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.t4 isoform g5942.t4 12943621 12946261
chr_2 g5942 g5942.t4 exon g5942.t4.exon1 12943621 12943763
chr_2 g5942 g5942.t4 TTS g5942.t4 12943666 12943666
chr_2 g5942 g5942.t4 cds g5942.t4.CDS1 12943693 12943763
chr_2 g5942 g5942.t4 exon g5942.t4.exon2 12943833 12944396
chr_2 g5942 g5942.t4 cds g5942.t4.CDS2 12943833 12944396
chr_2 g5942 g5942.t4 exon g5942.t4.exon3 12944457 12944805
chr_2 g5942 g5942.t4 cds g5942.t4.CDS3 12944457 12944805
chr_2 g5942 g5942.t4 exon g5942.t4.exon4 12946018 12946121
chr_2 g5942 g5942.t4 cds g5942.t4.CDS4 12946018 12946110
chr_2 g5942 g5942.t4 exon g5942.t4.exon5 12946187 12946261
chr_2 g5942 g5942.t4 TSS g5942.t4 12946276 12946276

Sequences

>g5942.t4 Gene=g5942 Length=1235
TTTGAAGTGTAAAGACTGAAAAGAATTTAAATAGCCATTTGATTTATCATTTAAGTTTGT
ACTTTTTAATAGAAGACAGCATAAACATGAAATTCTTAATCTTTTTTGCATTATTGATTG
GTGTGAGCTATGCAATTAAATTTTCTGAATTAGCTAAAGAAGAATGGGATGAATTTAAGG
CTCTTCACAAAAAAGAGTACAAAGATGAGACCGAAGAAAGATTCCGTTATAAAATCTATG
TAGATAATCGTCATAAGATCGCTAAACACAATAAACTCTTCCATACAAATGAAAAACCAT
ATAAAATGAGCCTTAACAAATATTCTGATATGTTGCATACTGAATTTGTTAAAACACTCA
ATGGATTCAATCGTTCATATGTTCATAGTGTTAATTCAGTTTATAAGTCATCAAGCCCAA
TTGATGAAGGCATCACATTTATTGCAGCTGAAAACCTTAACTTACCAGTATCAATGGATT
GGAGAACTAAGGGTGCTGTTACACCAATTAAGGATCAAGGCCATTGCGGTTCATGCTGGG
CATTTTCCACAACTGGCGCATTAGAAGGACAAACATTCCGTAAAACTGGAAAACTCATTT
CACTATCTGAACAAAATTTGGTAGATTGCTCAGGAAAATATGGCAATAACGGTTGCAATG
GAGGACTTATGGACAACGCATTCCAATATATCAAAGAAAATGGAGGAATTGACACAGAAA
AGTCCTATCCATATGAAGGAATTGATGATACTTGTCACTTTTCGAAACAAACTATTGGTG
CAACTGACAAAGGATTCGTTGATATTCCAGAGGGAGATGAAGATGCATTGTTGAAAGCTA
TTGCTTCAGTTGGACCTGTTTCAGTCGCTATTGATGCCAGTCACGAATCATTCCAATTCT
ACTCTGAAGGAGTTTACTATGAACCACAATGTGATAGTCAGCAATTAGACCATGGCGTTT
TGCTCGTTGGATATGGTACTGAAAAGGACAAGGATGGAAATGACCAAGACTATTGGTTAG
TTAAAAACAGTTGGGGCACATCTTGGGGTGATCAAGGCTATATTAAAATGGCTCGTAATA
AGGAAAATCACTCATTTATTTGCGTGTTTTTTCTTTATAACCATTTTTCATATTTTTTGA
ATCTATTAAGACTAGATTATTAATGTATAGCGAGAGAAAGAAATAAAAATTTCCTAATAA
AATTCAAAACTAAATTTTTCTCTTTTATTCCAGTT

>g5942.t4 Gene=g5942 Length=358
MKFLIFFALLIGVSYAIKFSELAKEEWDEFKALHKKEYKDETEERFRYKIYVDNRHKIAK
HNKLFHTNEKPYKMSLNKYSDMLHTEFVKTLNGFNRSYVHSVNSVYKSSSPIDEGITFIA
AENLNLPVSMDWRTKGAVTPIKDQGHCGSCWAFSTTGALEGQTFRKTGKLISLSEQNLVD
CSGKYGNNGCNGGLMDNAFQYIKENGGIDTEKSYPYEGIDDTCHFSKQTIGATDKGFVDI
PEGDEDALLKAIASVGPVSVAIDASHESFQFYSEGVYYEPQCDSQQLDHGVLLVGYGTEK
DKDGNDQDYWLVKNSWGTSWGDQGYIKMARNKENHSFICVFFLYNHFSYFLNLLRLDY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g5942.t4 CDD cd02248 Peptidase_C1A 127 334 1.27879E-120
10 g5942.t4 Gene3D G3DSA:3.90.70.10 Cysteine proteinases 18 343 7.4E-115
3 g5942.t4 PANTHER PTHR12411 CYSTEINE PROTEASE FAMILY C1-RELATED 13 333 3.0E-111
4 g5942.t4 PANTHER PTHR12411:SF57 CATHEPSIN L1 13 333 3.0E-111
5 g5942.t4 PRINTS PR00705 Papain cysteine protease (C1) family signature 144 159 2.1E-11
6 g5942.t4 PRINTS PR00705 Papain cysteine protease (C1) family signature 289 299 2.1E-11
7 g5942.t4 PRINTS PR00705 Papain cysteine protease (C1) family signature 309 315 2.1E-11
1 g5942.t4 Pfam PF08246 Cathepsin propeptide inhibitor domain (I29) 27 87 3.2E-10
2 g5942.t4 Pfam PF00112 Papain family cysteine protease 126 336 1.6E-84
13 g5942.t4 Phobius SIGNAL_PEPTIDE Signal peptide region 1 16 -
14 g5942.t4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
15 g5942.t4 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 11 -
17 g5942.t4 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 12 16 -
12 g5942.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 17 334 -
16 g5942.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 335 354 -
11 g5942.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 355 358 -
21 g5942.t4 ProSitePatterns PS00139 Eukaryotic thiol (cysteine) proteases cysteine active site. 144 155 -
20 g5942.t4 ProSitePatterns PS00639 Eukaryotic thiol (cysteine) proteases histidine active site. 287 297 -
19 g5942.t4 ProSitePatterns PS00640 Eukaryotic thiol (cysteine) proteases asparagine active site. 309 328 -
23 g5942.t4 SMART SM00848 Inhibitor_I29_2 27 87 4.2E-18
22 g5942.t4 SMART SM00645 pept_c1 126 346 1.7E-125
8 g5942.t4 SUPERFAMILY SSF54001 Cysteine proteinases 21 344 8.34E-116
9 g5942.t4 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.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5942.t4.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