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.t8 TSS g3021.t8 22170493 22170493
chr_3 g3021 g3021.t8 isoform g3021.t8 22170744 22171940
chr_3 g3021 g3021.t8 exon g3021.t8.exon1 22170744 22171379
chr_3 g3021 g3021.t8 cds g3021.t8.CDS1 22170777 22171379
chr_3 g3021 g3021.t8 exon g3021.t8.exon2 22171437 22171597
chr_3 g3021 g3021.t8 cds g3021.t8.CDS2 22171437 22171597
chr_3 g3021 g3021.t8 exon g3021.t8.exon3 22171661 22171940
chr_3 g3021 g3021.t8 cds g3021.t8.CDS3 22171661 22171940
chr_3 g3021 g3021.t8 TTS g3021.t8 22171996 22171996

Sequences

>g3021.t8 Gene=g3021 Length=1077
AGATATTATAGATCTGGTAATGAAATATATAGAATGGCAAAAATATACATGCAAGAAGGA
AATCATGAAAATGCGTACATCTTATTCCTAAGATTTTTAACTTTATTTGTTGAAAAGATA
AGAGAACATCCTAATTATAAAGAAGTACCAGCTGATTTCAAAAAATCTAACAAAGAGAAA
ATGACAGAAATTATGACATTAACAGAAAAATTGAAGGCGAAACTATTGGATCGTTATAAA
AAAGAATACGAACAATTTTTAATTGATCAAGAGAATGAGCGAAAGAAAGCGATTGAGGAA
GCTAAACGTAAAGAAATTGAAAATGCGAAAAATAAATCCAAAATAAGTGGACCTTCTGCA
GCATCTACAAACGTAATAATGCCTAGTGCACCTAACTTTGCTGATCTTGATCAAATCGTT
TACCCCAATGACTTTCCAACAGATCCAAAGAAGCCTACCCAAGCTGCTGCAAGAGATTAT
AAAGGTTTGCTCCCCGGTACAAAACCGCCTTCATATGATCGACTACTAAAACCATCGATT
TCTCTTATGGAAGGTGGTTTAAGAACTTTAAAAATACCTGACGATACTATGAAAAAGTTC
CTCGATGTTGCTGCTTCAAACACTATGAAAAATATCGAAACTTGTGGCATTCTCTGTGGA
AAATTACAAAATCATCAACTTTCTATAACTCATGTAATTTTACCAAAACAAACTGGAACT
TCAGACAGTTGTAATACAATGAACGAAGAAGAAATTTTTGATATACAAGATCAAATGAAT
TTAATTACTTTAGGGTGGATTCATACCCATCCTACTCAATCTGCATTTCTTTCATCGGTT
GATCTACATACACAATGTGGATATCAAATTATGCTACCAGAAGCTATTGCTATTGTTTGC
TCACCTAAATATGAAGAGCTTGGCTTCTTTACTTTAACTACTGAAGGCATTGATTTTATT
TCAAAATGTACACAAACCGGATTTCATCCACATCCTAACGATCAATTTATGGAAGCTATG
CATTACAAATTAGAAAAAGATAAACACATCATAATTACTGACTTGAGAGGTCGTTGA

>g3021.t8 Gene=g3021 Length=347
MAKIYMQEGNHENAYILFLRFLTLFVEKIREHPNYKEVPADFKKSNKEKMTEIMTLTEKL
KAKLLDRYKKEYEQFLIDQENERKKAIEEAKRKEIENAKNKSKISGPSAASTNVIMPSAP
NFADLDQIVYPNDFPTDPKKPTQAAARDYKGLLPGTKPPSYDRLLKPSISLMEGGLRTLK
IPDDTMKKFLDVAASNTMKNIETCGILCGKLQNHQLSITHVILPKQTGTSDSCNTMNEEE
IFDIQDQMNLITLGWIHTHPTQSAFLSSVDLHTQCGYQIMLPEAIAIVCSPKYEELGFFT
LTTEGIDFISKCTQTGFHPHPNDQFMEAMHYKLEKDKHIIITDLRGR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g3021.t8 CDD cd08066 MPN_AMSH_like 176 345 2.77049E-107
11 g3021.t8 Coils Coil Coil 65 101 -
10 g3021.t8 Gene3D G3DSA:1.20.58.280 Hypothetical protein 1500032h18. 1 103 1.4E-23
9 g3021.t8 Gene3D G3DSA:3.40.140.10 Cytidine Deaminase 167 346 1.3E-68
4 g3021.t8 PANTHER PTHR12947:SF4 FI19924P1 1 97 3.1E-96
6 g3021.t8 PANTHER PTHR12947 AMSH-LIKE PROTEASE 1 97 3.1E-96
3 g3021.t8 PANTHER PTHR12947:SF4 FI19924P1 129 345 3.1E-96
5 g3021.t8 PANTHER PTHR12947 AMSH-LIKE PROTEASE 129 345 3.1E-96
1 g3021.t8 Pfam PF08969 USP8 dimerisation domain 1 70 6.4E-18
2 g3021.t8 Pfam PF01398 JAB1/Mov34/MPN/PAD-1 ubiquitin protease 177 282 2.4E-19
14 g3021.t8 ProSiteProfiles PS50249 MPN domain profile. 179 307 29.999
13 g3021.t8 SMART SM00232 pad1_6 178 304 9.6E-16
8 g3021.t8 SUPERFAMILY SSF140856 USP8 N-terminal domain-like 2 85 2.75E-9
7 g3021.t8 SUPERFAMILY SSF102712 JAB1/MPN domain 177 301 4.45E-19

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