General information for g3227.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Splicing factor 3A subunit 1.
Parent gene
- The parent gene g3227 is located on chr_3: 23833987..23835499 (- 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 | g3227 | g3227.t3 | TTS | g3227.t3 | 23833070 | 23833070 |
| chr_3 | g3227 | g3227.t3 | isoform | g3227.t3 | 23833131 | 23835087 |
| chr_3 | g3227 | g3227.t3 | exon | g3227.t3.exon1 | 23833131 | 23833547 |
| chr_3 | g3227 | g3227.t3 | cds | g3227.t3.CDS1 | 23833132 | 23833547 |
| chr_3 | g3227 | g3227.t3 | exon | g3227.t3.exon2 | 23833603 | 23835087 |
| chr_3 | g3227 | g3227.t3 | cds | g3227.t3.CDS2 | 23833603 | 23834878 |
| chr_3 | g3227 | g3227.t3 | TSS | g3227.t3 | 23835557 | 23835557 |
Sequences
>g3227.t3 Gene=g3227 Length=1902
CTATTCCTGGCTTACAAAAGCTGTCAATTTCTCAAAAACAGCAAGAGCTACTGAAACAAG
CAACTGAACAGCAGTTTCAACCAAAAGATCCACCACCCGAATTTGAATTTATTGCTGATC
CACCTTCAATTTCAGCACTAGATCTTGATATTGTTAAACTCACAGCACAATTTGTAGCAC
GTAATGGACGTCAATTTCTTACAAACTTGATGAATCGTGAACAGAGAAACTTTCAATTTG
ATTTCTTACGTCCTCAACATTCACTCTTTCAATATTTCACAAAATTACTTGAACAATACA
CTAAAATTTTGATTCCACCCAAGGATTTATTGCCAAAATTGAGAGCTGAAATTGATATTA
ATAAAGAAGGAAGTGTTAATGCTATACTGGATTCAGTAAAATATCGAGCAAATTGGCTCA
AACATGAGGAAGCACAAAAAAGACGCGAAGAAGAGAAGGTTGAACGTGAACGAGTTGCAT
ATGCTCAAATAGATTGGCATGATTTTGTTGTAGTAGAAGTTGTAGAATATCAACCATTTG
AAAGCGGTAATTTTCCAGCGCCCACAACTCCTGAAGAAGTCGGTGCTCGTGTTATAATGG
AACAACGATATCAAGAAGATGATAACGATATAGAAATGCAAATTGAATCAGATGAAGAAG
TGCCAAATGATCAGCAAGTACCTCATCAAAATGTCAAGTTATCAGTTATGGAGAATCGTG
TTAAAGATAATACACAAGTGCAAGACATGGATGAAGCATCAAGTGATGATGATGCAGGTC
CTAGTCAACCAACACAAGTTGCTCCTGTCATGCCACCGACTCATGATAAAGTTATTGTCA
AGAAATATGATCCTAAACAAGCTCAAAAAGTCACTAAACCTGTGTCAACTACAGATGAAT
ATCTCATTTCTCCAATCACAGGTGAAAAAATACCAGCAAGTAAAGTTGCTGAACATATGC
GAATTGGATTACTTGATCCTCGTTGGGTTGAACAACGTGACAAGTTGATGGAAAAAGTTC
GTGAAGAAAATGTTTATGCACCAGGAGCTGCAATTGAAGCAAGCTTGAAACAATTGGCTG
AACGTCGTACTGATATTTTCGGTGTTGGTGATGAAGAAGCAGCAATTGGAAAGAAATTGG
GAGAAGAGCCAAGAAAAGATGATCGAGTAACATGGGATGGACATACGAGCAGCGTTGAGG
CCGCAACTAGAGCAGCAGCTAGAAATGTTTCACTCGAAGATCAAATTCATCAAATACATA
AAGTAAAAGGTCTTTTACCAGATGAAGAAAAAGAAAAAATTGGTCCTAAACCAATGTCTG
GATCGACTGTGTCAGCACCGCCTAAACCATCAATGCAAATCAGTAATCCTACAAATATTC
AGAATATTGCACATCATTCTGCTCCTCCAATGCCAGCTGTTCCACCGCCGCAAGTTTTGA
TGATGCCACAAATGAGACCACCATTACGTCCACCACCTTTAATTCCACCACCATTTCCTG
TTGGATTTCCTATGCCACAACTTGCTCCAGCACCGCCAGTGCAAATGGAAATGCCTAATG
AAGAAGAGCCCCCAAATAAGAAATCAAGACAAGAAGACAATCTCATTCCAGAAGATGTCT
TTATGCAACATCATAAGAGTCCAATTACAATTCAAGTTCAAGTTCCATCATCAACTGATA
AGCCAGAATGGAAATTAAATGGACAATTGCTCTCAATTAATATTGGTTTAGCTGATACAA
