Gene loci information

Transcript annotation

  • This transcript has been annotated as CCR4-NOT transcription complex subunit 3.

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 g10665 g10665.t11 isoform g10665.t11 11244174 11245783
chr_1 g10665 g10665.t11 exon g10665.t11.exon1 11244174 11244402
chr_1 g10665 g10665.t11 cds g10665.t11.CDS1 11244176 11244402
chr_1 g10665 g10665.t11 exon g10665.t11.exon2 11244472 11244937
chr_1 g10665 g10665.t11 cds g10665.t11.CDS2 11244472 11244937
chr_1 g10665 g10665.t11 exon g10665.t11.exon3 11244995 11245129
chr_1 g10665 g10665.t11 cds g10665.t11.CDS3 11244995 11245129
chr_1 g10665 g10665.t11 exon g10665.t11.exon4 11245258 11245355
chr_1 g10665 g10665.t11 cds g10665.t11.CDS4 11245258 11245355
chr_1 g10665 g10665.t11 exon g10665.t11.exon5 11245759 11245783
chr_1 g10665 g10665.t11 cds g10665.t11.CDS5 11245759 11245783
chr_1 g10665 g10665.t11 TSS g10665.t11 11246066 11246066
chr_1 g10665 g10665.t11 TTS g10665.t11 NA NA

Sequences

>g10665.t11 Gene=g10665 Length=953
ATGGCAGCCACGAGAAAACTACAAGGTGAAATTGATCGTTGTCTAAAAAAGGTGACGGAA
GGTGTTGAGACATTCGAAGATATTTGGCAAAAGGTTCATAATGCAACCAACAGCAATCAA
AAGGAAAAGTATGAAGCCGACCTCAAAAAAGAAATTAAGAAGCTGCAGAGACTTCGAGAT
CAAATCAAATCATGGATTGCATCAGGAGAAATTAAAGATAAAACATCACTCCTGGATAAT
AGACGACTTATAGAAACGCAAATGGAGAGATTTAAAGTAGTGGAAAGAGAGACGAAAACG
AAAGCATACTCAAAAGAAGGACTTGGAGCTGCACAAAAGCTTGATCCAGCACAGCGAGAA
AAAGAGTCTGTTAGTTGTTGGCTTCAAAATTCCATTAGTTCCCTACAAATACAAACTGAT
CAGTACGAGAGCGAAATTGAATCGCTGCTGGCGAATAAAAAAAAGCGTCTCGATAAAGAG
AAACAAGACAAAATGGACGATCTTAAGTCAAAACTTGAACGTCACAAGTTTCATATAACA
AAACTCGAAACTCTATTAAGGATGCTTGACAATGATAGTGTCGATGTAGAGCAGATAAGA
AAGATTCATGACGATGTGGAGTACTATATTGAATCATCACAAGAACCTGATTTCGAAGAG
AACGAATTCATATATGACGATATTGAAGGTCTTGATGAAGTGGAATTGAGTGGCGGTGAT
CAATGTTTACCATCAGTGGCTGGAACGACTGAGAGTAACAACAGTAATGAAACAGGGGAA
TCGCCGACAAGTACAGAGTCGACTAGTCCTATCAATTCAAATTCACCGGCACTTAACTGC
AGCGCGCCCACTACAGCGAATGTGACAAATAAACATAATCATAGTGGATCAACATCTGTG
GACTATACTGATTTGAAGAAAAATAAAGTAGTGTCTGAAAATTCCATCTCAAA

>g10665.t11 Gene=g10665 Length=317
MAATRKLQGEIDRCLKKVTEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRD
QIKSWIASGEIKDKTSLLDNRRLIETQMERFKVVERETKTKAYSKEGLGAAQKLDPAQRE
KESVSCWLQNSISSLQIQTDQYESEIESLLANKKKRLDKEKQDKMDDLKSKLERHKFHIT
KLETLLRMLDNDSVDVEQIRKIHDDVEYYIESSQEPDFEENEFIYDDIEGLDEVELSGGD
QCLPSVAGTTESNNSNETGESPTSTESTSPINSNSPALNCSAPTTANVTNKHNHSGSTSV
DYTDLKKNKVVSENSIS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g10665.t11 Coils Coil Coil 41 68 -
7 g10665.t11 Coils Coil Coil 132 152 -
5 g10665.t11 Coils Coil Coil 154 174 -
4 g10665.t11 MobiDBLite mobidb-lite consensus disorder prediction 245 317 -
2 g10665.t11 PANTHER PTHR23326:SF23 CCR4-NOT TRANSCRIPTION COMPLEX, SUBUNIT 3B 1 299 4.3E-133
3 g10665.t11 PANTHER PTHR23326 CCR4 NOT-RELATED 1 299 4.3E-133
8 g10665.t11 PIRSF PIRSF005290 NOT_su_3_5 1 316 8.5E-139
1 g10665.t11 Pfam PF04065 Not1 N-terminal domain, CCR4-Not complex component 4 229 4.5E-92

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:0006355 regulation of transcription, DNA-templated BP
GO:0030015 CCR4-NOT core complex CC

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. There were no conditions that were differentially expressed