Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Cathepsin L.

Parent gene

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_4 g16363 g16363.t2 TSS g16363.t2 9202397 9202397
chr_4 g16363 g16363.t2 isoform g16363.t2 9202433 9204272
chr_4 g16363 g16363.t2 exon g16363.t2.exon1 9202433 9202896
chr_4 g16363 g16363.t2 cds g16363.t2.CDS1 9202433 9202896
chr_4 g16363 g16363.t2 exon g16363.t2.exon2 9203061 9203165
chr_4 g16363 g16363.t2 cds g16363.t2.CDS2 9203061 9203165
chr_4 g16363 g16363.t2 exon g16363.t2.exon3 9203236 9203606
chr_4 g16363 g16363.t2 cds g16363.t2.CDS3 9203236 9203606
chr_4 g16363 g16363.t2 exon g16363.t2.exon4 9203676 9204272
chr_4 g16363 g16363.t2 cds g16363.t2.CDS4 9203676 9203773
chr_4 g16363 g16363.t2 TTS g16363.t2 9204953 9204953

Sequences

>g16363.t2 Gene=g16363 Length=1537
ATGAAAACTTTCGTGACTGTTTTATTTTGTGCCATTCTTTTGGTTTCTTCATCTTTTGCA
TTAAAAATTTCAATCAAAATTTCTGAAACTAAAAAAATTTCATCACTAAATAAAAATGCG
GAACTTTTCAACAATTTTTTGAAAGATTTCAATATTGAACTTTCGCCAGACGATAATTTC
GAAGAAAGACTTGCAGTTTTTATGGAAAATTATAGAAAAATTCAAGAACACAATAAAAAA
TATGAGAAAGGACTTGTTTCATTCAGCATGGGTTTAAATCAATTTACACATTTGAGAGAA
GATGAAATGGCAAATCTTAACAAATTTTATGATGATGAAGGAAATTTTGAGTTCAAAAAT
GTGACGACATTTCGATTTGATGATGAAAATTTCAGTTTACCGAAAAGCTTTGATTGGAAA
ACAAAGGGAGTTTTGCAACCAGTTCAAGATCAAAAAAATTGCGGTTCCTGCTATGTTTTT
GCTGGCATTGCTGCAATTGAAGCTCAAATGATGATTCAGTATAAAAATTATCAGAAATTA
TCAGAACAAGAAGCAATGGAATGCTTAGAAGGCTGTTCTGGAGGGTATCTCTATGAAGTT
TTGCAATATTCACATGATCACATGGGATGTGCATCAGGAAAATCTTATCCATATAAAGGT
CGTGTGTTTAATTCTTGTTCATTTGAAAGACCTCGCGTAAAAAATAGCAAAGTCAAAACA
TTTTTACGGTTTCAAGGCGAAAAATCAATCATGCAAAAATTAGTAGATGATGGTCCAGTC
ATAGCTTTGTTTAGTTTTTATCCAAGTATTCGTCACTACCATCAAGGGATATATGAAAAA
CTTCCGAATGAAGAGCAAGATGGATACCACGCGATTTTAATCGTTGGTTATGATGAAGAT
AGTTTTGGTAGGAAGTATTGGATTATCAGAAACTCATGGGGTCCACGATGGGGTGAAAGT
GGATATTTTAAGATGAAGAGAGGAGTTAACATGTGCAATATTGAGTCAATGAATTCTTAT
TTTGCACAAATTGAATAATTACTTCCACGCTTGCGATTAGAAATATTTTTTTATGATTAT
GAAAAACGCAATGGTTAATTTTTAATTTAAAAAAGGATAAATAAATGAAATAATTTTCAT
TATTAATAAAAAAAGTTATGCGGTTTTGATAATTTAAAAAATTTAAAATAAAACAAATAT
TTTTTGTTAAAGCTTATCATGTTTTGAAAATTTATTCACGAACAAAAATTTTTAAATTGA
TACTAAATAAAATATGCTCATAATCTAACGCTTAATAGGCTTTCATTATTATAGTGTCAA
TTTTTTTATTTGATTTCTTTAAAAAATATATTTTTGATTACAGAAAAGTTTATTTTAAAT
TTTCATTAAAATTACTTAGGTTGAAATTTTTTTGTTCCTATTTAAATTTTACCTCTAAAA
TAGACAAAAATAATATGGAAAAAATGTCCGTCTGACGAACTACTCGCAATTATTTTATAC
CAAAAAAATGATATTAATGTGTTTCATATATAACAGG

>g16363.t2 Gene=g16363 Length=345
MKTFVTVLFCAILLVSSSFALKISIKISETKKISSLNKNAELFNNFLKDFNIELSPDDNF
EERLAVFMENYRKIQEHNKKYEKGLVSFSMGLNQFTHLREDEMANLNKFYDDEGNFEFKN
VTTFRFDDENFSLPKSFDWKTKGVLQPVQDQKNCGSCYVFAGIAAIEAQMMIQYKNYQKL
SEQEAMECLEGCSGGYLYEVLQYSHDHMGCASGKSYPYKGRVFNSCSFERPRVKNSKVKT
FLRFQGEKSIMQKLVDDGPVIALFSFYPSIRHYHQGIYEKLPNEEQDGYHAILIVGYDED
SFGRKYWIIRNSWGPRWGESGYFKMKRGVNMCNIESMNSYFAQIE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g16363.t2 CDD cd02248 Peptidase_C1A 134 340 1.74734E-73
11 g16363.t2 Gene3D G3DSA:3.90.70.10 Cysteine proteinases 35 342 5.2E-84
3 g16363.t2 PANTHER PTHR12411 CYSTEINE PROTEASE FAMILY C1-RELATED 52 338 5.3E-57
4 g16363.t2 PANTHER PTHR12411:SF57 CATHEPSIN L1 52 338 5.3E-57
6 g16363.t2 PRINTS PR00705 Papain cysteine protease (C1) family signature 151 166 1.7E-6
5 g16363.t2 PRINTS PR00705 Papain cysteine protease (C1) family signature 290 300 1.7E-6
7 g16363.t2 PRINTS PR00705 Papain cysteine protease (C1) family signature 306 312 1.7E-6
1 g16363.t2 Pfam PF08246 Cathepsin propeptide inhibitor domain (I29) 43 102 2.4E-10
2 g16363.t2 Pfam PF00112 Papain family cysteine protease 133 340 2.1E-58
13 g16363.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 20 -
14 g16363.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
15 g16363.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 15 -
16 g16363.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 16 20 -
12 g16363.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 21 345 -
20 g16363.t2 ProSitePatterns PS00139 Eukaryotic thiol (cysteine) proteases cysteine active site. 151 162 -
19 g16363.t2 ProSitePatterns PS00639 Eukaryotic thiol (cysteine) proteases histidine active site. 288 298 -
18 g16363.t2 ProSitePatterns PS00640 Eukaryotic thiol (cysteine) proteases asparagine active site. 306 325 -
22 g16363.t2 SMART SM00848 Inhibitor_I29_2 43 103 1.6E-16
21 g16363.t2 SMART SM00645 pept_c1 133 342 2.8E-59
8 g16363.t2 SUPERFAMILY SSF54001 Cysteine proteinases 40 340 1.39E-79
10 g16363.t2 SignalP_EUK SignalP-noTM SignalP-noTM 1 20 -
9 g16363.t2 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 20 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

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.

Raw TPM values