Gene loci information

Transcript annotation

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

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.t5 TSS g3021.t5 22170493 22170493
chr_3 g3021 g3021.t5 isoform g3021.t5 22170555 22171940
chr_3 g3021 g3021.t5 exon g3021.t5.exon1 22170555 22170670
chr_3 g3021 g3021.t5 cds g3021.t5.CDS1 22170555 22170670
chr_3 g3021 g3021.t5 exon g3021.t5.exon2 22170746 22171379
chr_3 g3021 g3021.t5 cds g3021.t5.CDS2 22170746 22171379
chr_3 g3021 g3021.t5 exon g3021.t5.exon3 22171437 22171594
chr_3 g3021 g3021.t5 cds g3021.t5.CDS3 22171437 22171594
chr_3 g3021 g3021.t5 exon g3021.t5.exon4 22171661 22171940
chr_3 g3021 g3021.t5 cds g3021.t5.CDS4 22171661 22171940
chr_3 g3021 g3021.t5 TTS g3021.t5 22171996 22171996

Sequences

>g3021.t5 Gene=g3021 Length=1188
ATGGCAGATCTTATTAATTTTAATCAAATGGGGATTGTAGAACCTGAAAAGCGGTTAAAA
CAATTAAATGAGTCAGGTTCAAATATAAATGTCGATAAGAACCAGAATATCTTGAGATAT
TATAGATCTGGTAATGAAATATATAGAATGGCAAAAATATACATGCAAGAAGGAAATCAT
GAAAATGCGTACATCTTATTCCTAAGATTTTTAACTTTATTTGTTGAAAAGATAAGAGAA
CATCCTAATTATAAAGAAGTACCAGCTGATTTCAAAAAATCTAACAAAGAGAAAATGACA
GAAATTATGACATTAACAGAAAAATTGAAGGCGAAACTATTGGATCGTTATAAAAAAGAA
TACGAACAATTTTTAATTGATCAAGAGAATGAGCGAAAGAAAGCGATTGAGGAAGCTAAA
CGTAAAGAAATTGAAAATGCGAAAAATAAATCCAAAATAAGTGGACCTTCTGCAGCATCT
ACAAACGTAATAATGCCTAGTGCACCTAACTTTGCTGATCTTGATCAAATCGTTTACCCC
AATGACTTTCCAACAGATCCAAAGAAGCCTACCCAAGCTGCTGCAAGAGATTATAAAGGT
TTGCTCCCCGGTACAAAACCGCCTTCATATGATCGACTACTAAAACCATCGATTTCTCTT
ATGGAAGGTGGTTTAAGAACTTTAAAAATACCTGACGATACTATGAAAAAGTTCCTCGAT
GTTGCTGCTTCAAACACTATGAAAAATATCGAAACTTGTGGCATTCTCTGTGGAAAATTA
CAAAATCATCAACTTTCTATAACTCATGTAATTTTACCAAAACAAACTGGAACTTCAGAC
AGTTGTAATACAATGAACGAAGAAGAAATTTTTGATATACAAGATCAAATGAATTTAATT
ACTTTAGGGATTCATACCCATCCTACTCAATCTGCATTTCTTTCATCGGTTGATCTACAT
ACACAATGTGGATATCAAATTATGCTACCAGAAGCTATTGCTATTGTTTGCTCACCTAAA
TATGAAGAGCTTGGCTTCTTTACTTTAACTACTGAAGGCATTGATTTTATTTCAAAATGT
ACACAAACCGGATTTCATCCACATCCTAACGATCAATTTATGGAAGCTATGCATTACAAA
TTAGAAAAAGATAAACACATCATAATTACTGACTTGAGAGGTCGTTGA

>g3021.t5 Gene=g3021 Length=395
MADLINFNQMGIVEPEKRLKQLNESGSNINVDKNQNILRYYRSGNEIYRMAKIYMQEGNH
ENAYILFLRFLTLFVEKIREHPNYKEVPADFKKSNKEKMTEIMTLTEKLKAKLLDRYKKE
YEQFLIDQENERKKAIEEAKRKEIENAKNKSKISGPSAASTNVIMPSAPNFADLDQIVYP
NDFPTDPKKPTQAAARDYKGLLPGTKPPSYDRLLKPSISLMEGGLRTLKIPDDTMKKFLD
VAASNTMKNIETCGILCGKLQNHQLSITHVILPKQTGTSDSCNTMNEEEIFDIQDQMNLI
TLGIHTHPTQSAFLSSVDLHTQCGYQIMLPEAIAIVCSPKYEELGFFTLTTEGIDFISKC
TQTGFHPHPNDQFMEAMHYKLEKDKHIIITDLRGR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g3021.t5 CDD cd08066 MPN_AMSH_like 225 393 6.05929E-104
11 g3021.t5 Coils Coil Coil 114 150 -
10 g3021.t5 Gene3D G3DSA:1.20.58.280 Hypothetical protein 1500032h18. 8 152 2.1E-39
9 g3021.t5 Gene3D G3DSA:3.40.140.10 Cytidine Deaminase 216 394 7.7E-64
4 g3021.t5 PANTHER PTHR12947:SF4 FI19924P1 13 146 2.3E-101
6 g3021.t5 PANTHER PTHR12947 AMSH-LIKE PROTEASE 13 146 2.3E-101
3 g3021.t5 PANTHER PTHR12947:SF4 FI19924P1 170 393 2.3E-101
5 g3021.t5 PANTHER PTHR12947 AMSH-LIKE PROTEASE 170 393 2.3E-101
1 g3021.t5 Pfam PF08969 USP8 dimerisation domain 16 119 2.1E-27
2 g3021.t5 Pfam PF01398 JAB1/Mov34/MPN/PAD-1 ubiquitin protease 226 330 9.9E-15
14 g3021.t5 ProSiteProfiles PS50249 MPN domain profile. 228 355 22.35
13 g3021.t5 SMART SM00232 pad1_6 227 352 6.8E-11
8 g3021.t5 SUPERFAMILY SSF140856 USP8 N-terminal domain-like 18 133 3.79E-13
7 g3021.t5 SUPERFAMILY SSF102712 JAB1/MPN domain 226 349 2.62E-15

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