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.t21 TTS g5942.t21 12943666 12943666
chr_2 g5942 g5942.t21 isoform g5942.t21 12943795 12946276
chr_2 g5942 g5942.t21 exon g5942.t21.exon1 12943795 12944396
chr_2 g5942 g5942.t21 cds g5942.t21.CDS1 12943795 12944396
chr_2 g5942 g5942.t21 exon g5942.t21.exon2 12944457 12944789
chr_2 g5942 g5942.t21 cds g5942.t21.CDS2 12944457 12944789
chr_2 g5942 g5942.t21 exon g5942.t21.exon3 12946014 12946117
chr_2 g5942 g5942.t21 cds g5942.t21.CDS3 12946014 12946110
chr_2 g5942 g5942.t21 exon g5942.t21.exon4 12946187 12946276
chr_2 g5942 g5942.t21 TSS g5942.t21 12946276 12946276

Sequences

>g5942.t21 Gene=g5942 Length=1129
AGAGTAAAATTAAACTTTGAAGTGTAAAGACTGAAAAGAATTTAAATAGCCATTTGATTT
ATCATTTAAGTTTGTACTTTTTAATAGAAGCATAAACATGAAATTCTTAATCTTTTTTGC
ATTATTGATTGGTGTGAGCTATGCAATTAAATTTTCTGAATTAGCTAAAGAAGAATGGGA
TGAATTTAAGGTAAAGTACAAAGATGAGACCGAAGAAAGATTCCGTTATAAAATCTATGT
AGATAATCGTCATAAGATCGCTAAACACAATAAACTCTTCCATACAAATGAAAAACCATA
TAAAATGAGCCTTAACAAATATTCTGATATGTTGCATACTGAATTTGTTAAAACACTCAA
TGGATTCAATCGTTCATATGTTCATAGTGTTAATTCAGTTTATAAGTCATCAAGCCCAAT
TGATGAAGGCATCACATTTATTGCAGCTGAAAACCTTAACTTACCAGTATCAATGGATTG
GAGAACTAAGGGTGCTGTTACACCAATTAAGGATCAAGGCCATTGCGGTTCATGCTGGGC
ATTTTCCACAACTGGCGCATTAGAAGGACAAACATTCCGTAAAACTGGAAAACTCATTTC
ACTATCTGAACAAAATTTGGTAGATTGCTCAGGAAAATATGGCAATAACGGTTGCAATGG
AGGACTTATGGACAACGCATTCCAATATATCAAAGAAAATGGAGGAATTGACACAGAAAA
GTCCTATCCATATGAAGGAATTGATGATACTTGTCACTTTTCGAAACAAACTATTGGTGC
AACTGACAAAGGATTCGTTGATATTCCAGAGGGAGATGAAGATGCATTGTTGAAAGCTAT
TGCTTCAGTTGGACCTGTTTCAGTCGCTATTGATGCCAGTCACGAATCATTCCAATTCTA
CTCTGAAGGAGTTTACTATGAACCACAATGTGATAGTCAGCAATTAGACCATGGCGTTTT
GCTCGTTGGATATGGTACTGAAAAGGACAAGGATGGAAATGACCAAGACTATTGGTTAGT
TAAAAACAGTTGGGGCACATCTTGGGGTGATCAAGGCTATATTAAAATGGCTCGTAATAA
GGAAAATCACTGTGGAATTGCTACATCTGCAAGCTATCCATTAGTATAA

>g5942.t21 Gene=g5942 Length=343
MKFLIFFALLIGVSYAIKFSELAKEEWDEFKVKYKDETEERFRYKIYVDNRHKIAKHNKL
FHTNEKPYKMSLNKYSDMLHTEFVKTLNGFNRSYVHSVNSVYKSSSPIDEGITFIAAENL
NLPVSMDWRTKGAVTPIKDQGHCGSCWAFSTTGALEGQTFRKTGKLISLSEQNLVDCSGK
YGNNGCNGGLMDNAFQYIKENGGIDTEKSYPYEGIDDTCHFSKQTIGATDKGFVDIPEGD
EDALLKAIASVGPVSVAIDASHESFQFYSEGVYYEPQCDSQQLDHGVLLVGYGTEKDKDG
NDQDYWLVKNSWGTSWGDQGYIKMARNKENHCGIATSASYPLV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g5942.t21 CDD cd02248 Peptidase_C1A 123 341 1.2686E-127
10 g5942.t21 Gene3D G3DSA:3.90.70.10 Cysteine proteinases 18 343 7.6E-117
3 g5942.t21 PANTHER PTHR12411 CYSTEINE PROTEASE FAMILY C1-RELATED 14 339 1.5E-112
4 g5942.t21 PANTHER PTHR12411:SF57 CATHEPSIN L1 14 339 1.5E-112
5 g5942.t21 PRINTS PR00705 Papain cysteine protease (C1) family signature 140 155 1.8E-11
7 g5942.t21 PRINTS PR00705 Papain cysteine protease (C1) family signature 285 295 1.8E-11
6 g5942.t21 PRINTS PR00705 Papain cysteine protease (C1) family signature 305 311 1.8E-11
1 g5942.t21 Pfam PF08246 Cathepsin propeptide inhibitor domain (I29) 28 83 1.9E-9
2 g5942.t21 Pfam PF00112 Papain family cysteine protease 122 341 5.4E-89
12 g5942.t21 Phobius SIGNAL_PEPTIDE Signal peptide region 1 16 -
13 g5942.t21 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
14 g5942.t21 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 11 -
15 g5942.t21 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 12 16 -
11 g5942.t21 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 17 343 -
19 g5942.t21 ProSitePatterns PS00139 Eukaryotic thiol (cysteine) proteases cysteine active site. 140 151 -
18 g5942.t21 ProSitePatterns PS00639 Eukaryotic thiol (cysteine) proteases histidine active site. 283 293 -
17 g5942.t21 ProSitePatterns PS00640 Eukaryotic thiol (cysteine) proteases asparagine active site. 305 324 -
21 g5942.t21 SMART SM00848 Inhibitor_I29_2 27 83 3.1E-12
20 g5942.t21 SMART SM00645 pept_c1 122 342 1.7E-136
8 g5942.t21 SUPERFAMILY SSF54001 Cysteine proteinases 29 342 2.81E-117
9 g5942.t21 SignalP_EUK SignalP-noTM SignalP-noTM 1 16 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5942/g5942.t21; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5942.t21.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 transcript belongs to the following 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