General information for g3227.t1
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.t1 | TTS | g3227.t1 | 23829477 | 23829477 |
| chr_3 | g3227 | g3227.t1 | isoform | g3227.t1 | 23830119 | 23835499 |
| chr_3 | g3227 | g3227.t1 | exon | g3227.t1.exon1 | 23830119 | 23830247 |
| chr_3 | g3227 | g3227.t1 | cds | g3227.t1.CDS1 | 23830119 | 23830247 |
| chr_3 | g3227 | g3227.t1 | exon | g3227.t1.exon2 | 23830309 | 23831850 |
| chr_3 | g3227 | g3227.t1 | cds | g3227.t1.CDS2 | 23830309 | 23831850 |
| chr_3 | g3227 | g3227.t1 | exon | g3227.t1.exon3 | 23831913 | 23832081 |
| chr_3 | g3227 | g3227.t1 | cds | g3227.t1.CDS3 | 23831913 | 23832081 |
| chr_3 | g3227 | g3227.t1 | exon | g3227.t1.exon4 | 23832149 | 23832264 |
| chr_3 | g3227 | g3227.t1 | cds | g3227.t1.CDS4 | 23832149 | 23832264 |
| chr_3 | g3227 | g3227.t1 | exon | g3227.t1.exon5 | 23832335 | 23832573 |
| chr_3 | g3227 | g3227.t1 | cds | g3227.t1.CDS5 | 23832335 | 23832573 |
| chr_3 | g3227 | g3227.t1 | exon | g3227.t1.exon6 | 23833131 | 23833547 |
| chr_3 | g3227 | g3227.t1 | cds | g3227.t1.CDS6 | 23833131 | 23833547 |
| chr_3 | g3227 | g3227.t1 | exon | g3227.t1.exon7 | 23833603 | 23835087 |
| chr_3 | g3227 | g3227.t1 | cds | g3227.t1.CDS7 | 23833603 | 23835087 |
| chr_3 | g3227 | g3227.t1 | exon | g3227.t1.exon8 | 23835149 | 23835331 |
| chr_3 | g3227 | g3227.t1 | cds | g3227.t1.CDS8 | 23835149 | 23835331 |
| chr_3 | g3227 | g3227.t1 | exon | g3227.t1.exon9 | 23835403 | 23835499 |
| chr_3 | g3227 | g3227.t1 | cds | g3227.t1.CDS9 | 23835403 | 23835499 |
| chr_3 | g3227 | g3227.t1 | TSS | g3227.t1 | 23835557 | 23835557 |
Sequences
>g3227.t1 Gene=g3227 Length=4377
ATGACGGAATTAGCGCCTGCACCAGGATTTTCAGATCCAACGCAAACTCTTTCTGGGCCT
ATCATCGGAATTATTTACCCACCTCCAGAAGTTAGAAATATCGTCGATAAAACTGCAAGT
TTCGTTGCAAGAAATGGTTTTGAGTTCGAGAAAAGAATTCATCAGAGCGAAAAAGGCAAC
AAAAAGTTTAGTTTCCTAAATCCCGGTGACCCTTATCATGCCTATTATCAACATAAAGTT
CAAGAATTTAAAGGAACCGGAAAACAATTGACACAATCCACTATTCCTGGCTTACAAAAG
CTGTCAATTTCTCAAAAACAGCAAGAGCTACTGAAACAAGCAACTGAACAGCAGTTTCAA
CCAAAAGATCCACCACCCGAATTTGAATTTATTGCTGATCCACCTTCAATTTCAGCACTA
GATCTTGATATTGTTAAACTCACAGCACAATTTGTAGCACGTAATGGACGTCAATTTCTT
ACAAACTTGATGAATCGTGAACAGAGAAACTTTCAATTTGATTTCTTACGTCCTCAACAT
TCACTCTTTCAATATTTCACAAAATTACTTGAACAATACACTAAAATTTTGATTCCACCC
AAGGATTTATTGCCAAAATTGAGAGCTGAAATTGATATTAATAAAGAAGGAAGTGTTAAT
GCTATACTGGATTCAGTAAAATATCGAGCAAATTGGCTCAAACATGAGGAAGCACAAAAA
AGACGCGAAGAAGAGAAGGTTGAACGTGAACGAGTTGCATATGCTCAAATAGATTGGCAT
GATTTTGTTGTAGTAGAAGTTGTAGAATATCAACCATTTGAAAGCGGTAATTTTCCAGCG
