General information for g5981.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Digestive cysteine proteinase 1.
Parent gene
- The parent gene g5981 is located on chr_2: 13160413..13161578 (- 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 | g5981 | g5981.t3 | TTS | g5981.t3 | 13160303 | 13160303 |
| chr_2 | g5981 | g5981.t3 | isoform | g5981.t3 | 13160413 | 13161578 |
| chr_2 | g5981 | g5981.t3 | exon | g5981.t3.exon1 | 13160413 | 13160705 |
| chr_2 | g5981 | g5981.t3 | cds | g5981.t3.CDS1 | 13160413 | 13160705 |
| chr_2 | g5981 | g5981.t3 | exon | g5981.t3.exon2 | 13161156 | 13161578 |
| chr_2 | g5981 | g5981.t3 | cds | g5981.t3.CDS2 | 13161156 | 13161270 |
| chr_2 | g5981 | g5981.t3 | TSS | g5981.t3 | 13161676 | 13161676 |
Sequences
>g5981.t3 Gene=g5981 Length=716
ATGTACCTTGGTATTTTAGTCTTATTCACAAATTTAATAAACAGTTACATTGATAATCAT
GAATCAATAGAATTGTGGATGAAATTTAAAGTGAGTCATTTTTAAATTTTTTGTCTAGAT
TGCGTGAATTTCTACAACTCTCATTTTTTTATTCATAAGAGAGATGAGAAAAAAATTGCA
AAAAAAATTCTTTTCACTCTCAAAATCATGCATGAAAATATTTTTTTAAGGTTGACTACA
ACAGAAGCTATGAGACAACAAGAGAGGAAGAAATACGTAAAGAAATTTTCATGGATAATT
TAAGAAAAATGTTGTCACATAATCTCAAGCAATCTGCTGGCCTATATTCATTTAAATTTG
GTATTAATCAGTTTTCAGACATGACGTTTGAAGAATTTCTCAAAATAAACACAGAACCTG
GAAAATTGAAAAATGCACTTGTTAAATATGGACCAATTATAATTTCAATAGATCATTTAC
ATGAGAGTTTTATGAGATATTCAAGTGGAGTTTATCATGAAAGTGACTGTAAAAAACAAT
TTTCTCATGCTGCACTTTTGGTCGGTTATGGAAGTGAAAATGGCAAAGATTATTGGTTAG
TGAAAAACTCGTTTGGAACAACATGGGGTGAAAATGGATATTTTAGGATAGCAAGGAATC
GAAAAAATAATTGTGAAATTGCTACAGAACCGGTGATAATTAGCAGTGAAGATTAA
>g5981.t3 Gene=g5981 Length=135
MLSHNLKQSAGLYSFKFGINQFSDMTFEEFLKINTEPGKLKNALVKYGPIIISIDHLHES
FMRYSSGVYHESDCKKQFSHAALLVGYGSENGKDYWLVKNSFGTTWGENGYFRIARNRKN
NCEIATEPVIISSED
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5981.t3 | CDD | cd02248 | Peptidase_C1A | 39 | 131 | 0e+00 |
| 6 | g5981.t3 | Gene3D | G3DSA:3.90.70.10 | Cysteine proteinases | 31 | 134 | 0e+00 |
| 2 | g5981.t3 | PANTHER | PTHR12411 | CYSTEINE PROTEASE FAMILY C1-RELATED | 38 | 131 | 0e+00 |
| 3 | g5981.t3 | PANTHER | PTHR12411:SF734 | CATHEPSIN S, ORTHOLOG 1 | 38 | 131 | 0e+00 |
| 1 | g5981.t3 | Pfam | PF00112 | Papain family cysteine protease | 30 | 129 | 0e+00 |
| 5 | g5981.t3 | SMART | SM00645 | pept_c1 | 1 | 132 | 1e-07 |
| 4 | g5981.t3 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 39 | 129 | 0e+00 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5981/g5981.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5981.t3.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0008234 | cysteine-type peptidase activity | MF |
| GO:0006508 | proteolysis | BP |
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.
