Gene loci information

Transcript annotation

  • This transcript has been annotated as CCR4-NOT transcription complex subunit 4.

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_2 g4941 g4941.t8 isoform g4941.t8 6117292 6121250
chr_2 g4941 g4941.t8 exon g4941.t8.exon1 6117292 6117700
chr_2 g4941 g4941.t8 cds g4941.t8.CDS1 6117294 6117700
chr_2 g4941 g4941.t8 exon g4941.t8.exon2 6117922 6118711
chr_2 g4941 g4941.t8 cds g4941.t8.CDS2 6117922 6118711
chr_2 g4941 g4941.t8 exon g4941.t8.exon3 6118773 6119560
chr_2 g4941 g4941.t8 cds g4941.t8.CDS3 6118773 6118994
chr_2 g4941 g4941.t8 exon g4941.t8.exon4 6121205 6121250
chr_2 g4941 g4941.t8 TSS g4941.t8 6121253 6121253
chr_2 g4941 g4941.t8 TTS g4941.t8 NA NA

Sequences

>g4941.t8 Gene=g4941 Length=2033
ACTACAAAAAAATCTGAGTAAATTTTCTAAGAAAACTTTACAGAAGTTGGTGTTGCCTTC
CAATTTGCAGTGCTACAATTGAAAACATAAATTCATACCTTCAATATAATAAAAATAATA
CATATTCAGAAAATTGTGTTTGTGTGCATACATAATAACATCGTTGCACATTTCGTGAAA
CCCAATTTTATTATAAACAAGGAGATCACTCCATCTATCTAAGGTTACTTAAGCCTATAG
TCTTTTTCGCTAGGAGAGTGTATACGCGAATTAATACCGATACGTTTGTGCAGTTTAAAT
TTTTCTTCTCACAAATAGTTTTATACACCAAAAGAAACCAACGGTTCAAGTGTCGGAATA
TATATATAAACCTATATTCATACAACCAACGACATCACTGAAACAGACACAAAAACTGAA
CTGTACTCGTAAAAAAGAGAAAAGACGAGAGCGAGAGAAAGAGCGAAAATCCGACAACCA
TAACTATAGAAACAAAACCATCTGATAGAACCAGCTGAAGTGAAATTGTGTTTTTAATTG
GAACTATCGTCAATTTTTTTTTTTCTGCTTAATTCGTAGTTGAATAAAACCGATTGTTTA
CGTGTCATCATCATGAACGTCTTGAATACAAGCGGAGATGAATTACCTGAATGTCCATTG
TGCATGGAGCCTTTAGAAGTTGACGACTTAAGTTTCTATCCGTGTACTTGTGGTTATCAA
ATCTGTCGATTCTGTTGGCATCGGATTAGAACGGATGAGAATGAACTGTGTCCTGCATGC
AGGAAAGCTTATCCTGAAAATCCAGCTGATTTTAAGCCTCTTACTCAAGAGCAAATTTCT
GCTCTGAAAGCTGAGAAGCGTCAGCGCGATCAACAACGTAAGCAGAAGATTACGGAAAAC
CGAAAGCATTTAGCGAATGTTCGTGTTGTCCAGAAGAATCTGGTGTTTGTTGTTGGTCTT
CCTCCTAGACTAGCTGACGCTGAAATTCTTAAGAAGCACGAGTATTTCGGAAAGTATGGA
AAAATTCATAAAGTCGTCATAAATCCAAGTACAACGTATGCGGGTGTGCAAGGTCCATCG
GCATCGGCGTACGTGACTTATGTACATAATAATGATGCGCTCCGGGCAATTCAGAGTGTG
AATAATATTACAATTGACGGACGGTCGATAAAAACAAGTTTAGGAACCACAAAGTATTGT
TCTCATTTTATGAAGAATCAAGTTTGTCCCAAACCGGATTGTATGTATCTTCATGAATTG
GGAGATCCGGAAGCTAGTTTTACGAAGGAGGAAATGCATCAAGGAAAACATCAAGAATAT
GAAAAACGACTGCATGACGCACTTATTGCTCAAATGCAACAGCAGGCTCAAACGCCAACG
AGCAATGGTGGAAGTAGCAATCCAGCTTCGACAAGTCCTGTAAATGCAACAACCACAATT
TCAGGAATTGGCACTTCAAGTAATGGCTTAGTGAAACCGAATAGTGCAGAAACAAAGGAA
CTAACTGCTAGTGGAAGCAATAATGGAACGGTAAATAATGGACAAATTCAAAAAGAGGAG
GCATGGCCAAGCTTATCTACATCACCCGTAACAATAAAGGAAAATAAGACGAGTGTGAAA
GGAAATGCTAATCATAAGGAAAATCTAAAGAACGAAGCAAACAGAAAACACGAGAAGGTG
AAAGGAGAAAAATCAAAATCAAATTCGAAAAGTCAAAAGACTCTATCTTCGTCATCTTCC
TCTTCAACCACAAACAGTACTGCACGGGATAAAAATAAAAATAGTCTACATCTACAGTCA
AATAATAATTTCGAGGATGATTTAGGTGAAACAGACGAAAGCGACGACACTCCGTCTATC
AGTAGCATGACTGATAGCGGTACTGTTAGTGAAAGTGATAGCGGCAAAAGCTCGCCACCA
AGTTCATTCCCTGATCATCCACATAATGCACTTCAAAATAGCAGTAACCTCGTGACGGCA
ACATCACCAGATCAAATAACGAAGAGTCTACAAAATGAACAGCAAACTAAATC

