Gene loci information

Transcript annotation

  • This transcript has been annotated as 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_2 g5942 g5942.t6 TTS g5942.t6 12943666 12943666
chr_2 g5942 g5942.t6 isoform g5942.t6 12943795 12944784
chr_2 g5942 g5942.t6 exon g5942.t6.exon1 12943795 12944396
chr_2 g5942 g5942.t6 cds g5942.t6.CDS1 12943795 12944396
chr_2 g5942 g5942.t6 exon g5942.t6.exon2 12944457 12944784
chr_2 g5942 g5942.t6 cds g5942.t6.CDS2 12944457 12944679
chr_2 g5942 g5942.t6 TSS g5942.t6 NA NA

Sequences

>g5942.t6 Gene=g5942 Length=930
AAAGATGAGACCGAAGAAAGATTCCGTTATAAAATCTATGTAGATAATCGTCATAAGATC
GCTAAACACAATAAACTCTTCCATACAAATGAAAAACCATATAAAATGAGCCTTAACAAA
TATTCTGATATGTTGCATACTGAATTTGTTAAAACACTCAATGGATTCAATCGTTCATAT
GTTCATAGTGTTAATTCAGTTTATAAGTCATCAAGCCCAATTGATGAAGGCATCACATTT
ATTGCAGCTGAAAACCTTAACTTACCAGTATCAATGGATTGGAGAACTAAGGGTGCTGTT
ACACCAATTAAGGATCAAGGCCATTGCGGTTCATGCTGGGCATTTTCCACAACTGGCGCA
TTAGAAGGACAAACATTCCGTAAAACTGGAAAACTCATTTCACTATCTGAACAAAATTTG
GTAGATTGCTCAGGAAAATATGGCAATAACGGTTGCAATGGAGGACTTATGGACAACGCA
TTCCAATATATCAAAGAAAATGGAGGAATTGACACAGAAAAGTCCTATCCATATGAAGGA
ATTGATGATACTTGTCACTTTTCGAAACAAACTATTGGTGCAACTGACAAAGGATTCGTT
GATATTCCAGAGGGAGATGAAGATGCATTGTTGAAAGCTATTGCTTCAGTTGGACCTGTT
TCAGTCGCTATTGATGCCAGTCACGAATCATTCCAATTCTACTCTGAAGGAGTTTACTAT
GAACCACAATGTGATAGTCAGCAATTAGACCATGGCGTTTTGCTCGTTGGATATGGTACT
GAAAAGGACAAGGATGGAAATGACCAAGACTATTGGTTAGTTAAAAACAGTTGGGGCACA
TCTTGGGGTGATCAAGGCTATATTAAAATGGCTCGTAATAAGGAAAATCACTGTGGAATT
GCTACATCTGCAAGCTATCCATTAGTATAA

>g5942.t6 Gene=g5942 Length=274
MSLNKYSDMLHTEFVKTLNGFNRSYVHSVNSVYKSSSPIDEGITFIAAENLNLPVSMDWR
TKGAVTPIKDQGHCGSCWAFSTTGALEGQTFRKTGKLISLSEQNLVDCSGKYGNNGCNGG
LMDNAFQYIKENGGIDTEKSYPYEGIDDTCHFSKQTIGATDKGFVDIPEGDEDALLKAIA
SVGPVSVAIDASHESFQFYSEGVYYEPQCDSQQLDHGVLLVGYGTEKDKDGNDQDYWLVK
NSWGTSWGDQGYIKMARNKENHCGIATSASYPLV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g5942.t6 CDD cd02248 Peptidase_C1A 54 272 6.04122E-126
8 g5942.t6 Gene3D G3DSA:3.90.70.10 Cysteine proteinases 1 274 2.7E-106
2 g5942.t6 PANTHER PTHR12411 CYSTEINE PROTEASE FAMILY C1-RELATED 1 270 7.3E-103
3 g5942.t6 PANTHER PTHR12411:SF57 CATHEPSIN L1 1 270 7.3E-103
6 g5942.t6 PRINTS PR00705 Papain cysteine protease (C1) family signature 71 86 1.1E-11
4 g5942.t6 PRINTS PR00705 Papain cysteine protease (C1) family signature 216 226 1.1E-11
5 g5942.t6 PRINTS PR00705 Papain cysteine protease (C1) family signature 236 242 1.1E-11
1 g5942.t6 Pfam PF00112 Papain family cysteine protease 53 272 2.7E-89
12 g5942.t6 ProSitePatterns PS00139 Eukaryotic thiol (cysteine) proteases cysteine active site. 71 82 -
11 g5942.t6 ProSitePatterns PS00639 Eukaryotic thiol (cysteine) proteases histidine active site. 214 224 -
10 g5942.t6 ProSitePatterns PS00640 Eukaryotic thiol (cysteine) proteases asparagine active site. 236 255 -
13 g5942.t6 SMART SM00645 pept_c1 53 273 1.7E-136
7 g5942.t6 SUPERFAMILY SSF54001 Cysteine proteinases 2 273 6.1E-106

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5942/g5942.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5942.t6.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

Pathway

This gene does not belong to any pathways.

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