General information for g3021.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as STAM-binding protein-like A.
Parent gene
- The parent gene g3021 is located on chr_3: 22171600..22171940 (+ strand)
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.t1 | TSS | g3021.t1 | 22170493 | 22170493 |
| chr_3 | g3021 | g3021.t1 | isoform | g3021.t1 | 22170555 | 22171940 |
| chr_3 | g3021 | g3021.t1 | exon | g3021.t1.exon1 | 22170555 | 22170670 |
| chr_3 | g3021 | g3021.t1 | cds | g3021.t1.CDS1 | 22170555 | 22170670 |
| chr_3 | g3021 | g3021.t1 | exon | g3021.t1.exon2 | 22170746 | 22171379 |
| chr_3 | g3021 | g3021.t1 | cds | g3021.t1.CDS2 | 22170746 | 22171379 |
| chr_3 | g3021 | g3021.t1 | exon | g3021.t1.exon3 | 22171437 | 22171597 |
| chr_3 | g3021 | g3021.t1 | cds | g3021.t1.CDS3 | 22171437 | 22171597 |
| chr_3 | g3021 | g3021.t1 | exon | g3021.t1.exon4 | 22171661 | 22171940 |
| chr_3 | g3021 | g3021.t1 | cds | g3021.t1.CDS4 | 22171661 | 22171940 |
| chr_3 | g3021 | g3021.t1 | TTS | g3021.t1 | 22171996 | 22171996 |
Sequences
>g3021.t1 Gene=g3021 Length=1191
ATGGCAGATCTTATTAATTTTAATCAAATGGGGATTGTAGAACCTGAAAAGCGGTTAAAA
CAATTAAATGAGTCAGGTTCAAATATAAATGTCGATAAGAACCAGAATATCTTGAGATAT
TATAGATCTGGTAATGAAATATATAGAATGGCAAAAATATACATGCAAGAAGGAAATCAT
GAAAATGCGTACATCTTATTCCTAAGATTTTTAACTTTATTTGTTGAAAAGATAAGAGAA
CATCCTAATTATAAAGAAGTACCAGCTGATTTCAAAAAATCTAACAAAGAGAAAATGACA
GAAATTATGACATTAACAGAAAAATTGAAGGCGAAACTATTGGATCGTTATAAAAAAGAA
TACGAACAATTTTTAATTGATCAAGAGAATGAGCGAAAGAAAGCGATTGAGGAAGCTAAA
CGTAAAGAAATTGAAAATGCGAAAAATAAATCCAAAATAAGTGGACCTTCTGCAGCATCT
ACAAACGTAATAATGCCTAGTGCACCTAACTTTGCTGATCTTGATCAAATCGTTTACCCC
AATGACTTTCCAACAGATCCAAAGAAGCCTACCCAAGCTGCTGCAAGAGATTATAAAGGT
TTGCTCCCCGGTACAAAACCGCCTTCATATGATCGACTACTAAAACCATCGATTTCTCTT
ATGGAAGGTGGTTTAAGAACTTTAAAAATACCTGACGATACTATGAAAAAGTTCCTCGAT
GTTGCTGCTTCAAACACTATGAAAAATATCGAAACTTGTGGCATTCTCTGTGGAAAATTA
CAAAATCATCAACTTTCTATAACTCATGTAATTTTACCAAAACAAACTGGAACTTCAGAC
AGTTGTAATACAATGAACGAAGAAGAAATTTTTGATATACAAGATCAAATGAATTTAATT
ACTTTAGGGTGGATTCATACCCATCCTACTCAATCTGCATTTCTTTCATCGGTTGATCTA
CATACACAATGTGGATATCAAATTATGCTACCAGAAGCTATTGCTATTGTTTGCTCACCT
AAATATGAAGAGCTTGGCTTCTTTACTTTAACTACTGAAGGCATTGATTTTATTTCAAAA
TGTACACAAACCGGATTTCATCCACATCCTAACGATCAATTTATGGAAGCTATGCATTAC
AAATTAGAAAAAGATAAACACATCATAATTACTGACTTGAGAGGTCGTTGA
>g3021.t1 Gene=g3021 Length=396
MADLINFNQMGIVEPEKRLKQLNESGSNINVDKNQNILRYYRSGNEIYRMAKIYMQEGNH
ENAYILFLRFLTLFVEKIREHPNYKEVPADFKKSNKEKMTEIMTLTEKLKAKLLDRYKKE
YEQFLIDQENERKKAIEEAKRKEIENAKNKSKISGPSAASTNVIMPSAPNFADLDQIVYP
NDFPTDPKKPTQAAARDYKGLLPGTKPPSYDRLLKPSISLMEGGLRTLKIPDDTMKKFLD
VAASNTMKNIETCGILCGKLQNHQLSITHVILPKQTGTSDSCNTMNEEEIFDIQDQMNLI
TLGWIHTHPTQSAFLSSVDLHTQCGYQIMLPEAIAIVCSPKYEELGFFTLTTEGIDFISK
CTQTGFHPHPNDQFMEAMHYKLEKDKHIIITDLRGR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g3021.t1 | CDD | cd08066 | MPN_AMSH_like | 225 | 394 | 8.29867E-108 |
| 11 | g3021.t1 | Coils | Coil | Coil | 114 | 150 | - |
| 10 | g3021.t1 | Gene3D | G3DSA:1.20.58.280 | Hypothetical protein 1500032h18. | 8 | 152 | 2.1E-39 |
| 9 | g3021.t1 | Gene3D | G3DSA:3.40.140.10 | Cytidine Deaminase | 216 | 395 | 1.8E-68 |
| 4 | g3021.t1 | PANTHER | PTHR12947:SF4 | FI19924P1 | 13 | 146 | 1.9E-106 |
| 6 | g3021.t1 | PANTHER | PTHR12947 | AMSH-LIKE PROTEASE | 13 | 146 | 1.9E-106 |
| 3 | g3021.t1 | PANTHER | PTHR12947:SF4 | FI19924P1 | 170 | 394 | 1.9E-106 |
| 5 | g3021.t1 | PANTHER | PTHR12947 | AMSH-LIKE PROTEASE | 170 | 394 | 1.9E-106 |
| 1 | g3021.t1 | Pfam | PF08969 | USP8 dimerisation domain | 16 | 119 | 2.1E-27 |
| 2 | g3021.t1 | Pfam | PF01398 | JAB1/Mov34/MPN/PAD-1 ubiquitin protease | 226 | 331 | 3.1E-19 |
| 14 | g3021.t1 | ProSiteProfiles | PS50249 | MPN domain profile. | 228 | 356 | 29.999 |
| 13 | g3021.t1 | SMART | SM00232 | pad1_6 | 227 | 353 | 9.6E-16 |
| 8 | g3021.t1 | SUPERFAMILY | SSF140856 | USP8 N-terminal domain-like | 18 | 133 | 3.79E-13 |
| 7 | g3021.t1 | SUPERFAMILY | SSF102712 | JAB1/MPN domain | 226 | 350 | 5.89E-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
- This transcript has been annotated with K11866 (STAM-binding protein)
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.