CCCACAACTCCTGAAGAAGTCGGTGCTCGTGTTATAATGGAACAACGATATCAAGAAGAT
GATAACGATATAGAAATGCAAATTGAATCAGATGAAGAAGTGCCAAATGATCAGCAAGTA
CCTCATCAAAATGTCAAGTTATCAGTTATGGAGAATCGTGTTAAAGATAATACACAAGTG
CAAGACATGGATGAAGCATCAAGTGATGATGATGCAGGTCCTAGTCAACCAACACAAGTT
GCTCCTGTCATGCCACCGACTCATGATAAAGTTATTGTCAAGAAATATGATCCTAAACAA
GCTCAAAAAGTCACTAAACCTGTGTCAACTACAGATGAATATCTCATTTCTCCAATCACA
GGTGAAAAAATACCAGCAAGTAAAGTTGCTGAACATATGCGAATTGGATTACTTGATCCT
CGTTGGGTTGAACAACGTGACAAGTTGATGGAAAAAGTTCGTGAAGAAAATGTTTATGCA
CCAGGAGCTGCAATTGAAGCAAGCTTGAAACAATTGGCTGAACGTCGTACTGATATTTTC
GGTGTTGGTGATGAAGAAGCAGCAATTGGAAAGAAATTGGGAGAAGAGCCAAGAAAAGAT
GATCGAGTAACATGGGATGGACATACGAGCAGCGTTGAGGCCGCAACTAGAGCAGCAGCT
AGAAATGTTTCACTCGAAGATCAAATTCATCAAATACATAAAGTAAAAGGTCTTTTACCA
GATGAAGAAAAAGAAAAAATTGGTCCTAAACCAATGTCTGGATCGACTGTGTCAGCACCG
CCTAAACCATCAATGCAAATCAGTAATCCTACAAATATTCAGAATATTGCACATCATTCT
GCTCCTCCAATGCCAGCTGTTCCACCGCCGCAAGTTTTGATGATGCCACAAATGAGACCA
CCATTACGTCCACCACCTTTAATTCCACCACCATTTCCTGTTGGATTTCCTATGCCACAA
CTTGCTCCAGCACCGCCAGTGCAAATGGAAATGCCTAATGAAGAAGAGCCCCCAAATAAG
AAATCAAGACAAGAAGACAATCTCATTCCAGAAGATGTCTTTATGCAACATCATAAGAGT
CCAATTACAATTCAAGTTCAAGTTCCATCATCAACTGATAAGCCAGAATGGAAATTAAAT
GGACAATTGCTCTCAATTAATATTGGTTTAGCTGATACAATTCAGAAACTGAAGCAGAGA
GTCCAAGAGGAAACCGATATGCCTCCAGCTAAACAGAAAATCTCACATGATGGCATTTTC
TTTAAAGATAGCAACACAATTGCATATTACAATTTATTGTCAGGTGTAACTGTTCATTTA
CAAATTAAGGAAAGAGGTGGTCTATTAGCCAAAAAAGGTCCGTTGAGTCGGATATGGCTT
GCAGCGCATTGGGATAAAAAATTGACGAAGGCTCATGTTTTTGAGACGAATATAGAACAA
TCTGTAGATGGAATTTTACAGCCAAAAGTTAAATTAGCATTAAGAACATCCGGTCATTTG
TTACTTGGTGTAGCAAGAATTCATTCAAGAAAAGCAAAATATTTATTGGCTGATTGTAAT
GAAGCATTTGTCAAAATTAAGATGGCCTTTCGACCGGGTATGGTCGATTTGCCTGAAGAA
CATCGAGAAGCGGCAGTTAATGCAATTACTTTACCCGAAGTTTTTCATGACTTCGATACA
GCTCTTCCCGAACTAAATGACGTCGATATTGAAGCACAATTTTCTATTAATCAATCGAGA
GCTGATGAAATTACAATGAGAGAAGATTATGGCTCATTGCCTATGAATATGCATGATGAT
GGTTTTGGTGAGATTGGTTTTGATGGTTCTGATTTAGTTCGAGATGGATTAAATCCAACA
ATTGATGATGATTTATTTTCTGAAACAATACATCAAGGACCAGATATAGATCAAAGTAAA
ACAGCATCTTCTCGTTCAATGCTTGGTGGCATTGATGCACATCCTTTAGATGATGACTTT
GGAGACGATTTTGGTGAATCGGGTGGTTTATTTGAAGGCGATATTTTTTCTGATCCACAT
ACTGCCATGGATGAACCTTCAGCGCCTGTTAATCAAGGAAATATGACTTCAAGAACAGAC
GATGATGACTCAGATGATGATGGTGGTCATTTTGATGGAGGGGCATCACCTGCTTTATCT
AGTACAAGCTCCAGACCTCCTTCAACAATTCAAGCACCAATCAATCAATTTCATTCAGAT
GGGCAAACAAATTTCATCAACAATCTTAATCAACAGCCAGGAACAAGTAAAGATTTATTG
AATGATAGTGATCCGAATAAAACAAATTTGCTGGGCAATGAAGAAGAATCATTTGCTTTA
GCGCCTATTGATGCATCAGCGTTAAAAGGTGTAACCAAAGCAAAACGTAAACGAAAATTG
ATTATTGACGAAGTTAAAAATATTTCGGGCGAAGAAATGAAGGCACAATTAGCAAATACA
