General information for g10306.t4
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.t4 | TTS | g10306.t4 | 8868381 | 8868381 |
| chr_1 | g10306 | g10306.t4 | isoform | g10306.t4 | 8868464 | 8869896 |
| chr_1 | g10306 | g10306.t4 | exon | g10306.t4.exon1 | 8868464 | 8868474 |
| chr_1 | g10306 | g10306.t4 | exon | g10306.t4.exon2 | 8868850 | 8869896 |
| chr_1 | g10306 | g10306.t4 | cds | g10306.t4.CDS1 | 8868910 | 8869890 |
| chr_1 | g10306 | g10306.t4 | TSS | g10306.t4 | NA | NA |
Sequences
>g10306.t4 Gene=g10306 Length=1058
GTATCAATGTGTTTAGTTAAATTCAGCGTTGATGGTAAAAGTTATTTAGCATGCGGTGTT
GTTAAAGACATGCAGTTAAATCCACGACAAATTGGTTCTGGCTATATCGATTTATATCGA
GTCGATAATCAATGTGCAACGCTGAATTTGATTCATAGAACAGAAGTTGAAGATATTCCA
TCAGCAATAGCACCTTTTCAAGGTAAACTATTAGTTGGAGTTGGAAAGATTTTGCGAGTT
TATGATTTAGGCAAGAAAAAGTTATTAAGAAAATGCGAAAATAAGCACATCCCTAATCAA
ATTGTCAATATTCAAACGAGAGCTTTACGTGTATTTTGCTCAGATGTACAAGAAAGTGTT
TATTGTCTCACATACAAGCGAAATGAAAATCAATTGATTATTTTTGCTGATGACACTTTC
CCTCGATGGATAACAACAACAGCAATTTTGGATTATGATACAATAGCTACAGGTGACAAG
TTTGGAAATATTGCCATTTTGAGACTACCGCATTCTATCAATGATGATGTGGACGAAGAT
CCAACGGGAAACAAAGCACTTTGGGATCGAGGTTTGCTAAATGGAGCATCACAAAAAGCT
GAAAACATAATCACATTCCATATTGGTGAGATAGTAATGTCGCTACAAAAATCAATGTTG
ATTCCTGGTGGTCCAGAACTTTTAATTTATACAACAATTAGCGGTACAATTGGTGCATTA
GTTCCATTTACAGGAAGAGAAGATTTTGATTTCTTTCAACATTTAGAAATGCACATGAGA
AATGAAAATCCACCATTGTGTGGTAGAGATCATTTGAGTTATAGATCTTACTATTATCCA
GTAAAGAATGTCATTGATGGTGATTTGTGTGAACAGTTTACATCTTTAGATCCAGCAAAA
CAAAAGAGTATTGCATCGGATTTAAGTCGAAGTGCAACTGAGGTGGCAAAGAAGCTTGAA
GATATTAGAACAAGATACGCATTTTAAATTTTTTCACAGTCAAGTAAGTGTTTTATATGA
AAATAATTCTTTTTATGTAATTTTACTGTTTTCTTTAA
>g10306.t4 Gene=g10306 Length=326
MCLVKFSVDGKSYLACGVVKDMQLNPRQIGSGYIDLYRVDNQCATLNLIHRTEVEDIPSA
IAPFQGKLLVGVGKILRVYDLGKKKLLRKCENKHIPNQIVNIQTRALRVFCSDVQESVYC
LTYKRNENQLIIFADDTFPRWITTTAILDYDTIATGDKFGNIAILRLPHSINDDVDEDPT
GNKALWDRGLLNGASQKAENIITFHIGEIVMSLQKSMLIPGGPELLIYTTISGTIGALVP
FTGREDFDFFQHLEMHMRNENPPLCGRDHLSYRSYYYPVKNVIDGDLCEQFTSLDPAKQK
SIASDLSRSATEVAKKLEDIRTRYAF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g10306.t4 | Gene3D | G3DSA:2.130.10.10 | - | 1 | 240 | 0.0e+00 |
| 5 | g10306.t4 | Gene3D | G3DSA:3.30.980.30 | - | 244 | 323 | 5.3e-06 |
| 2 | g10306.t4 | PANTHER | PTHR10644 | DNA REPAIR/RNA PROCESSING CPSF FAMILY | 1 | 319 | 0.0e+00 |
| 3 | g10306.t4 | PANTHER | PTHR10644:SF1 | SPLICING FACTOR 3B SUBUNIT 3 | 1 | 319 | 0.0e+00 |
| 1 | g10306.t4 | Pfam | PF03178 | CPSF A subunit region | 1 | 292 | 0.0e+00 |
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.
