General information for g5982.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Cathepsin L-like.
Parent gene
- The parent gene g5982 is located on chr_2: 13162513..13163608 (- 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 | g5982 | g5982.t1 | isoform | g5982.t1 | 13162513 | 13163608 |
| chr_2 | g5982 | g5982.t1 | exon | g5982.t1.exon1 | 13162513 | 13163442 |
| chr_2 | g5982 | g5982.t1 | cds | g5982.t1.CDS1 | 13162513 | 13163442 |
| chr_2 | g5982 | g5982.t1 | exon | g5982.t1.exon2 | 13163498 | 13163608 |
| chr_2 | g5982 | g5982.t1 | cds | g5982.t1.CDS2 | 13163498 | 13163608 |
| chr_2 | g5982 | g5982.t1 | TSS | g5982.t1 | NA | NA |
| chr_2 | g5982 | g5982.t1 | TTS | g5982.t1 | NA | NA |
Sequences
>g5982.t1 Gene=g5982 Length=1041
ATGATATCTCTTGGATTTTTAATTTTAGGATTAAATTTTTTGTCATATCAAAAAAGTGAA
AATGAGAGAAATAATCAAACTCAAACGAAGAATGTCTTTGATGAGTATTGTAATGACTTC
AACAAGTCTTATCATTCAAAGCAAGAATATGGTGTGCGGAAGGAAATATTTTTAAAAAAT
CTAAACGCTATTAATAAACACAATGGCAATAATAGTGAAACATATAAAATGTCTATTAAT
CAATTTACTGATATGACGTTTAAAGAACTTTACGATCTAAACTATCCAGATGAAGGCGAA
TCCTCTTCTAAAATGGACACTACAAAATACACATCACCTGAGACTGAAAATTTATTGAGT
GACTCATTTGAGGAAAATGTTCCTGATTCTTTTGATTGGAGAAATTTTGATGTAATTTCA
AACATAAAAGATCAAAAATTGTGTGGCAGTTGTTTTATTTATGCAGTTCTTGAAGAAATT
GAAAGTCAAATTAAAATTAAAACAAATCAATCTTATGAATTTTCACGTCAAGAAATTCTC
GATTGTGCTAGAAAAGGATATGGATCGCTTGGATGTAGTGGTGGTTCACTGTATGGTGTT
CATTCTTATATTAAAAATAGAGGTGGAATTTCTGAAGAAAAATTTTATCCTTATGAAGCA
AAAGAAAATTTGTGTCGTAGTGAAAAATTTCCAAAAATTGACATCGATCTCAAAGGCATA
AAAATATTTGACACAGAAGATGAAGACATTCTGAAAAGAGCTTTATATACTTTAGGACCA
ATAACTGTAATAATTGATAATCTTCATGACTCATTCTTTCGTTATTCAAGTGGAATTTAT
TATGAGCAAGAATGCAATGAATCTGATGCATATTCTCATGCAGTTGTGATAATTGGTTAT
GGAAGTTCAAATGGTAAAGATTATTGGACAATTAAAAATTCTTATGGAGAAAAATGGGGA
GAAAAAGGATATATGAGAATTGCAAGAAATCAAAATAATCACTGCAAAATATCATCATTT
AATATGGTCACAAAATTATAA
>g5982.t1 Gene=g5982 Length=346
MISLGFLILGLNFLSYQKSENERNNQTQTKNVFDEYCNDFNKSYHSKQEYGVRKEIFLKN
LNAINKHNGNNSETYKMSINQFTDMTFKELYDLNYPDEGESSSKMDTTKYTSPETENLLS
DSFEENVPDSFDWRNFDVISNIKDQKLCGSCFIYAVLEEIESQIKIKTNQSYEFSRQEIL
DCARKGYGSLGCSGGSLYGVHSYIKNRGGISEEKFYPYEAKENLCRSEKFPKIDIDLKGI
KIFDTEDEDILKRALYTLGPITVIIDNLHDSFFRYSSGIYYEQECNESDAYSHAVVIIGY
GSSNGKDYWTIKNSYGEKWGEKGYMRIARNQNNHCKISSFNMVTKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g5982.t1 | CDD | cd02248 | Peptidase_C1A | 128 | 340 | 6.89376E-76 |
| 10 | g5982.t1 | Gene3D | G3DSA:3.90.70.10 | Cysteine proteinases | 23 | 344 | 2.0E-88 |
| 3 | g5982.t1 | PANTHER | PTHR12411 | CYSTEINE PROTEASE FAMILY C1-RELATED | 28 | 343 | 4.3E-64 |
| 4 | g5982.t1 | PANTHER | PTHR12411:SF734 | CATHEPSIN S, ORTHOLOG 1 | 28 | 343 | 4.3E-64 |
| 7 | g5982.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 145 | 160 | 3.1E-5 |
| 6 | g5982.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 293 | 303 | 3.1E-5 |
| 5 | g5982.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 308 | 314 | 3.1E-5 |
| 1 | g5982.t1 | Pfam | PF08246 | Cathepsin propeptide inhibitor domain (I29) | 33 | 89 | 7.4E-13 |
| 2 | g5982.t1 | Pfam | PF00112 | Papain family cysteine protease | 127 | 342 | 3.1E-62 |
| 12 | g5982.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 15 | - |
| 13 | g5982.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 14 | g5982.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 11 | - |
| 15 | g5982.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 12 | 15 | - |
| 11 | g5982.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 16 | 346 | - |
| 18 | g5982.t1 | SMART | SM00848 | Inhibitor_I29_2 | 33 | 90 | 1.9E-17 |
| 17 | g5982.t1 | SMART | SM00645 | pept_c1 | 127 | 345 | 1.3E-66 |
| 8 | g5982.t1 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 27 | 340 | 4.26E-89 |
| 9 | g5982.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5982/g5982.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5982.t1.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. There were no conditions that were differentially expressed