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.t5 TSS g10505.t5 10270294 10270294
chr_1 g10505 g10505.t5 isoform g10505.t5 10270519 10271981
chr_1 g10505 g10505.t5 exon g10505.t5.exon1 10270519 10271498
chr_1 g10505 g10505.t5 cds g10505.t5.CDS1 10270634 10271498
chr_1 g10505 g10505.t5 exon g10505.t5.exon2 10271557 10271981
chr_1 g10505 g10505.t5 cds g10505.t5.CDS2 10271557 10271981
chr_1 g10505 g10505.t5 TTS g10505.t5 10272160 10272160

Sequences

>g10505.t5 Gene=g10505 Length=1405
ATGACAGAAAGGGCTGAAGTTGGTAAGTAAAATATTCATTCATTGATTATATTGTCATGA
ATTTCGTTAATATAATAAGCTACAGGACACTTTATTTAAATTTGAGTAGAGAGTAATGTT
TATTAATTCATTTACAGAGGCATTCGATAATGATGCCGTAGAAGAACGTGTGATTAACGA
AGAATACAAGATTTGGAAAAAGAATACGCCATTTCTGTATGATCTAGTAATGACTCATGC
ATTGGAATGGCCTTCATTGACTGCTCAATGGTTGCCTGATGTTACAAAACCAGAAGGAAA
AGACTATACCGTACATCGTCTCATTCTCGGTACTCATACTTCAGATGAACAAAATCATTT
GCTTATTGCTAGCGTTCAATTGCCTAATGAAGATTTCCAATTTGATGCAAGTCACTATGA
TAATGAGAAAGGAGAATTTGGTGGCTTTGGTAGTGTGTCTGGGAAAATTGAGATTGAAAT
TAAAATTAATCATGAAGGTGAAGTTAATCGGGCTCGCTTTATGCCACAGAATCCATGTGT
GATTGCAACAAAAACTCCATCATCCGATGTTCTTGTTTTTGATTATACAAAGCATCCTAG
CAAACCCGAACCATCTGGAGAATGTCATCCAGATTTGCGATTAAGAGGTCATCAAAAAGA
GGGCTATGGATTGTCATGGAATCCAAATTTGAATGGTTATTTACTTTCGGCAAGTGATGA
TCATACTATTTGTTTATGGGACATCAATGCAACACCGAAAGAATATCGAATTATTGATGC
AAAGAACATTTTCACTGGACATACTGCGGTGGTTGAAGATGTTGCATGGCATTTATTGCA
TGAATCTCTTTTCGGTTCAGTTGCTGATGATCAAAAGCTTATGATTTGGGACACTAGAGT
CAACAACACCACAAAACCATCACACACCGTTGATGCGCATACTGCTGAAGTCAATTGCTT
AAGTTTCAATCCTTATTCAGAATTTATTTTGGCTACTGGGTCTGCTGATAAAACAGTAGC
ATTATGGGATTTACGTAATTTGAAGTTGAAACTTCATTCATTTGAATCGCATAAAGACGA
AATTTTCCAAGTTCAATGGTCACCACATAATGAAACCATCTTGGCTAGTAGTGGAACTGA
TCGTCGATTACATGTATGGGATTTGTCAAAGATCGGCGAAGAACAAACTGCTGAAGATGC
GGAAGATGGTCCTCCAGAACTTCTTTTCATTCATGGAGGACATACCGCAAAAATTTCAGA
CTTTTCATGGAATCCTAATGAACCTTGGGTTATTTGCTCGGTTTCAGAGGATAATATCAT
GCAAGTTTGGCAAATGGCGGAAAACATTTACAACGATGAAGAGCCTGAAGCAACTGCAAA
TGAAATCGAACCGGCAAATGCTTAA

>g10505.t5 Gene=g10505 Length=429
MFINSFTEAFDNDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTKPE
GKDYTVHRLILGTHTSDEQNHLLIASVQLPNEDFQFDASHYDNEKGEFGGFGSVSGKIEI
EIKINHEGEVNRARFMPQNPCVIATKTPSSDVLVFDYTKHPSKPEPSGECHPDLRLRGHQ
KEGYGLSWNPNLNGYLLSASDDHTICLWDINATPKEYRIIDAKNIFTGHTAVVEDVAWHL
LHESLFGSVADDQKLMIWDTRVNNTTKPSHTVDAHTAEVNCLSFNPYSEFILATGSADKT
VALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLHVWDLSKIGEEQTAE
DAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEEPEAT
ANEIEPANA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g10505.t5 CDD cd00200 WD40 125 406 4.24736E-40
13 g10505.t5 Gene3D G3DSA:2.130.10.10 - 5 429 8.9E-172
7 g10505.t5 PANTHER PTHR22850:SF82 HISTONE-BINDING PROTEIN RBBP7 12 426 6.1E-273
8 g10505.t5 PANTHER PTHR22850 WD40 REPEAT FAMILY 12 426 6.1E-273
9 g10505.t5 PRINTS PR00320 G protein beta WD-40 repeat signature 196 210 1.7E-8
11 g10505.t5 PRINTS PR00320 G protein beta WD-40 repeat signature 292 306 1.7E-8
10 g10505.t5 PRINTS PR00320 G protein beta WD-40 repeat signature 336 350 1.7E-8
1 g10505.t5 Pfam PF12265 Histone-binding protein RBBP4 or subunit C of CAF1 complex 22 91 4.7E-28
2 g10505.t5 Pfam PF00400 WD domain, G-beta repeat 177 209 0.044
3 g10505.t5 Pfam PF00400 WD domain, G-beta repeat 225 259 0.1
5 g10505.t5 Pfam PF00400 WD domain, G-beta repeat 267 305 2.2E-7
4 g10505.t5 Pfam PF00400 WD domain, G-beta repeat 313 349 1.5E-4
6 g10505.t5 Pfam PF00400 WD domain, G-beta repeat 370 405 0.0019
15 g10505.t5 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 196 210 -
17 g10505.t5 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 292 306 -
16 g10505.t5 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 336 350 -
24 g10505.t5 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 176 415 36.543
28 g10505.t5 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 176 218 12.614
25 g10505.t5 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 226 268 9.305
26 g10505.t5 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 272 308 13.85
27 g10505.t5 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 316 358 12.981
29 g10505.t5 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 373 407 9.272
19 g10505.t5 SMART SM00320 WD40_4 115 156 7.7
18 g10505.t5 SMART SM00320 WD40_4 169 209 4.4E-6
21 g10505.t5 SMART SM00320 WD40_4 219 259 0.082
20 g10505.t5 SMART SM00320 WD40_4 265 305 5.2E-10
22 g10505.t5 SMART SM00320 WD40_4 309 349 2.7E-7
23 g10505.t5 SMART SM00320 WD40_4 366 406 1.8E-4
12 g10505.t5 SUPERFAMILY SSF50978 WD40 repeat-like 117 412 1.12E-55

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