General information for g10306.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Splicing factor 3B subunit 3.
Parent gene
- The parent gene g10306 is located on chr_1: 8873421..8873811 (- 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_1 | g10306 | g10306.t2 | TTS | g10306.t2 | 8868381 | 8868381 |
| chr_1 | g10306 | g10306.t2 | isoform | g10306.t2 | 8868464 | 8871539 |
| chr_1 | g10306 | g10306.t2 | exon | g10306.t2.exon1 | 8868464 | 8868474 |
| chr_1 | g10306 | g10306.t2 | cds | g10306.t2.CDS1 | 8868464 | 8868474 |
| chr_1 | g10306 | g10306.t2 | exon | g10306.t2.exon2 | 8868660 | 8868696 |
| chr_1 | g10306 | g10306.t2 | cds | g10306.t2.CDS2 | 8868660 | 8868696 |
| chr_1 | g10306 | g10306.t2 | exon | g10306.t2.exon3 | 8868894 | 8868970 |
| chr_1 | g10306 | g10306.t2 | cds | g10306.t2.CDS3 | 8868894 | 8868970 |
| chr_1 | g10306 | g10306.t2 | exon | g10306.t2.exon4 | 8869038 | 8870868 |
| chr_1 | g10306 | g10306.t2 | cds | g10306.t2.CDS4 | 8869038 | 8870868 |
| chr_1 | g10306 | g10306.t2 | exon | g10306.t2.exon5 | 8871059 | 8871366 |
| chr_1 | g10306 | g10306.t2 | cds | g10306.t2.CDS5 | 8871059 | 8871366 |
| chr_1 | g10306 | g10306.t2 | exon | g10306.t2.exon6 | 8871527 | 8871539 |
| chr_1 | g10306 | g10306.t2 | cds | g10306.t2.CDS6 | 8871527 | 8871539 |
| chr_1 | g10306 | g10306.t2 | TSS | g10306.t2 | NA | NA |
Sequences
>g10306.t2 Gene=g10306 Length=2277
ATGTTGTGGAAAGATGAATTTGATGCATACATCATTGTATCTTTCGTAAATGCTACCTTG
GTATTGAGCATTGGTGACACTGTTGAGGAAGTAACAGATAGTGGATTTTTAGGAACTACT
CCTACACTTTGCTGCGCTTCACTTGGAGATGATGCTTTGGTTCAGATTTATCCTGATGGT
ATTAGACACATTCGAGCTGATCGAAGAGTAAACGAATGGAAAGCACCAAATAAAAAGACA
ATTGTGAAATGTGCAGTTAATCAGCGTCAAGTTGTAATTGCTTTATCTGGTGGTGATCTC
GTTTATTTTGAAATGGATCCGACTGGTCAATTAAATGAGTTTACTGAACGAAGAAAAATG
ATGGCTGATATATTGTGTATGACATTAGCTTCAATAAAACCTGGTGAACTACAATCTCCG
TTTTTAGCAGTTGGTTTAGCTGACAGCACAGTTCGAGTCATATCACTACAGAGACAAGAT
TGTCTTCAACCACGCTCAATGCAAGCTTTACCATCGCCAGCAGAATCATTATGTTTGGTA
GAAATGGGAATTGGTGAGACTGAAGAAGATGAAGATGGTGTCATTATTCATAAAGGAGGA
AAAGAAAAAGGATCATTATATCTCAACATAGGTCTGCAAAATGGTGTTTTATTGCGAACA
GTATTGGATAAGATATCGGGTGATTTGACTGATACACGAACACGTTATTTAGGATCGCGT
GGTGTAAAGCTTTTTAGAATTAAAGTACAAGGAAGTGAAGCTGTTCTGGCAATGTCTTCA
AGATCGTGGCTCAGTTATTATTATCAAAATCGTTTTCATTTAACACCATTAAGTTATGAG
ACACTCGAATATGCATCAGGATTCTCATCAGAGCAGTGTTCAGAAGGTATTGTTGCAATT
TCAACGAATACATTACGAATTTTGGCATTGGAAAAACTAGGAGCTGTTTTCAATCAAATT
TCATTTCCTCTCGAGTATACGCCCAAAAGATTCGTTGTTCATACTGATACTTCACGATTA
ATTGTTGCTGAAACAGATCATAATGCATACACTGAGGCAACGAAAAATCTCAGAAAACGT
CAAATGGCTGATGAAATGATTGAAGCTGCAGGCGAGAATGAACAAGAATTAGCACAAGAG
CTTGCTGATGCTTTTATTAATGAAGTTTTACCCGAAGATACATTTTCAGCACCAAAAGCA