>g4941.t8 Gene=g4941 Length=473
MNVLNTSGDELPECPLCMEPLEVDDLSFYPCTCGYQICRFCWHRIRTDENELCPACRKAY
PENPADFKPLTQEQISALKAEKRQRDQQRKQKITENRKHLANVRVVQKNLVFVVGLPPRL
ADAEILKKHEYFGKYGKIHKVVINPSTTYAGVQGPSASAYVTYVHNNDALRAIQSVNNIT
IDGRSIKTSLGTTKYCSHFMKNQVCPKPDCMYLHELGDPEASFTKEEMHQGKHQEYEKRL
HDALIAQMQQQAQTPTSNGGSSNPASTSPVNATTTISGIGTSSNGLVKPNSAETKELTAS
GSNNGTVNNGQIQKEEAWPSLSTSPVTIKENKTSVKGNANHKENLKNEANRKHEKVKGEK
SKSNSKSQKTLSSSSSSSTTNSTARDKNKNSLHLQSNNNFEDDLGETDESDDTPSISSMT
DSGTVSESDSGKSSPPSSFPDHPHNALQNSSNLVTATSPDQITKSLQNEQQTK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g4941.t8 CDD cd16618 mRING-HC-C4C4_CNOT4 14 58 1.01155E-30
11 g4941.t8 CDD cd12438 RRM_CNOT4 104 201 8.59317E-60
9 g4941.t8 Coils Coil Coil 339 362 -
8 g4941.t8 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 3 78 2.7E-27
7 g4941.t8 Gene3D G3DSA:3.30.70.330 - 110 190 1.7E-27
18 g4941.t8 MobiDBLite mobidb-lite consensus disorder prediction 249 269 -
15 g4941.t8 MobiDBLite mobidb-lite consensus disorder prediction 295 473 -
17 g4941.t8 MobiDBLite mobidb-lite consensus disorder prediction 295 334 -
13 g4941.t8 MobiDBLite mobidb-lite consensus disorder prediction 335 364 -
16 g4941.t8 MobiDBLite mobidb-lite consensus disorder prediction 365 401 -
14 g4941.t8 MobiDBLite mobidb-lite consensus disorder prediction 411 473 -
3 g4941.t8 PANTHER PTHR12603:SF0 CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 4 9 465 4.4E-139
4 g4941.t8 PANTHER PTHR12603 CCR4-NOT TRANSCRIPTION COMPLEX RELATED 9 465 4.4E-139
1 g4941.t8 Pfam PF14570 RING/Ubox like zinc-binding domain 14 60 1.7E-19
2 g4941.t8 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 111 187 6.6E-6
20 g4941.t8 ProSiteProfiles PS50089 Zinc finger RING-type profile. 14 57 10.129
21 g4941.t8 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 109 193 11.094
19 g4941.t8 ProSiteProfiles PS50103 Zinc finger C3H1-type profile. 190 217 9.516
12 g4941.t8 SMART SM00361 rrm2_1 110 189 7.7E-17
6 g4941.t8 SUPERFAMILY SSF57850 RING/U-box 9 73 8.24E-17
5 g4941.t8 SUPERFAMILY SSF54928 RNA-binding domain, RBD 103 187 2.15E-16

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:0046872 metal ion binding MF
GO:0030014 CCR4-NOT complex CC
GO:0004842 ubiquitin-protein transferase activity MF
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