ACTGATATTATTACATCTCTTGATCTTGCGCCACCGACAAAGAGACTCATGAATTGGAAA
GAAACGGGAGGCGTAGAAAAACTTTTTGCACTTCCATCTCGATTACTTCCTGCACGTGCA
CTCTCAAAAATATATCAAATGAATCTGGTATTTACAACTGGTATTATTGATGAAGATTTT
TCAACATTGGGACCTGCAGATATTCTCGCGTTAGATTCACACTCGTTAGAACCATTATCA
GAGTCACCTTCAAAGAGAGGAAGAAAACGAAAGAATATTGAAGATGTTGATCCATCTGAC
ATGTCTTTACCAGAGCCTCTTCGAGATGTCAACGATTTACCACCACAAACACCTGCACCA
ATCGAATTAAAAGGAGATCTTGGTTTAGATACGAATCAATCATACGGTAATGGTGATATG
AAATTAATGCCGCCACCTCCACAAATAACAAGTCCAAGACAATCAATGATGGGAATGTCT
AGTCCTCCTTCAACACCGCATATACCAATGACACCTGGTAATTTAACACATGGAAGTATG
ACTCCCGCAGGTTTTCATCATGGTCTTGATGACAACAATCCAATGTTGAGCGATCCTGCT
TTAAATAATTTGGATACAATTCCAAATTTGAATGCTGAAACTGTGAGCTCAATTCTTGAT
GGTACAAATGGAATGGATCAACATTTCGCAAACATGGGTTACGATGCACAAGCATCACCA
AGTGGAGGCATTTCTGAGAGAATAGCAAGTGATTGGAATGATTACGATTATCCTGCGTCT
GTTGGTCAAACGGGAGATGAGCAAATGGTGGATGAGTCAATAGAACAATTTGAAGAACGT
GTGCTAAATAAAAGAGCGGCACAATTGTTTGTGAATATAAGATCAAAATTACAGAAGCAA
GACAAAATTTATTTGTCTGATATGACATATAGGAATAGCAAGAAACAAGCTGCACAAAAA
TTCTACTCATTACTTGTTTTGAAGAAATTTCAAATGCTTGATATAGATCAAGAGAGACCG
TTTGCTGATATTGTTTGTTCGCGTGGTGAGGCATTCAACGATAACAAAACACTGTAA
>g3227.t1 Gene=g3227 Length=1458
MTELAPAPGFSDPTQTLSGPIIGIIYPPPEVRNIVDKTASFVARNGFEFEKRIHQSEKGN
KKFSFLNPGDPYHAYYQHKVQEFKGTGKQLTQSTIPGLQKLSISQKQQELLKQATEQQFQ
PKDPPPEFEFIADPPSISALDLDIVKLTAQFVARNGRQFLTNLMNREQRNFQFDFLRPQH
SLFQYFTKLLEQYTKILIPPKDLLPKLRAEIDINKEGSVNAILDSVKYRANWLKHEEAQK
RREEEKVERERVAYAQIDWHDFVVVEVVEYQPFESGNFPAPTTPEEVGARVIMEQRYQED
DNDIEMQIESDEEVPNDQQVPHQNVKLSVMENRVKDNTQVQDMDEASSDDDAGPSQPTQV
APVMPPTHDKVIVKKYDPKQAQKVTKPVSTTDEYLISPITGEKIPASKVAEHMRIGLLDP
RWVEQRDKLMEKVREENVYAPGAAIEASLKQLAERRTDIFGVGDEEAAIGKKLGEEPRKD
DRVTWDGHTSSVEAATRAAARNVSLEDQIHQIHKVKGLLPDEEKEKIGPKPMSGSTVSAP
PKPSMQISNPTNIQNIAHHSAPPMPAVPPPQVLMMPQMRPPLRPPPLIPPPFPVGFPMPQ
LAPAPPVQMEMPNEEEPPNKKSRQEDNLIPEDVFMQHHKSPITIQVQVPSSTDKPEWKLN
GQLLSINIGLADTIQKLKQRVQEETDMPPAKQKISHDGIFFKDSNTIAYYNLLSGVTVHL
QIKERGGLLAKKGPLSRIWLAAHWDKKLTKAHVFETNIEQSVDGILQPKVKLALRTSGHL
LLGVARIHSRKAKYLLADCNEAFVKIKMAFRPGMVDLPEEHREAAVNAITLPEVFHDFDT
ALPELNDVDIEAQFSINQSRADEITMREDYGSLPMNMHDDGFGEIGFDGSDLVRDGLNPT
IDDDLFSETIHQGPDIDQSKTASSRSMLGGIDAHPLDDDFGDDFGESGGLFEGDIFSDPH
TAMDEPSAPVNQGNMTSRTDDDDSDDDGGHFDGGASPALSSTSSRPPSTIQAPINQFHSD
GQTNFINNLNQQPGTSKDLLNDSDPNKTNLLGNEEESFALAPIDASALKGVTKAKRKRKL
IIDEVKNISGEEMKAQLANTTDIITSLDLAPPTKRLMNWKETGGVEKLFALPSRLLPARA
LSKIYQMNLVFTTGIIDEDFSTLGPADILALDSHSLEPLSESPSKRGRKRKNIEDVDPSD
MSLPEPLRDVNDLPPQTPAPIELKGDLGLDTNQSYGNGDMKLMPPPPQITSPRQSMMGMS
SPPSTPHIPMTPGNLTHGSMTPAGFHHGLDDNNPMLSDPALNNLDTIPNLNAETVSSILD
GTNGMDQHFANMGYDAQASPSGGISERIASDWNDYDYPASVGQTGDEQMVDESIEQFEER
