Gene loci information

Transcript annotation

  • This transcript has been annotated as STAM-binding protein.

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.t4 TSS g3021.t4 22170493 22170493
chr_3 g3021 g3021.t4 isoform g3021.t4 22170555 22171940
chr_3 g3021 g3021.t4 exon g3021.t4.exon1 22170555 22170670
chr_3 g3021 g3021.t4 exon g3021.t4.exon2 22170746 22171115
chr_3 g3021 g3021.t4 exon g3021.t4.exon3 22171186 22171379
chr_3 g3021 g3021.t4 cds g3021.t4.CDS1 22171290 22171379
chr_3 g3021 g3021.t4 exon g3021.t4.exon4 22171437 22171597
chr_3 g3021 g3021.t4 cds g3021.t4.CDS2 22171437 22171597
chr_3 g3021 g3021.t4 exon g3021.t4.exon5 22171661 22171940
chr_3 g3021 g3021.t4 cds g3021.t4.CDS3 22171661 22171940
chr_3 g3021 g3021.t4 TTS g3021.t4 22171996 22171996

Sequences

>g3021.t4 Gene=g3021 Length=1121
ATGGCAGATCTTATTAATTTTAATCAAATGGGGATTGTAGAACCTGAAAAGCGGTTAAAA
CAATTAAATGAGTCAGGTTCAAATATAAATGTCGATAAGAACCAGAATATCTTGAGATAT
TATAGATCTGGTAATGAAATATATAGAATGGCAAAAATATACATGCAAGAAGGAAATCAT
GAAAATGCGTACATCTTATTCCTAAGATTTTTAACTTTATTTGTTGAAAAGATAAGAGAA
CATCCTAATTATAAAGAAGTACCAGCTGATTTCAAAAAATCTAACAAAGAGAAAATGACA
GAAATTATGACATTAACAGAAAAATTGAAGGCGAAACTATTGGATCGTTATAAAAAAGAA
TACGAACAATTTTTAATTGATCAAGAGAATGAGCGAAAGAAAGCGATTGAGGAAGCTAAA
CGTAAAGAAATTGAAAATGCGAAAAATAAATCCAAAATAAGTGGACCTTCTGCAGCATCT
ACAAACATCCAAAGAAGCCTACCCAAGCTGCTGCAAGAGATTATAAAGGTTTGCTCCCCG
GTACAAAACCGCCTTCATATGATCGACTACTAAAACCATCGATTTCTCTTATGGAAGGTG
GTTTAAGAACTTTAAAAATACCTGACGATACTATGAAAAAGTTCCTCGATGTTGCTGCTT
CAAACACTATGAAAAATATCGAAACTTGTGGCATTCTCTGTGGAAAATTACAAAATCATC
AACTTTCTATAACTCATGTAATTTTACCAAAACAAACTGGAACTTCAGACAGTTGTAATA
CAATGAACGAAGAAGAAATTTTTGATATACAAGATCAAATGAATTTAATTACTTTAGGGT
GGATTCATACCCATCCTACTCAATCTGCATTTCTTTCATCGGTTGATCTACATACACAAT
GTGGATATCAAATTATGCTACCAGAAGCTATTGCTATTGTTTGCTCACCTAAATATGAAG
AGCTTGGCTTCTTTACTTTAACTACTGAAGGCATTGATTTTATTTCAAAATGTACACAAA
CCGGATTTCATCCACATCCTAACGATCAATTTATGGAAGCTATGCATTACAAATTAGAAA
AAGATAAACACATCATAATTACTGACTTGAGAGGTCGTTGA

>g3021.t4 Gene=g3021 Length=176
MEGGLRTLKIPDDTMKKFLDVAASNTMKNIETCGILCGKLQNHQLSITHVILPKQTGTSD
SCNTMNEEEIFDIQDQMNLITLGWIHTHPTQSAFLSSVDLHTQCGYQIMLPEAIAIVCSP
KYEELGFFTLTTEGIDFISKCTQTGFHPHPNDQFMEAMHYKLEKDKHIIITDLRGR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g3021.t4 CDD cd08066 MPN_AMSH_like 5 174 0.000
6 g3021.t4 Gene3D G3DSA:3.40.140.10 Cytidine Deaminase 1 175 0.000
2 g3021.t4 PANTHER PTHR12947:SF4 FI19924P1 3 174 0.000
3 g3021.t4 PANTHER PTHR12947 AMSH-LIKE PROTEASE 3 174 0.000
1 g3021.t4 Pfam PF01398 JAB1/Mov34/MPN/PAD-1 ubiquitin protease 6 111 0.000
7 g3021.t4 ProSiteProfiles PS50249 MPN domain profile. 8 136 29.999
5 g3021.t4 SMART SM00232 pad1_6 7 133 0.000
4 g3021.t4 SUPERFAMILY SSF102712 JAB1/MPN domain 6 131 0.000

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:0061578 Lys63-specific deubiquitinase activity MF
GO:0008237 metallopeptidase activity MF
GO:0005515 protein binding MF
GO:0016579 protein deubiquitination BP
GO:0070122 isopeptidase activity MF
GO:0070536 protein K63-linked deubiquitination 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