GGCTATGGAATGTGGGCATCACAAATTAGAATTATGGATCCTGTCAAAGGTCAGACGTTA
TTCAAAGTACCACTTGAACAGAATGAAGCAGTTGTATCAATGTGTTTAGTTAAATTCAGC
GTTGATGGTAAAAGTTATTTAGCATGCGGTGTTGTTAAAGACATGCAGTTAAATCCACGA
CAAATTGGTTCTGGCTATATCGATTTATATCGAGTCGATAATCAATGTGCAACGCTGAAT
TTGATTCATAGAACAGAAGTTGAAGATATTCCATCAGCAATAGCACCTTTTCAAGGTAAA
CTATTAGTTGGAGTTGGAAAGATTTTGCGAGTTTATGATTTAGGCAAGAAAAAGTTATTA
AGAAAATGCGAAAATAAGCACATCCCTAATCAAATTGTCAATATTCAAACGAGAGCTTTA
CGTGTATTTTGCTCAGATGTACAAGAAAGTGTTTATTGTCTCACATACAAGCGAAATGAA
AATCAATTGATTATTTTTGCTGATGACACTTTCCCTCGATGGATAACAACAACAGCAATT
TTGGATTATGATACAATAGCTACAGGTGACAAGTTTGGAAATATTGCCATTTTGAGACTA
CCGCATTCTATCAATGATGATGTGGACGAAGATCCAACGGGAAACAAAGCACTTTGGGAT
CGAGGTTTGCTAAATGGAGCATCACAAAAAGCTGAAAACATAATCACATTCCATATTGGT
GAGATAGTAATGTCGCTACAAAAATCAATGTTGATTCCTGGTGGTCCAGAACTTTTAATT
TATACAACAATTAGCGGTACAATTGGTGCATTAGTTCCATTTACAGGAAGAGAAGATTTT
GATTTCTTTCAACATTTAGAAATGCACATGAGAAATGAAAATCCACCATTGTGTGGTAGA
GATCATTTGAGTTATAGATCTTACTATTATCCAGTAAAGAATGTCATTGATGTCGAAGTG
CAACTGAGGTGGCAAAGAAGCTTGAAGATATTAGAACAAGATACGCATTTTAAATTTTTT
CACAGTCAAATTGTAATTTTAAAAAGTGACGGTAGTGAAAATGAATGTTTTCTTTAA
>g10306.t2 Gene=g10306 Length=758
MLWKDEFDAYIIVSFVNATLVLSIGDTVEEVTDSGFLGTTPTLCCASLGDDALVQIYPDG
IRHIRADRRVNEWKAPNKKTIVKCAVNQRQVVIALSGGDLVYFEMDPTGQLNEFTERRKM
MADILCMTLASIKPGELQSPFLAVGLADSTVRVISLQRQDCLQPRSMQALPSPAESLCLV
EMGIGETEEDEDGVIIHKGGKEKGSLYLNIGLQNGVLLRTVLDKISGDLTDTRTRYLGSR
GVKLFRIKVQGSEAVLAMSSRSWLSYYYQNRFHLTPLSYETLEYASGFSSEQCSEGIVAI
STNTLRILALEKLGAVFNQISFPLEYTPKRFVVHTDTSRLIVAETDHNAYTEATKNLRKR
QMADEMIEAAGENEQELAQELADAFINEVLPEDTFSAPKAGYGMWASQIRIMDPVKGQTL
FKVPLEQNEAVVSMCLVKFSVDGKSYLACGVVKDMQLNPRQIGSGYIDLYRVDNQCATLN
LIHRTEVEDIPSAIAPFQGKLLVGVGKILRVYDLGKKKLLRKCENKHIPNQIVNIQTRAL
RVFCSDVQESVYCLTYKRNENQLIIFADDTFPRWITTTAILDYDTIATGDKFGNIAILRL
PHSINDDVDEDPTGNKALWDRGLLNGASQKAENIITFHIGEIVMSLQKSMLIPGGPELLI
YTTISGTIGALVPFTGREDFDFFQHLEMHMRNENPPLCGRDHLSYRSYYYPVKNVIDVEV
QLRWQRSLKILEQDTHFKFFHSQIVILKSDGSENECFL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g10306.t2 | Gene3D | G3DSA:2.130.10.10 | - | 2 | 314 | 0 |
| 3 | g10306.t2 | PANTHER | PTHR10644 | DNA REPAIR/RNA PROCESSING CPSF FAMILY | 6 | 718 | 0 |
| 4 | g10306.t2 | PANTHER | PTHR10644:SF1 | SPLICING FACTOR 3B SUBUNIT 3 | 6 | 718 | 0 |
| 1 | g10306.t2 | Pfam | PF10433 | Mono-functional DNA-alkylating methyl methanesulfonate N-term | 4 | 129 | 0 |
| 2 | g10306.t2 | Pfam | PF03178 | CPSF A subunit region | 406 | 722 | 0 |
| 5 | g10306.t2 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 86 | 604 | 0 |
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:0005634 | nucleus | CC |
| GO:0005515 | protein binding | MF |
| GO:0003676 | nucleic acid 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.