VLNKRAAQLFVNIRSKLQKQDKIYLSDMTYRNSKKQAAQKFYSLLVLKKFQMLDIDQERP
FADIVCSRGEAFNDNKTL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g3227.t1 | CDD | cd01800 | Ubl_SF3a120 | 641 | 723 | 6.48573E-34 |
| 16 | g3227.t1 | Coils | Coil | Coil | 233 | 253 | - |
| 15 | g3227.t1 | Gene3D | G3DSA:1.10.10.790 | - | 30 | 86 | 1.5E-25 |
| 14 | g3227.t1 | Gene3D | G3DSA:1.10.10.790 | - | 137 | 195 | 5.4E-25 |
| 13 | g3227.t1 | Gene3D | G3DSA:3.10.20.90 | - | 618 | 728 | 9.4E-31 |
| 22 | g3227.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 341 | 366 | - |
| 23 | g3227.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1177 | 1212 | - |
| 21 | g3227.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1179 | 1202 | - |
| 7 | g3227.t1 | PANTHER | PTHR15316:SF1 | SPLICING FACTOR 3A SUBUNIT 1 | 17 | 727 | 2.1E-194 |
| 8 | g3227.t1 | PANTHER | PTHR15316 | SPLICEOSOME ASSOCIATED PROTEIN 114/SWAP SPLICING FACTOR-RELATED | 17 | 727 | 2.1E-194 |
| 4 | g3227.t1 | Pfam | PF01805 | Surp module | 32 | 83 | 1.7E-20 |
| 3 | g3227.t1 | Pfam | PF01805 | Surp module | 142 | 193 | 1.4E-20 |
| 1 | g3227.t1 | Pfam | PF12230 | Pre-mRNA splicing factor PRP21 like protein | 220 | 455 | 7.4E-45 |
| 5 | g3227.t1 | Pfam | PF00240 | Ubiquitin family | 659 | 725 | 3.0E-12 |
| 6 | g3227.t1 | Pfam | PF04825 | N terminus of Rad21 / Rec8 like protein | 728 | 824 | 4.5E-35 |
| 2 | g3227.t1 | Pfam | PF04824 | Conserved region of Rad21 / Rec8 like protein | 1401 | 1452 | 5.1E-13 |
| 26 | g3227.t1 | ProSiteProfiles | PS50128 | SURP motif repeat profile. | 34 | 76 | 18.188 |
| 25 | g3227.t1 | ProSiteProfiles | PS50128 | SURP motif repeat profile. | 144 | 186 | 17.269 |
| 24 | g3227.t1 | ProSiteProfiles | PS50053 | Ubiquitin domain profile. | 642 | 727 | 18.606 |
| 18 | g3227.t1 | SMART | SM00648 | surpneu2 | 32 | 85 | 1.2E-22 |
| 19 | g3227.t1 | SMART | SM00648 | surpneu2 | 142 | 195 | 8.4E-23 |
| 20 | g3227.t1 | SMART | SM00213 | ubq_7 | 652 | 723 | 8.0E-11 |
| 11 | g3227.t1 | SUPERFAMILY | SSF109905 | Surp module (SWAP domain) | 19 | 84 | 1.83E-23 |
| 12 | g3227.t1 | SUPERFAMILY | SSF109905 | Surp module (SWAP domain) | 116 | 194 | 9.05E-25 |
| 10 | g3227.t1 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 619 | 727 | 4.14E-23 |
| 9 | g3227.t1 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 1387 | 1452 | 2.99E-10 |
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 transcript has been annotated with K12825 (splicing factor 3A subunit 1)
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.
