Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable histone-binding protein Caf1.

Parent gene

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.t4 TSS g10505.t4 10270294 10270294
chr_1 g10505 g10505.t4 isoform g10505.t4 10270519 10271489
chr_1 g10505 g10505.t4 exon g10505.t4.exon1 10270519 10270540
chr_1 g10505 g10505.t4 cds g10505.t4.CDS1 10270519 10270540
chr_1 g10505 g10505.t4 exon g10505.t4.exon2 10270656 10271489
chr_1 g10505 g10505.t4 cds g10505.t4.CDS2 10270656 10271488
chr_1 g10505 g10505.t4 TTS g10505.t4 10272160 10272160

Sequences

>g10505.t4 Gene=g10505 Length=856
ATGACAGAAAGGGCTGAAGTTGAGGCATTCGATAATGATGCCGTAGAAGAACGTGTGATT
AACGAAGAATACAAGATTTGGAAAAAGAATACGCCATTTCTGTATGATCTAGTAATGACT
CATGCATTGGAATGGCCTTCATTGACTGCTCAATGGTTGCCTGATGTTACAAAACCAGAA
GGAAAAGACTATACCGTACATCGTCTCATTCTCGGTACTCATACTTCAGATGAACAAAAT
CATTTGCTTATTGCTAGCGTTCAATTGCCTAATGAAGATTTCCAATTTGATGCAAGTCAC
TATGATAATGAGAAAGGAGAATTTGGTGGCTTTGGTAGTGTGTCTGGGAAAATTGAGATT
GAAATTAAAATTAATCATGAAGGTGAAGTTAATCGGGCTCGCTTTATGCCACAGAATCCA
TGTGTGATTGCAACAAAAACTCCATCATCCGATGTTCTTGTTTTTGATTATACAAAGCAT
CCTAGCAAACCCGAACCATCTGGAGAATGTCATCCAGATTTGCGATTAAGAGGTCATCAA
AAAGAGGGCTATGGATTGTCATGGAATCCAAATTTGAATGGTTATTTACTTTCGGCAAGT
GATGATCATACTATTTGTTTATGGGACATCAATGCAACACCGAAAGAATATCGAATTATT
GATGCAAAGAACATTTTCACTGGACATACTGCGGTGGTTGAAGATGTTGCATGGCATTTA
TTGCATGAATCTCTTTTCGGTTCAGTTGCTGATGATCAAAAGCTTATGATTTGGGACACT
AGAGTCAACAACACCACAAAACCATCACACACCGTTGATGCGCATACTGCTGAAGTCAAT
TGCTTAAGTTTCAATC

>g10505.t4 Gene=g10505 Length=285
MTERAEVEAFDNDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTKPE
GKDYTVHRLILGTHTSDEQNHLLIASVQLPNEDFQFDASHYDNEKGEFGGFGSVSGKIEI
EIKINHEGEVNRARFMPQNPCVIATKTPSSDVLVFDYTKHPSKPEPSGECHPDLRLRGHQ
KEGYGLSWNPNLNGYLLSASDDHTICLWDINATPKEYRIIDAKNIFTGHTAVVEDVAWHL
LHESLFGSVADDQKLMIWDTRVNNTTKPSHTVDAHTAEVNCLSFN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g10505.t4 Gene3D G3DSA:2.130.10.10 - 5 285 1.2E-107
4 g10505.t4 PANTHER PTHR22850:SF82 HISTONE-BINDING PROTEIN RBBP7 8 285 5.1E-176
5 g10505.t4 PANTHER PTHR22850 WD40 REPEAT FAMILY 8 285 5.1E-176
1 g10505.t4 Pfam PF12265 Histone-binding protein RBBP4 or subunit C of CAF1 complex 22 91 2.4E-28
3 g10505.t4 Pfam PF00400 WD domain, G-beta repeat 176 209 0.025
2 g10505.t4 Pfam PF00400 WD domain, G-beta repeat 225 259 0.058
10 g10505.t4 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 196 210 -
12 g10505.t4 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 176 285 18.853
14 g10505.t4 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 176 218 12.614
13 g10505.t4 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 226 268 9.305
8 g10505.t4 SMART SM00320 WD40_4 115 156 7.7
7 g10505.t4 SMART SM00320 WD40_4 169 209 4.4E-6
9 g10505.t4 SMART SM00320 WD40_4 219 259 0.082
6 g10505.t4 SUPERFAMILY SSF50978 WD40 repeat-like 120 285 9.47E-26

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

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.

Raw TPM values