General information for g10306.t5
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.t5 | TTS | g10306.t5 | 8868381 | 8868381 |
| chr_1 | g10306 | g10306.t5 | isoform | g10306.t5 | 8868464 | 8870476 |
| chr_1 | g10306 | g10306.t5 | exon | g10306.t5.exon1 | 8868464 | 8868474 |
| chr_1 | g10306 | g10306.t5 | exon | g10306.t5.exon2 | 8868890 | 8870476 |
| chr_1 | g10306 | g10306.t5 | cds | g10306.t5.CDS1 | 8868910 | 8870418 |
| chr_1 | g10306 | g10306.t5 | TSS | g10306.t5 | NA | NA |
Sequences
>g10306.t5 Gene=g10306 Length=1598
ATCGCGTGGTGTAAAGCTTTTTAGAATTAAAGTACAAGGAAGTGAAGCTGTTCTGGCAAT
GTCTTCAAGATCGTGGCTCAGTTATTATTATCAAAATCGTTTTCATTTAACACCATTAAG
TTATGAGACACTCGAATATGCATCAGGATTCTCATCAGAGCAGTGTTCAGAAGGTATTGT
TGCAATTTCAACGAATACATTACGAATTTTGGCATTGGAAAAACTAGGAGCTGTTTTCAA
TCAAATTTCATTTCCTCTCGAGTATACGCCCAAAAGATTCGTTGTTCATACTGATACTTC
ACGATTAATTGTTGCTGAAACAGATCATAATGCATACACTGAGGCAACGAAAAATCTCAG
AAAACGTCAAATGGCTGATGAAATGATTGAAGCTGCAGGCGAGAATGAACAAGAATTAGC
ACAAGAGCTTGCTGATGCTTTTATTAATGAAGTTTTACCCGAAGATACATTTTCAGCACC
AAAAGCAGGCTATGGAATGTGGGCATCACAAATTAGAATTATGGATCCTGTCAAAGGTCA
GACGTTATTCAAAGTACCACTTGAACAGAATGAAGCAGTTGTATCAATGTGTTTAGTTAA
ATTCAGCGTTGATGGTAAAAGTTATTTAGCATGCGGTGTTGTTAAAGACATGCAGTTAAA
TCCACGACAAATTGGTTCTGGCTATATCGATTTATATCGAGTCGATAATCAATGTGCAAC
GCTGAATTTGATTCATAGAACAGAAGTTGAAGATATTCCATCAGCAATAGCACCTTTTCA
AGGTAAACTATTAGTTGGAGTTGGAAAGATTTTGCGAGTTTATGATTTAGGCAAGAAAAA
GTTATTAAGAAAATGCGAAAATAAGCACATCCCTAATCAAATTGTCAATATTCAAACGAG
AGCTTTACGTGTATTTTGCTCAGATGTACAAGAAAGTGTTTATTGTCTCACATACAAGCG
AAATGAAAATCAATTGATTATTTTTGCTGATGACACTTTCCCTCGATGGATAACAACAAC
AGCAATTTTGGATTATGATACAATAGCTACAGGTGACAAGTTTGGAAATATTGCCATTTT
GAGACTACCGCATTCTATCAATGATGATGTGGACGAAGATCCAACGGGAAACAAAGCACT
TTGGGATCGAGGTTTGCTAAATGGAGCATCACAAAAAGCTGAAAACATAATCACATTCCA
TATTGGTGAGATAGTAATGTCGCTACAAAAATCAATGTTGATTCCTGGTGGTCCAGAACT
TTTAATTTATACAACAATTAGCGGTACAATTGGTGCATTAGTTCCATTTACAGGAAGAGA
AGATTTTGATTTCTTTCAACATTTAGAAATGCACATGAGAAATGAAAATCCACCATTGTG
TGGTAGAGATCATTTGAGTTATAGATCTTACTATTATCCAGTAAAGAATGTCATTGATGG
TGATTTGTGTGAACAGTTTACATCTTTAGATCCAGCAAAACAAAAGAGTATTGCATCGGA
TTTAAGTCGAAGTGCAACTGAGGTGGCAAAGAAGCTTGAAGATATTAGAACAAGATACGC
ATTTTAAATTTTTTCACAGTCAAGTAAGTTTTCTTTAA
>g10306.t5 Gene=g10306 Length=502
MSSRSWLSYYYQNRFHLTPLSYETLEYASGFSSEQCSEGIVAISTNTLRILALEKLGAVF
NQISFPLEYTPKRFVVHTDTSRLIVAETDHNAYTEATKNLRKRQMADEMIEAAGENEQEL
AQELADAFINEVLPEDTFSAPKAGYGMWASQIRIMDPVKGQTLFKVPLEQNEAVVSMCLV
KFSVDGKSYLACGVVKDMQLNPRQIGSGYIDLYRVDNQCATLNLIHRTEVEDIPSAIAPF
QGKLLVGVGKILRVYDLGKKKLLRKCENKHIPNQIVNIQTRALRVFCSDVQESVYCLTYK
RNENQLIIFADDTFPRWITTTAILDYDTIATGDKFGNIAILRLPHSINDDVDEDPTGNKA
LWDRGLLNGASQKAENIITFHIGEIVMSLQKSMLIPGGPELLIYTTISGTIGALVPFTGR
EDFDFFQHLEMHMRNENPPLCGRDHLSYRSYYYPVKNVIDGDLCEQFTSLDPAKQKSIAS
DLSRSATEVAKKLEDIRTRYAF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g10306.t5 | Gene3D | G3DSA:2.130.10.10 | - | 26 | 416 | 0.0e+00 |
| 6 | g10306.t5 | Gene3D | G3DSA:3.30.980.30 | - | 420 | 499 | 1.1e-05 |
| 2 | g10306.t5 | PANTHER | PTHR10644 | DNA REPAIR/RNA PROCESSING CPSF FAMILY | 1 | 495 | 0.0e+00 |
| 3 | g10306.t5 | PANTHER | PTHR10644:SF1 | SPLICING FACTOR 3B SUBUNIT 3 | 1 | 495 | 0.0e+00 |
| 1 | g10306.t5 | Pfam | PF03178 | CPSF A subunit region | 149 | 468 | 0.0e+00 |
| 4 | g10306.t5 | SUPERFAMILY | SSF50998 | Quinoprotein alcohol dehydrogenase-like | 150 | 313 | 3.9e-06 |
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.
