Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative AMSH-like protease.

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 g3021 g3021.t6 TSS g3021.t6 22170493 22170493
chr_3 g3021 g3021.t6 isoform g3021.t6 22170555 22171940
chr_3 g3021 g3021.t6 exon g3021.t6.exon1 22170555 22170670
chr_3 g3021 g3021.t6 cds g3021.t6.CDS1 22170555 22170670
chr_3 g3021 g3021.t6 exon g3021.t6.exon2 22170746 22171379
chr_3 g3021 g3021.t6 cds g3021.t6.CDS2 22170746 22171379
chr_3 g3021 g3021.t6 exon g3021.t6.exon3 22171437 22171631
chr_3 g3021 g3021.t6 cds g3021.t6.CDS3 22171437 22171601
chr_3 g3021 g3021.t6 exon g3021.t6.exon4 22171744 22171940
chr_3 g3021 g3021.t6 TTS g3021.t6 22171996 22171996

Sequences

>g3021.t6 Gene=g3021 Length=1142
ATGGCAGATCTTATTAATTTTAATCAAATGGGGATTGTAGAACCTGAAAAGCGGTTAAAA
CAATTAAATGAGTCAGGTTCAAATATAAATGTCGATAAGAACCAGAATATCTTGAGATAT
TATAGATCTGGTAATGAAATATATAGAATGGCAAAAATATACATGCAAGAAGGAAATCAT
GAAAATGCGTACATCTTATTCCTAAGATTTTTAACTTTATTTGTTGAAAAGATAAGAGAA
CATCCTAATTATAAAGAAGTACCAGCTGATTTCAAAAAATCTAACAAAGAGAAAATGACA
GAAATTATGACATTAACAGAAAAATTGAAGGCGAAACTATTGGATCGTTATAAAAAAGAA
TACGAACAATTTTTAATTGATCAAGAGAATGAGCGAAAGAAAGCGATTGAGGAAGCTAAA
CGTAAAGAAATTGAAAATGCGAAAAATAAATCCAAAATAAGTGGACCTTCTGCAGCATCT
ACAAACGTAATAATGCCTAGTGCACCTAACTTTGCTGATCTTGATCAAATCGTTTACCCC
AATGACTTTCCAACAGATCCAAAGAAGCCTACCCAAGCTGCTGCAAGAGATTATAAAGGT
TTGCTCCCCGGTACAAAACCGCCTTCATATGATCGACTACTAAAACCATCGATTTCTCTT
ATGGAAGGTGGTTTAAGAACTTTAAAAATACCTGACGATACTATGAAAAAGTTCCTCGAT
GTTGCTGCTTCAAACACTATGAAAAATATCGAAACTTGTGGCATTCTCTGTGGAAAATTA
CAAAATCATCAACTTTCTATAACTCATGTAATTTTACCAAAACAAACTGGAACTTCAGAC
AGTTGTAATACAATGAACGAAGAAGAAATTTTTGATATACAAGATCAAATGAATTTAATT
ACTTTAGGGTGGTGAGTGTTTTTAAAAAAATTTTATTAAGTGTATAAGCTATTGCTATTG
TTTGCTCACCTAAATATGAAGAGCTTGGCTTCTTTACTTTAACTACTGAAGGCATTGATT
TTATTTCAAAATGTACACAAACCGGATTTCATCCACATCCTAACGATCAATTTATGGAAG
CTATGCATTACAAATTAGAAAAAGATAAACACATCATAATTACTGACTTGAGAGGTCGTT
GA

>g3021.t6 Gene=g3021 Length=304
MADLINFNQMGIVEPEKRLKQLNESGSNINVDKNQNILRYYRSGNEIYRMAKIYMQEGNH
ENAYILFLRFLTLFVEKIREHPNYKEVPADFKKSNKEKMTEIMTLTEKLKAKLLDRYKKE
YEQFLIDQENERKKAIEEAKRKEIENAKNKSKISGPSAASTNVIMPSAPNFADLDQIVYP
NDFPTDPKKPTQAAARDYKGLLPGTKPPSYDRLLKPSISLMEGGLRTLKIPDDTMKKFLD
VAASNTMKNIETCGILCGKLQNHQLSITHVILPKQTGTSDSCNTMNEEEIFDIQDQMNLI
TLGW

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g3021.t6 Coils Coil Coil 114 150 -
8 g3021.t6 Gene3D G3DSA:1.20.58.280 Hypothetical protein 1500032h18. 8 152 1.1E-39
7 g3021.t6 Gene3D G3DSA:3.40.140.10 Cytidine Deaminase 216 304 6.0E-29
4 g3021.t6 PANTHER PTHR12947 AMSH-LIKE PROTEASE 14 157 2.8E-61
3 g3021.t6 PANTHER PTHR12947 AMSH-LIKE PROTEASE 179 304 2.8E-61
1 g3021.t6 Pfam PF08969 USP8 dimerisation domain 16 119 1.2E-27
2 g3021.t6 Pfam PF01398 JAB1/Mov34/MPN/PAD-1 ubiquitin protease 226 295 1.0E-7
10 g3021.t6 ProSiteProfiles PS50249 MPN domain profile. 228 304 18.881
6 g3021.t6 SUPERFAMILY SSF140856 USP8 N-terminal domain-like 18 134 2.09E-13
5 g3021.t6 SUPERFAMILY SSF102712 JAB1/MPN domain 226 304 6.8E-6

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:0008237 metallopeptidase activity MF
GO:0005515 protein binding MF
GO:0070122 isopeptidase activity MF

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