Gene loci information

Transcript annotation

  • This transcript has been annotated as CCR4-NOT transcription complex subunit 7.

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_3 g176 g176.t10 TSS g176.t10 1493551 1493551
chr_3 g176 g176.t10 isoform g176.t10 1493837 1495009
chr_3 g176 g176.t10 exon g176.t10.exon1 1493837 1494069
chr_3 g176 g176.t10 cds g176.t10.CDS1 1493892 1494069
chr_3 g176 g176.t10 exon g176.t10.exon2 1494122 1494299
chr_3 g176 g176.t10 cds g176.t10.CDS2 1494122 1494299
chr_3 g176 g176.t10 exon g176.t10.exon3 1494375 1494682
chr_3 g176 g176.t10 cds g176.t10.CDS3 1494375 1494682
chr_3 g176 g176.t10 exon g176.t10.exon4 1494745 1495009
chr_3 g176 g176.t10 cds g176.t10.CDS4 1494745 1494863
chr_3 g176 g176.t10 TTS g176.t10 1495441 1495441

Sequences

>g176.t10 Gene=g176 Length=984
AACTGAATATATTAATATTATAGCTACTGATCGGATAGACGATAAAATATTAACAATGCC
ATCAGCAATCGTTGCCGCTCAGCAATCCAACCAATTACAACATCAAGGTGATGATATTAA
TCAAGAATGTGGAATACGCGATGTTTGGCGACATAATCTTGAAGAAGAGTTTGTTCTAAT
TCGTAAAATTGTCACAAAATATTGCTATGTTGCAATGGACACTGAATTTCCAGGCGTCGT
TGCTCGGCCAATTGGTGAATTCAGATCAACCTCTGATTATCAGTATCAACTATTAAGATG
CAATGTAGATCTTTTGAAAATCATTCAACTTGGATTAACTTTCATGGATGAAGATGGCAA
CACAGCTCCTGAATTTTCTACTTTTCAATTCAATTTCAAATTCAGTCTTACTGATGATAT
GTATGCTCAAGATTCTATTGATTTACTTCAAAATTCTGGCATACAATTTAAAAAGCACGA
AGAAGATGGCATTGATCCAATTGAATTTGCTGAACTGCTCATGACAAGTGGCATTGTTCT
TATGGATAACATAAAATGGCTCAGTTTCCATTCAGGATATGATTTCGGTTATCTCTTAAA
AGTTCTAACCGATCAGAACTTGCCTAGCGATGAAAGTGAATTCTTTGAACTTTTGCGAAT
CTACTTTCCTACTATTTATGATGTCAAGTATCTAATGAAGTCTTGCAAAAATTTAAAAGG
TGGATTGCAAGAAGTTGCAGAACAATTAGATATCAGAAGAATTGGACCTCAACATCAAGC
TGGTTCCGATTCACTTCTAACTGGAATGGCCTTTTTCAAAATGAGAGAAGTATGGTGAAA
ATGATTTAAGTTAACACCTGAAACTAATATTTTATTAATTTTTTGTAGATGTTTTTTGAA
GATAATATCGATAACGACAAGTACTCAGGTCATTTATTTGGTTTGTCTTTCAATCAGAAT
GATCGTGTAGTGTCGGCTGAATAA

>g176.t10 Gene=g176 Length=260
MPSAIVAAQQSNQLQHQGDDINQECGIRDVWRHNLEEEFVLIRKIVTKYCYVAMDTEFPG
VVARPIGEFRSTSDYQYQLLRCNVDLLKIIQLGLTFMDEDGNTAPEFSTFQFNFKFSLTD
DMYAQDSIDLLQNSGIQFKKHEEDGIDPIEFAELLMTSGIVLMDNIKWLSFHSGYDFGYL
LKVLTDQNLPSDESEFFELLRIYFPTIYDVKYLMKSCKNLKGGLQEVAEQLDIRRIGPQH
QAGSDSLLTGMAFFKMREVW

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g176.t10 Gene3D G3DSA:3.30.420.10 - 14 260 0
3 g176.t10 PANTHER PTHR10797 CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 23 259 0
4 g176.t10 PANTHER PTHR10797:SF1 CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 8 23 259 0
1 g176.t10 Pfam PF04857 CAF1 family ribonuclease 30 146 0
2 g176.t10 Pfam PF04857 CAF1 family ribonuclease 162 253 0
5 g176.t10 SUPERFAMILY SSF53098 Ribonuclease H-like 27 259 0

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

## Warning: Removed 1 row(s) containing missing values (geom_path).

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0004535 poly(A)-specific ribonuclease activity MF
GO:0030014 CCR4-NOT complex CC
GO:0006351 transcription, DNA-templated BP
GO:0003676 nucleic acid 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