TTCAGAAACTGAAGCAGAGAGTCCAAGAGGAAACCGATATGCCTCCAGCTAAACAGAAAA
TCTCACATGATGGCATTTTCTTTAAAGATAGCAACACAATTGCATATTACAATTTATTGT
CAGGTGTAACTGTTCATTTACAAATTAAGGAAAGAGGTGGTC
>g3227.t3 Gene=g3227 Length=564
MNREQRNFQFDFLRPQHSLFQYFTKLLEQYTKILIPPKDLLPKLRAEIDINKEGSVNAIL
DSVKYRANWLKHEEAQKRREEEKVERERVAYAQIDWHDFVVVEVVEYQPFESGNFPAPTT
PEEVGARVIMEQRYQEDDNDIEMQIESDEEVPNDQQVPHQNVKLSVMENRVKDNTQVQDM
DEASSDDDAGPSQPTQVAPVMPPTHDKVIVKKYDPKQAQKVTKPVSTTDEYLISPITGEK
IPASKVAEHMRIGLLDPRWVEQRDKLMEKVREENVYAPGAAIEASLKQLAERRTDIFGVG
DEEAAIGKKLGEEPRKDDRVTWDGHTSSVEAATRAAARNVSLEDQIHQIHKVKGLLPDEE
KEKIGPKPMSGSTVSAPPKPSMQISNPTNIQNIAHHSAPPMPAVPPPQVLMMPQMRPPLR
PPPLIPPPFPVGFPMPQLAPAPPVQMEMPNEEEPPNKKSRQEDNLIPEDVFMQHHKSPIT
IQVQVPSSTDKPEWKLNGQLLSINIGLADTIQKLKQRVQEETDMPPAKQKISHDGIFFKD
SNTIAYYNLLSGVTVHLQIKERGG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g3227.t3 | CDD | cd01800 | Ubl_SF3a120 | 478 | 560 | 3.10583E-34 |
| 13 | g3227.t3 | Coils | Coil | Coil | 70 | 90 | - |
| 12 | g3227.t3 | Gene3D | G3DSA:1.10.10.790 | - | 1 | 32 | 2.6E-8 |
| 11 | g3227.t3 | Gene3D | G3DSA:3.10.20.90 | - | 455 | 564 | 2.8E-31 |
| 16 | g3227.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 178 | 203 | - |
| 4 | g3227.t3 | PANTHER | PTHR15316:SF1 | SPLICING FACTOR 3A SUBUNIT 1 | 1 | 564 | 6.0E-129 |
| 5 | g3227.t3 | PANTHER | PTHR15316 | SPLICEOSOME ASSOCIATED PROTEIN 114/SWAP SPLICING FACTOR-RELATED | 1 | 564 | 6.0E-129 |
| 6 | g3227.t3 | PRINTS | PR00348 | Ubiquitin signature | 499 | 519 | 4.8E-5 |
| 8 | g3227.t3 | PRINTS | PR00348 | Ubiquitin signature | 520 | 540 | 4.8E-5 |
| 7 | g3227.t3 | PRINTS | PR00348 | Ubiquitin signature | 541 | 562 | 4.8E-5 |
| 2 | g3227.t3 | Pfam | PF01805 | Surp module | 1 | 30 | 1.2E-6 |
| 1 | g3227.t3 | Pfam | PF12230 | Pre-mRNA splicing factor PRP21 like protein | 57 | 292 | 1.3E-45 |
| 3 | g3227.t3 | Pfam | PF00240 | Ubiquitin family | 496 | 562 | 9.0E-13 |
| 18 | g3227.t3 | ProSiteProfiles | PS50128 | SURP motif repeat profile. | 1 | 23 | 9.209 |
| 17 | g3227.t3 | ProSiteProfiles | PS50053 | Ubiquitin domain profile. | 479 | 564 | 18.606 |
| 15 | g3227.t3 | SMART | SM00213 | ubq_7 | 489 | 560 | 8.0E-11 |
| 10 | g3227.t3 | SUPERFAMILY | SSF109905 | Surp module (SWAP domain) | 1 | 38 | 8.67E-8 |
| 9 | g3227.t3 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 456 | 564 | 1.47E-23 |
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:0006396 | RNA processing | BP |
| GO:0003723 | RNA binding | MF |
| GO:0005515 | protein binding | MF |
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.
