATGA
AATATAATCATAAATTGGTTATTGCAAATATTCTACAAACTAGAAGAAATCGTGTTGTTT
TTGTCACACCTACATCTTCTGAAGAAATTATATTGACAAAGGAACAAGCTTTATCTGGAT
TAGAAATTGAGGAGCCCATAGTTTGCGAAATTATTAAACGACACGAAGAGTTTCAAGCAA
CTGTTGCTCAATGA
>g3996.t2 Gene=g3996 Length=208
MLEINDREHTENPSINVKPDSVDILLPILRKYKEAQESNRLLYINFTSVSDYLWLLRAAC
EALASFEKRALLFLAAAVSDFYVPQDDMPKHKIQSSGAPKISLQLVPKILKPLVGNWVPQ
AFVVSFKLETDDSLLIAKSRESLMKYNHKLVIANILQTRRNRVVFVTPTSSEEIILTKEQ
ALSGLEIEEPIVCEIIKRHEEFQATVAQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g3996.t2 | Gene3D | G3DSA:3.40.50.10300 | - | 1 | 206 | 0 |
| 2 | g3996.t2 | PANTHER | PTHR12290:SF2 | PHOSPHOPANTOTHENATE–CYSTEINE LIGASE | 7 | 202 | 0 |
| 3 | g3996.t2 | PANTHER | PTHR12290 | CORNICHON-RELATED | 7 | 202 | 0 |
| 1 | g3996.t2 | Pfam | PF04127 | DNA / pantothenate metabolism flavoprotein | 63 | 159 | 0 |
| 4 | g3996.t2 | SUPERFAMILY | SSF102645 | CoaB-like | 4 | 201 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
