General information for g10505.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Histone-binding protein RBBP4.
Parent gene
- The parent gene g10505 is located on chr_1: 10271981..10273519 (+ 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 | g10505 | g10505.t3 | TSS | g10505.t3 | 10270294 | 10270294 |
| chr_1 | g10505 | g10505.t3 | isoform | g10505.t3 | 10270519 | 10271150 |
| chr_1 | g10505 | g10505.t3 | exon | g10505.t3.exon1 | 10270519 | 10270540 |
| chr_1 | g10505 | g10505.t3 | cds | g10505.t3.CDS1 | 10270519 | 10270540 |
| chr_1 | g10505 | g10505.t3 | exon | g10505.t3.exon2 | 10270656 | 10270828 |
| chr_1 | g10505 | g10505.t3 | cds | g10505.t3.CDS2 | 10270656 | 10270828 |
| chr_1 | g10505 | g10505.t3 | exon | g10505.t3.exon3 | 10270911 | 10271150 |
| chr_1 | g10505 | g10505.t3 | cds | g10505.t3.CDS3 | 10270911 | 10271060 |
| chr_1 | g10505 | g10505.t3 | TTS | g10505.t3 | 10272160 | 10272160 |
Sequences
>g10505.t3 Gene=g10505 Length=435
ATGACAGAAAGGGCTGAAGTTGAGGCATTCGATAATGATGCCGTAGAAGAACGTGTGATT
AACGAAGAATACAAGATTTGGAAAAAGAATACGCCATTTCTGTATGATCTAGTAATGACT
CATGCATTGGAATGGCCTTCATTGACTGCTCAATGGTTGCCTGATGTTACAAAACCAGAA
GGAAAAGACTATACCATTTCCAATTTGATGCAAGTCACTATGATAATGAGAAAGGAGAAT
TTGGTGGCTTTGGTAGTGTGTCTGGGAAAATTGAGATTGAAATTAAAATTAATCATGAAG
GTGAAGTTAATCGGGCTCGCTTTATGCCACAGAATCCATGTGTGATTGCAACAAAAACTC
CATCATCCGATGTTCTTGTTTTTGATTATACAAAGCATCCTAGCAAACCCGAACCATCTG
GAGAATGTCATCCAG
>g10505.t3 Gene=g10505 Length=114
MTERAEVEAFDNDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTKPE
GKDYTISNLMQVTMIMRKENLVALVVCLGKLRLKLKLIMKVKLIGLALCHRIHV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g10505.t3 | Gene3D | G3DSA:2.130.10.10 | - | 5 | 92 | 0 |
| 2 | g10505.t3 | PANTHER | PTHR22850 | WD40 REPEAT FAMILY | 8 | 83 | 0 |
| 3 | g10505.t3 | PANTHER | PTHR22850:SF90 | HISTONE-BINDING PROTEIN RBBP4 | 8 | 83 | 0 |
| 1 | g10505.t3 | Pfam | PF12265 | Histone-binding protein RBBP4 or subunit C of CAF1 complex | 22 | 68 | 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: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. There were no conditions that were differentially expressed