General information for g5979.t3
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Sepiapterin reductase.
Parent gene
- The parent gene g5979 is located on chr_2: 13158794..13159690 (- 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_2 | g5979 | g5979.t3 | TTS | g5979.t3 | 13158330 | 13158330 |
| chr_2 | g5979 | g5979.t3 | isoform | g5979.t3 | 13158794 | 13159674 |
| chr_2 | g5979 | g5979.t3 | exon | g5979.t3.exon1 | 13158794 | 13159674 |
| chr_2 | g5979 | g5979.t3 | cds | g5979.t3.CDS1 | 13158893 | 13159390 |
| chr_2 | g5979 | g5979.t3 | TSS | g5979.t3 | 13160236 | 13160236 |
Sequences
>g5979.t3 Gene=g5979 Length=881
TTGATTTAAATAATAAATTAGTGTATCTGATAATCACTGGAGCAAGCAGAGGCATAGGTA
AAGAATTGGCCATTGAAACATCTAAAAATTTTAAAACTGGTTCTACTGTTGTTTTACTTG
CTCGCTCAAAAGAGGGATTAGAAAACACAAAAAAAGTCATTAACGAAACAAATAAAAATG
TTGAAGTCATTATTAAATCAATTGATTTAACAAAACCAAGTGTTGAGGAATTAGATGAGA
TTATTAATAATTCATTTGATGCATCTAAAAATTATGACCTAACAATGATAATACATAATG
TAGGCACACTTGGTGATATTTCAAAATGGTCCAATGATATGAACGATTATAACGAGTTGG
AACAATATTTCAGCACTAATGTTTTTGCACCAGTAATTCTCAACAATCGCTTACTTAAAG
TCATTCCAAAAAGTATGAAAACATTTATTGTGAATATCACATCGAAAGCTGCTTTGCATG
CATTTAAAAGCTTTGGATTTTACTGTATGGGAAAAGCTGCACGTGAAATGTACTTTAAGA
TGATTGCTGAAGAATTCAAGGATCTTTTGGTTCTCAATTATTCACCAGGACCAGTTGAAA
GTGATATGACTGTGTATGCACAAAACGCATCTATTTCAGAAGAGACATCTGGAATGTTTA
AGCAACTACGAAATGAGGGAACAATCTTAACCACAGCAATGACTACTAAACGATTTTTAG
AAGTTGTTGCTGCTGGAAAATATAATTCTGGAGATCATGTAGATTATTTTGATGAAATTT
AAATATCATATATATTCCATTATATACTTACACAAACTAAATCAATACTCATTAAAAGTT
GATTAACCTACCTAATTAAAATTTTCTTTCATTTTCTTGTT
>g5979.t3 Gene=g5979 Length=165
MIIHNVGTLGDISKWSNDMNDYNELEQYFSTNVFAPVILNNRLLKVIPKSMKTFIVNITS
KAALHAFKSFGFYCMGKAAREMYFKMIAEEFKDLLVLNYSPGPVESDMTVYAQNASISEE
TSGMFKQLRNEGTILTTAMTTKRFLEVVAAGKYNSGDHVDYFDEI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g5979.t3 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 164 | 0 |
| 2 | g5979.t3 | PANTHER | PTHR44085 | SEPIAPTERIN REDUCTASE | 1 | 164 | 0 |
| 1 | g5979.t3 | Pfam | PF00106 | short chain dehydrogenase | 1 | 111 | 0 |
| 3 | g5979.t3 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 2 | 156 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5979/g5979.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5979.t3.fa.iupred3.txt does not exist
GO terms from InterProScan
## [1] "No matching GO terms"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.
