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.t2 TTS g2993.t2 21867629 21867629
chr_3 g2993 g2993.t2 isoform g2993.t2 21867665 21869132
chr_3 g2993 g2993.t2 exon g2993.t2.exon1 21867665 21867821
chr_3 g2993 g2993.t2 cds g2993.t2.CDS1 21867812 21867821
chr_3 g2993 g2993.t2 exon g2993.t2.exon2 21867916 21868355
chr_3 g2993 g2993.t2 cds g2993.t2.CDS2 21867916 21868355
chr_3 g2993 g2993.t2 exon g2993.t2.exon3 21868412 21868479
chr_3 g2993 g2993.t2 cds g2993.t2.CDS3 21868412 21868479
chr_3 g2993 g2993.t2 exon g2993.t2.exon4 21868542 21868694
chr_3 g2993 g2993.t2 cds g2993.t2.CDS4 21868542 21868694
chr_3 g2993 g2993.t2 exon g2993.t2.exon5 21868752 21868992
chr_3 g2993 g2993.t2 cds g2993.t2.CDS5 21868752 21868992
chr_3 g2993 g2993.t2 exon g2993.t2.exon6 21869064 21869132
chr_3 g2993 g2993.t2 cds g2993.t2.CDS6 21869064 21869132
chr_3 g2993 g2993.t2 TSS g2993.t2 21869220 21869220

Sequences

>g2993.t2 Gene=g2993 Length=1128
ATGAAATATTTCATATTATTTGCTGCATTGACAGCAGTTTGCTTTGGAGCTGACATTTTT
TCTGATGAATTCATCAATGAAATTAATAAAAAAGCAACAACATGGAAGGCTGGCCATAAT
TTTCATCCAGATACTAATTTGAAATATATCAAGAATTTACTTGGTGTTCATTCCGATTCT
AAGCATTTTAAACTACCTGAGTTATTGCATGACTCACGGGACATAAAAGATTTACCTGAA
AATTTTGATGCTCGTGAACAATGGCCTGATTGTCCAACATTGAGAGAAATAAGAGATCAA
GGAAGTTGTGGATCTTGTTGGGCTTTTGGCGCTGTTGAGGCAATGAGTGACAGAGTATGC
ATTCATAGCAACGCAACTGAACATTTCCACTTTTCTGCTGAACATTTGGTTTCTTGCTGT
CACACTTGTGGATTTGGTTGCAATGGTGGCTTTCCAGGATCAGCTTGGAGCTATTGGGTT
AGAAAAGGTATTGTTAGTGGTGGACCATACAATTCTTCAATTGGATGTCAGCCATATGAA
ATCGCTCCTTGTGAACATCATGTCAATGGAACTCGTATGCCATGCTCTGGAGAAGGACAT
ACACCAAAATGCATGAATAAATGCTCGAATCCCGCTTATAAAGTTGATTTCAAAACAGAC
AAACACTTTGGCAAATCAAGCTATTCAGTAAAGCGTAATGAAGATCAAATTCGTTTGGAA
ATTTTCAAAAATGGTCCAGTTGAAGGTGCATTCACAGTCTATGAAGATTTCGTTCAATAT
AAATCTGGAGTTTATCAACATGTTACTGGTAAAGCACTTGGTGGCCATGCTATTAAAATT
TTCGGATGGGGAGTTGAAAATGGTGTCAAATACTGGTTGATTGCTAATAGCTGGAATTCA
GGTATGTTTATTGAATTTCTGCCTAAATATAAACTAGAAGATTTATTTTTTTTAAAAAAA
AATAGATTGGGATCAAGATAATTATAAAAATGTTGTGATCAGCATTCACAGTTGATCATC
TTTTAACCTTTCCGCGATTTACTTCGTATTTGTTTTTATTTTTCTTTCTCATTTTGATTT
CAATTAATCTTACTGATAATGTAATTTTTTTCTTTATTAAAAACTGAA

>g2993.t2 Gene=g2993 Length=326
MKYFILFAALTAVCFGADIFSDEFINEINKKATTWKAGHNFHPDTNLKYIKNLLGVHSDS
KHFKLPELLHDSRDIKDLPENFDAREQWPDCPTLREIRDQGSCGSCWAFGAVEAMSDRVC
IHSNATEHFHFSAEHLVSCCHTCGFGCNGGFPGSAWSYWVRKGIVSGGPYNSSIGCQPYE
IAPCEHHVNGTRMPCSGEGHTPKCMNKCSNPAYKVDFKTDKHFGKSSYSVKRNEDQIRLE
IFKNGPVEGAFTVYEDFVQYKSGVYQHVTGKALGGHAIKIFGWGVENGVKYWLIANSWNS
GMFIEFLPKYKLEDLFFLKKNRLGSR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g2993.t2 CDD cd02620 Peptidase_C1A_CathepsinB 79 301 1.4372E-131
10 g2993.t2 Gene3D G3DSA:3.90.70.10 Cysteine proteinases 16 304 6.8E-102
3 g2993.t2 PANTHER PTHR12411:SF737 CATHEPSIN B 13 299 8.9E-92
4 g2993.t2 PANTHER PTHR12411 CYSTEINE PROTEASE FAMILY C1-RELATED 13 299 8.9E-92
5 g2993.t2 PRINTS PR00705 Papain cysteine protease (C1) family signature 100 115 2.6E-8
7 g2993.t2 PRINTS PR00705 Papain cysteine protease (C1) family signature 276 286 2.6E-8
6 g2993.t2 PRINTS PR00705 Papain cysteine protease (C1) family signature 291 297 2.6E-8
1 g2993.t2 Pfam PF08127 Peptidase family C1 propeptide 20 59 9.0E-19
2 g2993.t2 Pfam PF00112 Papain family cysteine protease 78 300 1.1E-55
12 g2993.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 16 -
13 g2993.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
14 g2993.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 11 -
15 g2993.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 12 16 -
11 g2993.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 17 326 -
17 g2993.t2 ProSitePatterns PS00139 Eukaryotic thiol (cysteine) proteases cysteine active site. 100 111 -
18 g2993.t2 SMART SM00645 pept_c1 78 312 2.8E-75
8 g2993.t2 SUPERFAMILY SSF54001 Cysteine proteinases 21 300 5.42E-90
9 g2993.t2 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.

Raw TPM values