General information for g3996.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TSS | g3996.t1 | 29409557 | 29409557 |
| chr_3 | g3996 | g3996.t1 | isoform | g3996.t1 | 29409655 | 29410662 |
| chr_3 | g3996 | g3996.t1 | exon | g3996.t1.exon1 | 29409655 | 29409790 |
| chr_3 | g3996 | g3996.t1 | cds | g3996.t1.CDS1 | 29409655 | 29409790 |
| chr_3 | g3996 | g3996.t1 | exon | g3996.t1.exon2 | 29409857 | 29410662 |
| chr_3 | g3996 | g3996.t1 | cds | g3996.t1.CDS2 | 29409857 | 29410662 |
| chr_3 | g3996 | g3996.t1 | TTS | g3996.t1 | NA | NA |
Sequences
>g3996.t1 Gene=g3996 Length=942
ATGACATCTTGGGAAGAATTCTATGCTTGTCATTTACCACCATCAGATTTTGAAGACAAT
AGACAATTGTTGAAACAATTTTGTGAAAACCACTTGAAAAATAAGAATCAGAATATAGTT
CTCATCACTTCAGGAGGCACTATTGCACCACTTGAGCACAACACTGTAAGATTTGTCGAT
AATTTTAGCGCTGGTAATCGTGGTAGTGCATCAGCTGAATTTTTCTTAGATCGAGGATAT
GCGGTTATTTTCCTCTTTCGCACAAAATCACTAGAGCCATTTACAAGACATTTTAGTGGA
CAACAATTTTTAGATATGCTCGAAATTAATGACAGAGAGCATACAGAAAATCCAAGCATA
AATGTAAAGCCTGATTCTGTGGATATTTTATTACCAATTTTAAGAAAGTATAAAGAAGCT
CAAGAGAGTAATCGACTGCTCTATATTAACTTTACAAGTGTAAGCGATTATTTATGGCTG
TTGAGAGCTGCTTGTGAGGCACTTGCCTCATTCGAAAAAAGGGCATTGCTTTTTCTTGCT
GCAGCCGTAAGTGATTTTTATGTTCCTCAAGATGACATGCCAAAACACAAAATTCAATCG
AGCGGTGCACCAAAAATATCATTGCAATTAGTTCCAAAAATTTTGAAACCTTTAGTTGGC
AATTGGGTACCACAGGCATTTGTCGTATCATTTAAACTAGAAACGGATGACTCCTTACTC
ATTGCAAAATCTAGAGAAAGTTTGATGAAATATAATCATAAATTGGTTATTGCAAATATT
CTACAAACTAGAAGAAATCGTGTTGTTTTTGTCACACCTACATCTTCTGAAGAAATTATA
TTGACAAAGGAACAAGCTTTATCTGGATTAGAAATTGAGGAGCCCATAGTTTGCGAAATT
ATTAAACGACACGAAGAGTTTCAAGCAACTGTTGCTCAATGA
>g3996.t1 Gene=g3996 Length=313
MTSWEEFYACHLPPSDFEDNRQLLKQFCENHLKNKNQNIVLITSGGTIAPLEHNTVRFVD
NFSAGNRGSASAEFFLDRGYAVIFLFRTKSLEPFTRHFSGQQFLDMLEINDREHTENPSI
NVKPDSVDILLPILRKYKEAQESNRLLYINFTSVSDYLWLLRAACEALASFEKRALLFLA
AAVSDFYVPQDDMPKHKIQSSGAPKISLQLVPKILKPLVGNWVPQAFVVSFKLETDDSLL
IAKSRESLMKYNHKLVIANILQTRRNRVVFVTPTSSEEIILTKEQALSGLEIEEPIVCEI
IKRHEEFQATVAQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3996.t1 | Gene3D | G3DSA:3.40.50.10300 | - | 20 | 311 | 0.0e+00 |
| 3 | g3996.t1 | PANTHER | PTHR12290:SF2 | PHOSPHOPANTOTHENATE–CYSTEINE LIGASE | 4 | 307 | 0.0e+00 |
| 4 | g3996.t1 | PANTHER | PTHR12290 | CORNICHON-RELATED | 4 | 307 | 0.0e+00 |
| 2 | g3996.t1 | Pfam | PF04127 | DNA / pantothenate metabolism flavoprotein | 39 | 92 | 1.6e-05 |
| 1 | g3996.t1 | Pfam | PF04127 | DNA / pantothenate metabolism flavoprotein | 168 | 264 | 0.0e+00 |
| 5 | g3996.t1 | SUPERFAMILY | SSF102645 | CoaB-like | 33 | 306 | 0.0e+00 |
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 transcript has been annotated with K01922 (phosphopantothenate—cysteine ligase (ATP))
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.
