Gene loci information

Transcript annotation

  • This transcript has been annotated as Cathepsin B.

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_3 g2993 g2993.t24 TTS g2993.t24 21867629 21867629
chr_3 g2993 g2993.t24 isoform g2993.t24 21867833 21869132
chr_3 g2993 g2993.t24 exon g2993.t24.exon1 21867833 21867921
chr_3 g2993 g2993.t24 cds g2993.t24.CDS1 21867833 21867921
chr_3 g2993 g2993.t24 exon g2993.t24.exon2 21867986 21868355
chr_3 g2993 g2993.t24 cds g2993.t24.CDS2 21867986 21868355
chr_3 g2993 g2993.t24 exon g2993.t24.exon3 21868417 21868479
chr_3 g2993 g2993.t24 cds g2993.t24.CDS3 21868417 21868479
chr_3 g2993 g2993.t24 exon g2993.t24.exon4 21868546 21868694
chr_3 g2993 g2993.t24 cds g2993.t24.CDS4 21868546 21868694
chr_3 g2993 g2993.t24 exon g2993.t24.exon5 21868752 21868992
chr_3 g2993 g2993.t24 cds g2993.t24.CDS5 21868752 21868992
chr_3 g2993 g2993.t24 exon g2993.t24.exon6 21869064 21869132
chr_3 g2993 g2993.t24 cds g2993.t24.CDS6 21869064 21869132
chr_3 g2993 g2993.t24 TSS g2993.t24 21869220 21869220

Sequences

>g2993.t24 Gene=g2993 Length=981
ATGAAATATTTCATATTATTTGCTGCATTGACAGCAGTTTGCTTTGGAGCTGACATTTTT
TCTGATGAATTCATCAATGAAATTAATAAAAAAGCAACAACATGGAAGGCTGGCCATAAT
TTTCATCCAGATACTAATTTGAAATATATCAAGAATTTACTTGGTGTTCATTCCGATTCT
AAGCATTTTAAACTACCTGAGTTATTGCATGACTCACGGGACATAAAAGATTTACCTGAA
AATTTTGATGCTCGTGAACAATGGCCTGATTGTCCAACATTGAGAGAAATAAGAGATCAA
GGAAGTTGTGGATCTTGTTGGGCTTTTGGCGCTGTTGAGGCAATGAGTGACAGAGTATGC
ATTCATAGCAACGCAACTGAACATTTCCACTTTTCTGCTGAACATTTGGTTTCTTGCTGT
CACACTTGTGGATTTGGTTGCAATGGTGGCTTTCCAGGACTTGGAGCTATTGGGTTAGAA
AAGGTATTGTTAGTGGTGGACCATACAATTCTTCAATTGGATCCATATGAAATCGCTCCT
TGTGAACATCATGTCAATGGAACTCGTATGCCATGCTCTGGAGAAGGACATACACCAAAA
TGCATGAATAAATGCTCGAATCCCGCTTATAAAGTTGATTTCAAAACAGACAAACACTTT
GGCAAATCAAGCTATTCAGTAAAGCGTAATGAAGATCAAATTCGTTTGGAAATTTTCAAA
AATGGTCCAGTTGAAGGTGCATTCACAGTCTATGAAGATTTCGTTCAATATAAATCTGGA
GTTTATCAACATGTTACTGGTAAAGCACTTGGTGGCCATGCTATTAAAATTTTCGGATGG
GGAGTTGAAAATGGTGTCAAATACTGGTTGATTGCTAATAGCTGGAATTCAGATTGGGGT
GATAATGGAACCTTCAAAATATTGCGAGGAGAAGACCATGTCGGTATTGAGAGTGAGATT
AGCGCTGGTTTGCCAAAGTAA

>g2993.t24 Gene=g2993 Length=326
MKYFILFAALTAVCFGADIFSDEFINEINKKATTWKAGHNFHPDTNLKYIKNLLGVHSDS
KHFKLPELLHDSRDIKDLPENFDAREQWPDCPTLREIRDQGSCGSCWAFGAVEAMSDRVC
IHSNATEHFHFSAEHLVSCCHTCGFGCNGGFPGLGAIGLEKVLLVVDHTILQLDPYEIAP
CEHHVNGTRMPCSGEGHTPKCMNKCSNPAYKVDFKTDKHFGKSSYSVKRNEDQIRLEIFK
NGPVEGAFTVYEDFVQYKSGVYQHVTGKALGGHAIKIFGWGVENGVKYWLIANSWNSDWG
DNGTFKILRGEDHVGIESEISAGLPK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g2993.t24 CDD cd02620 Peptidase_C1A_CathepsinB 79 323 2.08125E-138
10 g2993.t24 Gene3D G3DSA:3.90.70.10 Cysteine proteinases 16 326 1.5E-103
3 g2993.t24 PANTHER PTHR12411:SF737 CATHEPSIN B 13 323 2.3E-90
4 g2993.t24 PANTHER PTHR12411 CYSTEINE PROTEASE FAMILY C1-RELATED 13 323 2.3E-90
5 g2993.t24 PRINTS PR00705 Papain cysteine protease (C1) family signature 100 115 2.6E-8
7 g2993.t24 PRINTS PR00705 Papain cysteine protease (C1) family signature 273 283 2.6E-8
6 g2993.t24 PRINTS PR00705 Papain cysteine protease (C1) family signature 288 294 2.6E-8
1 g2993.t24 Pfam PF08127 Peptidase family C1 propeptide 20 59 9.0E-19
2 g2993.t24 Pfam PF00112 Papain family cysteine protease 78 323 2.3E-58
12 g2993.t24 Phobius SIGNAL_PEPTIDE Signal peptide region 1 16 -
13 g2993.t24 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
14 g2993.t24 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 11 -
15 g2993.t24 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 12 16 -
11 g2993.t24 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 17 326 -
17 g2993.t24 ProSitePatterns PS00139 Eukaryotic thiol (cysteine) proteases cysteine active site. 100 111 -
18 g2993.t24 SMART SM00645 pept_c1 78 324 3.3E-87
8 g2993.t24 SUPERFAMILY SSF54001 Cysteine proteinases 21 325 2.95E-93
9 g2993.t24 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.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0008234 cysteine-type peptidase activity MF
GO:0006508 proteolysis BP
GO:0004197 cysteine-type endopeptidase activity MF
GO:0050790 regulation of catalytic activity BP

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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. There were no conditions that were differentially expressed