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 g5981 g5981.t2 TTS g5981.t2 13160303 13160303
chr_2 g5981 g5981.t2 isoform g5981.t2 13160413 13161578
chr_2 g5981 g5981.t2 exon g5981.t2.exon1 13160413 13161348
chr_2 g5981 g5981.t2 cds g5981.t2.CDS1 13160413 13161270
chr_2 g5981 g5981.t2 exon g5981.t2.exon2 13161485 13161578
chr_2 g5981 g5981.t2 TSS g5981.t2 13161676 13161676

Sequences

>g5981.t2 Gene=g5981 Length=1030
ATGTACCTTGGTATTTTAGTCTTATTCACAAATTTAATAAACAGTTACATTGATAATCAT
GAATCAATAGAATTGTGGATGAAATTTAAAGTGAGTTGACTACAACAGAAGCTATGAGAC
AACAAGAGAGGAAGAAATACGTAAAGAAATTTTCATGGATAATTTAAGAAAAATGTTGTC
ACATAATCTCAAGCAATCTGCTGGCCTATATTCATTTAAATTTGGTATTAATCAGTTTTC
AGACATGACGTTTGAAGAATTTCTCAAAATAAACACAGAACCTGGAAGTCGAGACAAATC
ATTAGAGCAAAATTTTAATGCAATTGTCATTCATGATCTTACAAGTGATCCAAGTAATTA
TACATCATTCGATTGGCGTGATCATGGTGCAGTGACGAGTATTAAAAATCAAGGATATAA
ATGTGGATCATGTTATGCATTTGCATCAATTGCAGCTATAGAATCTCATATATTTTTGAA
AACAGGAAAACTTCTTGATTTATCAGAGCAAGAAATTGTTGATTGTGCACAAGGTTATTT
TACAGCTGGCTGTTATGGTGGTTATGAAATTGGAGCACTTAATTATATACAAAATAATGG
TGATATAACTTTTGAAGAATCATATCCTTATAAAGGAATACAAGAAAAATGTTTACGAAG
TGTCAATGGCACAGATCTTTCAAAAATTAAAATTACAATCAAACAAATTTCACAACCGCC
AAGAGAAAATGAAGAAGAATTGAAAAATGCACTTGTTAAATATGGACCAATTATAATTTC
AATAGATCATTTACATGAGAGTTTTATGAGATATTCAAGTGGAGTTTATCATGAAAGTGA
CTGTAAAAAACAATTTTCTCATGCTGCACTTTTGGTCGGTTATGGAAGTGAAAATGGCAA
AGATTATTGGTTAGTGAAAAACTCGTTTGGAACAACATGGGGTGAAAATGGATATTTTAG
GATAGCAAGGAATCGAAAAAATAATTGTGAAATTGCTACAGAACCGGTGATAATTAGCAG
TGAAGATTAA

>g5981.t2 Gene=g5981 Length=285
MLSHNLKQSAGLYSFKFGINQFSDMTFEEFLKINTEPGSRDKSLEQNFNAIVIHDLTSDP
SNYTSFDWRDHGAVTSIKNQGYKCGSCYAFASIAAIESHIFLKTGKLLDLSEQEIVDCAQ
GYFTAGCYGGYEIGALNYIQNNGDITFEESYPYKGIQEKCLRSVNGTDLSKIKITIKQIS
QPPRENEEELKNALVKYGPIIISIDHLHESFMRYSSGVYHESDCKKQFSHAALLVGYGSE
NGKDYWLVKNSFGTTWGENGYFRIARNRKNNCEIATEPVIISSED

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g5981.t2 CDD cd02248 Peptidase_C1A 64 281 0e+00
9 g5981.t2 Gene3D G3DSA:3.90.70.10 Cysteine proteinases 1 281 0e+00
2 g5981.t2 PANTHER PTHR12411 CYSTEINE PROTEASE FAMILY C1-RELATED 3 277 0e+00
3 g5981.t2 PANTHER PTHR12411:SF57 CATHEPSIN L1 3 277 0e+00
6 g5981.t2 PRINTS PR00705 Papain cysteine protease (C1) family signature 81 96 6e-07
5 g5981.t2 PRINTS PR00705 Papain cysteine protease (C1) family signature 230 240 6e-07
4 g5981.t2 PRINTS PR00705 Papain cysteine protease (C1) family signature 245 251 6e-07
1 g5981.t2 Pfam PF00112 Papain family cysteine protease 64 279 0e+00
8 g5981.t2 SMART SM00645 pept_c1 62 282 0e+00
7 g5981.t2 SUPERFAMILY SSF54001 Cysteine proteinases 3 279 0e+00

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5981/g5981.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5981.t2.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