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.t18 TTS g5942.t18 12943666 12943666
chr_2 g5942 g5942.t18 isoform g5942.t18 12943795 12946276
chr_2 g5942 g5942.t18 exon g5942.t18.exon1 12943795 12944805
chr_2 g5942 g5942.t18 cds g5942.t18.CDS1 12943795 12944805
chr_2 g5942 g5942.t18 exon g5942.t18.exon2 12946018 12946121
chr_2 g5942 g5942.t18 cds g5942.t18.CDS2 12946018 12946110
chr_2 g5942 g5942.t18 exon g5942.t18.exon3 12946187 12946276
chr_2 g5942 g5942.t18 TSS g5942.t18 12946276 12946276

Sequences

>g5942.t18 Gene=g5942 Length=1205
AGAGTAAAATTAAACTTTGAAGTGTAAAGACTGAAAAGAATTTAAATAGCCATTTGATTT
ATCATTTAAGTTTGTACTTTTTAATAGAAGACAGCATAAACATGAAATTCTTAATCTTTT
TTGCATTATTGATTGGTGTGAGCTATGCAATTAAATTTTCTGAATTAGCTAAAGAAGAAT
GGGATGAATTTAAGGCTCTTCACAAAAAAGAGTACAAAGATGAGACCGAAGAAAGATTCC
GTTATAAAATCTATGTAGATAATCGTCATAAGATCGCTAAACACAATAAACTCTTCCATA
CAAATGAAAAACCATATAAAATGAGCCTTAACAAATATTCTGATATGTTGCATACTGAAT
TTGTTAAAACACTCAATGGATTCAATCGTTCATATGTTCATAGTGTTAATTCAGTTTATA
AGTCATCAAGCCCAATTGATGAAGGCATCACATTTATTGCAGCTGAAAACCTTAACTTAC
CAGTATCAATGGATTGGAGAACTAAGGGTGCTGTTACACCAATTAAGGATCAAGGCCATT
GCGGTAAATACTTTAAAAATCTTTTATCTTTTTTGTTTTTGATAAAATTTTATAATTATG
CAGGTTCATGCTGGGCATTTTCCACAACTGGCGCATTAGAAGGACAAACATTCCGTAAAA
CTGGAAAACTCATTTCACTATCTGAACAAAATTTGGTAGATTGCTCAGGAAAATATGGCA
ATAACGGTTGCAATGGAGGACTTATGGACAACGCATTCCAATATATCAAAGAAAATGGAG
GAATTGACACAGAAAAGTCCTATCCATATGAAGGAATTGATGATACTTGTCACTTTTCGA
AACAAACTATTGGTGCAACTGACAAAGGATTCGTTGATATTCCAGAGGGAGATGAAGATG
CATTGTTGAAAGCTATTGCTTCAGTTGGACCTGTTTCAGTCGCTATTGATGCCAGTCACG
AATCATTCCAATTCTACTCTGAAGGAGTTTACTATGAACCACAATGTGATAGTCAGCAAT
TAGACCATGGCGTTTTGCTCGTTGGATATGGTACTGAAAAGGACAAGGATGGAAATGACC
AAGACTATTGGTTAGTTAAAAACAGTTGGGGCACATCTTGGGGTGATCAAGGCTATATTA
AAATGGCTCGTAATAAGGAAAATCACTGTGGAATTGCTACATCTGCAAGCTATCCATTAG
TATAA

>g5942.t18 Gene=g5942 Length=367
MKFLIFFALLIGVSYAIKFSELAKEEWDEFKALHKKEYKDETEERFRYKIYVDNRHKIAK
HNKLFHTNEKPYKMSLNKYSDMLHTEFVKTLNGFNRSYVHSVNSVYKSSSPIDEGITFIA
AENLNLPVSMDWRTKGAVTPIKDQGHCGKYFKNLLSFLFLIKFYNYAGSCWAFSTTGALE
GQTFRKTGKLISLSEQNLVDCSGKYGNNGCNGGLMDNAFQYIKENGGIDTEKSYPYEGID
DTCHFSKQTIGATDKGFVDIPEGDEDALLKAIASVGPVSVAIDASHESFQFYSEGVYYEP
QCDSQQLDHGVLLVGYGTEKDKDGNDQDYWLVKNSWGTSWGDQGYIKMARNKENHCGIAT
SASYPLV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g5942.t18 CDD cd02248 Peptidase_C1A 127 365 4.78418E-123
12 g5942.t18 Gene3D G3DSA:3.90.70.10 Cysteine proteinases 18 367 3.6E-116
4 g5942.t18 PANTHER PTHR12411 CYSTEINE PROTEASE FAMILY C1-RELATED 13 148 3.7E-108
6 g5942.t18 PANTHER PTHR12411:SF57 CATHEPSIN L1 13 148 3.7E-108
3 g5942.t18 PANTHER PTHR12411 CYSTEINE PROTEASE FAMILY C1-RELATED 165 363 3.7E-108
5 g5942.t18 PANTHER PTHR12411:SF57 CATHEPSIN L1 165 363 3.7E-108
9 g5942.t18 PRINTS PR00705 Papain cysteine protease (C1) family signature 164 179 2.4E-8
7 g5942.t18 PRINTS PR00705 Papain cysteine protease (C1) family signature 309 319 2.4E-8
8 g5942.t18 PRINTS PR00705 Papain cysteine protease (C1) family signature 329 335 2.4E-8
1 g5942.t18 Pfam PF08246 Cathepsin propeptide inhibitor domain (I29) 27 87 3.4E-10
2 g5942.t18 Pfam PF00112 Papain family cysteine protease 166 365 3.4E-77
14 g5942.t18 Phobius SIGNAL_PEPTIDE Signal peptide region 1 16 -
15 g5942.t18 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
16 g5942.t18 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 11 -
17 g5942.t18 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 12 16 -
13 g5942.t18 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 17 367 -
20 g5942.t18 ProSitePatterns PS00639 Eukaryotic thiol (cysteine) proteases histidine active site. 307 317 -
19 g5942.t18 ProSitePatterns PS00640 Eukaryotic thiol (cysteine) proteases asparagine active site. 329 348 -
22 g5942.t18 SMART SM00848 Inhibitor_I29_2 27 87 4.2E-18
21 g5942.t18 SMART SM00645 pept_c1 126 366 7.1E-126
10 g5942.t18 SUPERFAMILY SSF54001 Cysteine proteinases 24 366 8.81E-112
11 g5942.t18 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.t18; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5942.t18.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