General information for g5458.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Serine protease snake.
Parent gene
- The parent gene g5458 is located on chr_2: 9679335..9698759 (- 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 | g5458 | g5458.t6 | TTS | g5458.t6 | 9677650 | 9677650 |
| chr_2 | g5458 | g5458.t6 | isoform | g5458.t6 | 9677666 | 9679335 |
| chr_2 | g5458 | g5458.t6 | exon | g5458.t6.exon1 | 9677666 | 9677851 |
| chr_2 | g5458 | g5458.t6 | cds | g5458.t6.CDS1 | 9677850 | 9677851 |
| chr_2 | g5458 | g5458.t6 | exon | g5458.t6.exon2 | 9677969 | 9678407 |
| chr_2 | g5458 | g5458.t6 | cds | g5458.t6.CDS2 | 9677969 | 9678407 |
| chr_2 | g5458 | g5458.t6 | exon | g5458.t6.exon3 | 9678468 | 9678514 |
| chr_2 | g5458 | g5458.t6 | cds | g5458.t6.CDS3 | 9678468 | 9678514 |
| chr_2 | g5458 | g5458.t6 | exon | g5458.t6.exon4 | 9678608 | 9678661 |
| chr_2 | g5458 | g5458.t6 | cds | g5458.t6.CDS4 | 9678608 | 9678661 |
| chr_2 | g5458 | g5458.t6 | exon | g5458.t6.exon5 | 9678733 | 9678753 |
| chr_2 | g5458 | g5458.t6 | cds | g5458.t6.CDS5 | 9678733 | 9678753 |
| chr_2 | g5458 | g5458.t6 | exon | g5458.t6.exon6 | 9678820 | 9678942 |
| chr_2 | g5458 | g5458.t6 | cds | g5458.t6.CDS6 | 9678820 | 9678942 |
| chr_2 | g5458 | g5458.t6 | exon | g5458.t6.exon7 | 9679004 | 9679210 |
| chr_2 | g5458 | g5458.t6 | cds | g5458.t6.CDS7 | 9679004 | 9679210 |
| chr_2 | g5458 | g5458.t6 | exon | g5458.t6.exon8 | 9679278 | 9679335 |
| chr_2 | g5458 | g5458.t6 | cds | g5458.t6.CDS8 | 9679278 | 9679335 |
| chr_2 | g5458 | g5458.t6 | TSS | g5458.t6 | 9679356 | 9679356 |
Sequences
>g5458.t6 Gene=g5458 Length=1135
ATGAAAAGAATAATAATCATTGAGTTTGTGATTTTTACGGTGGTTTGGGGTCAAACACCA
TGCACCGTTTCAAAGACAAAACAAGTAGGTGAGTGCATGTTCATTAGTAACTGCCCTGAG
GTTCTTAAAACTTTCAAAGAATCTGGTGAAATGCCGACAATATGTGACCGTGTTCTGCGT
ACTATTTGTTGTCCTTTAAAAACCACTACAACGTCTACAACTACAACAACAACTACTCAT
TCACCTATTCGTATAAGTGTCAAAAAATGTAAAGAATATGGTCAACTGGTGTATGAAAAA
AAAATTGTAAACAGTTCAATTATTGGCGAACCAAGTGTCGTTAAAATGATATCAAAGTGT
AATCACGAATCAGTGCCACTTATTGTTGGTGGTGAAGATGCAAAGGATGGGGAATTCCCT
CACATGGCGTTAATAGGGTTTGGGGATGGCAATAGAATGGAAGATTATCAATGTGGAGGT
TCGATGATTTCTGAACAGTGGATTCTCTCAGCGGCTCATTGTGTCAGTACTGGTGGTTTA
ACAGCAAATTTTGCAAAAGTTGGTAATGTGGTTCGAGGACGAGACACATTGAATTCATGG
ACTTATAAAATAATTCAAAGAATTCCTCATCCAAATTATAATTCAAGATTTGCAGATGAT
GATATTGCATTATTTAAACTTGAAAAACCTGCACAATTAAATGTTCATGTTATACCAATT
TGTTTACCAGATAAAGAATTACTTACTACAAAATCAGCTATAGCAAGTGGCTATGGACGT
ACTGGATTTGCTGATGATGTTAGTGAAAAATTGATGAAAGTTATAATTGAATATTTTAAG
CCAGCAGATTGTAATGAAGCATTTGCGGATAACACAAAACTTTCAAATAATCAAATAAAT
TGGGATAAAATGGTTTGTGCGGGGTCTCATAATAAAACTGGTGACACTTAATTAATGTTT
TATTTTGATAGGTCCATTGCAAATTTATCATTCTGATGTCTATTGCATGTATAAAATAAT
TGGTATCACATCCTTTGGTCATGCTTACTGCGGTTTTCCTGGTGTCCCTGCTATTTATAC
AAAGGTCTATCACTATTTAGATTGGATTGAATCTATTGTTTGGCCAAATCAATAA
>g5458.t6 Gene=g5458 Length=316
MKRIIIIEFVIFTVVWGQTPCTVSKTKQVGECMFISNCPEVLKTFKESGEMPTICDRVLR
TICCPLKTTTTSTTTTTTTHSPIRISVKKCKEYGQLVYEKKIVNSSIIGEPSVVKMISKC
NHESVPLIVGGEDAKDGEFPHMALIGFGDGNRMEDYQCGGSMISEQWILSAAHCVSTGGL
TANFAKVGNVVRGRDTLNSWTYKIIQRIPHPNYNSRFADDDIALFKLEKPAQLNVHVIPI
CLPDKELLTTKSAIASGYGRTGFADDVSEKLMKVIIEYFKPADCNEAFADNTKLSNNQIN
WDKMVCAGSHNKTGDT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g5458.t6 | CDD | cd00190 | Tryp_SPc | 128 | 316 | 3.16569E-48 |
| 8 | g5458.t6 | Gene3D | G3DSA:2.40.10.10 | - | 119 | 316 | 1.0E-42 |
| 2 | g5458.t6 | PANTHER | PTHR24260:SF107 | EG:BACR7A4.3 PROTEIN-RELATED | 5 | 312 | 1.8E-43 |
| 3 | g5458.t6 | PANTHER | PTHR24260 | - | 5 | 312 | 1.8E-43 |
| 5 | g5458.t6 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 159 | 174 | 5.9E-8 |
| 4 | g5458.t6 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 217 | 231 | 5.9E-8 |
| 1 | g5458.t6 | Pfam | PF00089 | Trypsin | 128 | 310 | 4.5E-33 |
| 10 | g5458.t6 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 17 | - |
| 11 | g5458.t6 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 12 | g5458.t6 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 12 | - |
| 13 | g5458.t6 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 13 | 17 | - |
| 9 | g5458.t6 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 18 | 316 | - |
| 16 | g5458.t6 | ProSitePatterns | PS00134 | Serine proteases, trypsin family, histidine active site. | 169 | 174 | - |
| 18 | g5458.t6 | ProSiteProfiles | PS51888 | Clip domain profile. | 20 | 64 | 7.142 |
| 17 | g5458.t6 | ProSiteProfiles | PS50240 | Serine proteases, trypsin domain profile. | 128 | 316 | 18.858 |
| 15 | g5458.t6 | SMART | SM00020 | trypsin_2 | 127 | 316 | 2.2E-23 |
| 6 | g5458.t6 | SUPERFAMILY | SSF50494 | Trypsin-like serine proteases | 118 | 312 | 8.4E-47 |
| 7 | g5458.t6 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 17 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5458/g5458.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5458.t6.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0004252 | serine-type endopeptidase 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