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.t20 TTS g2993.t20 21867629 21867629
chr_3 g2993 g2993.t20 isoform g2993.t20 21867833 21869132
chr_3 g2993 g2993.t20 exon g2993.t20.exon1 21867833 21867921
chr_3 g2993 g2993.t20 cds g2993.t20.CDS1 21867833 21867921
chr_3 g2993 g2993.t20 exon g2993.t20.exon2 21867986 21868326
chr_3 g2993 g2993.t20 cds g2993.t20.CDS2 21867986 21868326
chr_3 g2993 g2993.t20 exon g2993.t20.exon3 21868412 21868479
chr_3 g2993 g2993.t20 cds g2993.t20.CDS3 21868412 21868479
chr_3 g2993 g2993.t20 exon g2993.t20.exon4 21868542 21868694
chr_3 g2993 g2993.t20 cds g2993.t20.CDS4 21868542 21868562
chr_3 g2993 g2993.t20 exon g2993.t20.exon5 21868752 21868992
chr_3 g2993 g2993.t20 exon g2993.t20.exon6 21869064 21869132
chr_3 g2993 g2993.t20 TSS g2993.t20 21869220 21869220

Sequences

>g2993.t20 Gene=g2993 Length=961
ATGAAATATTTCATATTATTTGCTGCATTGACAGCAGTTTGCTTTGGAGCTGACATTTTT
TCTGATGAATTCATCAATGAAATTAATAAAAAAGCAACAACATGGAAGGCTGGCCATAAT
TTTCATCCAGATACTAATTTGAAATATATCAAGAATTTACTTGGTGTTCATTCCGATTCT
AAGCATTTTAAACTACCTGAGTTATTGCATGACTCACGGGACATAAAAGATTTACCTGAA
AATTTTGATGCTCGTGAACAATGGCCTGATTGTCCAACATTGAGAGAAATAAGAGATCAA
GGAAGTTGTGGATCTTGTTGGGCTTTTGGCGCTGTTGAGGCAATGAGTGACAGAGTATGC
ATTCATAGCAACGCAACTGAACATTTCCACTTTTCTGCTGAACATTTGGTTTCTTGCTGT
CACACTTGTGGATTTGGTTGCAATGGTGGCTTTCCAGGATCAGCTTGGAGCTATTGGGTT
AGAAAAGGTATTGTTAGTGGTGGACCATACAATTCTTCAATTGGATGTCAGTGTCAATGG
AACTCGTATGCCATGCTCTGGAGAAGGACATACACCAAAATGCATGAATAAATGCTCGAA
TCCCGCTTATAAAGTTGATTTCAAAACAGACAAACACTTTGGCAAATCAAGCTATTCAGT
AAAGCGTAATGAAGATCAAATTCGTTTGGAAATTTTCAAAAATGGTCCAGTTGAAGGTGC
ATTCACAGTCTATGAAGATTTCGTTCAATATAAATCTGGAGTTTATCAACATGTTACTGG
TAAAGCACTTGGTGGCCATGCTATTAAAATTTTCGGATGGGGAGTTGAAAATGGTGTCAA
ATACTGGTTGATTGCTAATAGCTGGAATTCAGATTGGGGTGATAATGGAACCTTCAAAAT
ATTGCGAGGAGAAGACCATGTCGGTATTGAGAGTGAGATTAGCGCTGGTTTGCCAAAGTA
A

>g2993.t20 Gene=g2993 Length=172
MVAFQDQLGAIGLEKVLLVVDHTILQLDVSVNGTRMPCSGEGHTPKCMNKCSNPAYKVDF
KTDKHFGKSSYSVKRNEDQIRLEIFKNGPVEGAFTVYEDFVQYKSGVYQHVTGKALGGHA
IKIFGWGVENGVKYWLIANSWNSDWGDNGTFKILRGEDHVGIESEISAGLPK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g2993.t20 Gene3D G3DSA:3.90.70.10 Cysteine proteinases 19 172 0
2 g2993.t20 PANTHER PTHR12411:SF737 CATHEPSIN B 41 169 0
3 g2993.t20 PANTHER PTHR12411 CYSTEINE PROTEASE FAMILY C1-RELATED 41 169 0
1 g2993.t20 Pfam PF00112 Papain family cysteine protease 45 169 0
5 g2993.t20 SMART SM00645 pept_c1 11 170 0
4 g2993.t20 SUPERFAMILY SSF54001 Cysteine proteinases 27 171 0

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

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