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.t9 TSS g3021.t9 22170493 22170493
chr_3 g3021 g3021.t9 isoform g3021.t9 22171044 22171940
chr_3 g3021 g3021.t9 exon g3021.t9.exon1 22171044 22171379
chr_3 g3021 g3021.t9 cds g3021.t9.CDS1 22171122 22171379
chr_3 g3021 g3021.t9 exon g3021.t9.exon2 22171437 22171594
chr_3 g3021 g3021.t9 cds g3021.t9.CDS2 22171437 22171594
chr_3 g3021 g3021.t9 exon g3021.t9.exon3 22171661 22171940
chr_3 g3021 g3021.t9 cds g3021.t9.CDS3 22171661 22171940
chr_3 g3021 g3021.t9 TTS g3021.t9 22171996 22171996

Sequences

>g3021.t9 Gene=g3021 Length=774
GCTAAACGTAAAGAAATTGAAAATGCGAAAAATAAATCCAAAATAAGTGGACCTTCTGCA
GCATCTACAAACGTAATAATGCCTAGTGCACCTAACTTTGCTGATCTTGATCAAATCGTT
TACCCCAATGACTTTCCAACAGATCCAAAGAAGCCTACCCAAGCTGCTGCAAGAGATTAT
AAAGGTTTGCTCCCCGGTACAAAACCGCCTTCATATGATCGACTACTAAAACCATCGATT
TCTCTTATGGAAGGTGGTTTAAGAACTTTAAAAATACCTGACGATACTATGAAAAAGTTC
CTCGATGTTGCTGCTTCAAACACTATGAAAAATATCGAAACTTGTGGCATTCTCTGTGGA
AAATTACAAAATCATCAACTTTCTATAACTCATGTAATTTTACCAAAACAAACTGGAACT
TCAGACAGTTGTAATACAATGAACGAAGAAGAAATTTTTGATATACAAGATCAAATGAAT
TTAATTACTTTAGGGATTCATACCCATCCTACTCAATCTGCATTTCTTTCATCGGTTGAT
CTACATACACAATGTGGATATCAAATTATGCTACCAGAAGCTATTGCTATTGTTTGCTCA
CCTAAATATGAAGAGCTTGGCTTCTTTACTTTAACTACTGAAGGCATTGATTTTATTTCA
AAATGTACACAAACCGGATTTCATCCACATCCTAACGATCAATTTATGGAAGCTATGCAT
TACAAATTAGAAAAAGATAAACACATCATAATTACTGACTTGAGAGGTCGTTGA

>g3021.t9 Gene=g3021 Length=231
MPSAPNFADLDQIVYPNDFPTDPKKPTQAAARDYKGLLPGTKPPSYDRLLKPSISLMEGG
LRTLKIPDDTMKKFLDVAASNTMKNIETCGILCGKLQNHQLSITHVILPKQTGTSDSCNT
MNEEEIFDIQDQMNLITLGIHTHPTQSAFLSSVDLHTQCGYQIMLPEAIAIVCSPKYEEL
GFFTLTTEGIDFISKCTQTGFHPHPNDQFMEAMHYKLEKDKHIIITDLRGR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g3021.t9 CDD cd08066 MPN_AMSH_like 61 229 0.00
6 g3021.t9 Gene3D G3DSA:3.40.140.10 Cytidine Deaminase 52 230 0.00
2 g3021.t9 PANTHER PTHR12947:SF4 FI19924P1 42 229 0.00
3 g3021.t9 PANTHER PTHR12947 AMSH-LIKE PROTEASE 42 229 0.00
1 g3021.t9 Pfam PF01398 JAB1/Mov34/MPN/PAD-1 ubiquitin protease 62 166 0.00
7 g3021.t9 ProSiteProfiles PS50249 MPN domain profile. 64 191 22.35
5 g3021.t9 SMART SM00232 pad1_6 63 188 0.00
4 g3021.t9 SUPERFAMILY SSF102712 JAB1/MPN domain 62 185 0.00

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

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