General information for g4941.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as CCR4-NOT transcription complex subunit 4.
Parent gene
- The parent gene g4941 is located on chr_2: 6118788..6121250 (- strand)
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.t12 | isoform | g4941.t12 | 6117928 | 6121250 |
| chr_2 | g4941 | g4941.t12 | exon | g4941.t12.exon1 | 6117928 | 6118711 |
| chr_2 | g4941 | g4941.t12 | cds | g4941.t12.CDS1 | 6117929 | 6118711 |
| chr_2 | g4941 | g4941.t12 | exon | g4941.t12.exon2 | 6118773 | 6119027 |
| chr_2 | g4941 | g4941.t12 | cds | g4941.t12.CDS2 | 6118773 | 6118994 |
| chr_2 | g4941 | g4941.t12 | exon | g4941.t12.exon3 | 6121205 | 6121250 |
| chr_2 | g4941 | g4941.t12 | TSS | g4941.t12 | 6121253 | 6121253 |
| chr_2 | g4941 | g4941.t12 | TTS | g4941.t12 | NA | NA |
Sequences
>g4941.t12 Gene=g4941 Length=1085
ACTACAAAAAAATCTGAGTAAATTTTCTAAGAAAACTTTACAGAAGTTGAATAAAACCGA
TTGTTTACGTGTCATCATCATGAACGTCTTGAATACAAGCGGAGATGAATTACCTGAATG
TCCATTGTGCATGGAGCCTTTAGAAGTTGACGACTTAAGTTTCTATCCGTGTACTTGTGG
TTATCAAATCTGTCGATTCTGTTGGCATCGGATTAGAACGGATGAGAATGAACTGTGTCC
TGCATGCAGGAAAGCTTATCCTGAAAATCCAGCTGATTTTAAGCCTCTTACTCAAGAGCA
AATTTCTGCTCTGAAAGCTGAGAAGCGTCAGCGCGATCAACAACGTAAGCAGAAGATTAC
GGAAAACCGAAAGCATTTAGCGAATGTTCGTGTTGTCCAGAAGAATCTGGTGTTTGTTGT
TGGTCTTCCTCCTAGACTAGCTGACGCTGAAATTCTTAAGAAGCACGAGTATTTCGGAAA
GTATGGAAAAATTCATAAAGTCGTCATAAATCCAAGTACAACGTATGCGGGTGTGCAAGG
TCCATCGGCATCGGCGTACGTGACTTATGTACATAATAATGATGCGCTCCGGGCAATTCA
GAGTGTGAATAATATTACAATTGACGGACGGTCGATAAAAACAAGTTTAGGAACCACAAA
GTATTGTTCTCATTTTATGAAGAATCAAGTTTGTCCCAAACCGGATTGTATGTATCTTCA
TGAATTGGGAGATCCGGAAGCTAGTTTTACGAAGGAGGAAATGCATCAAGGAAAACATCA
AGAATATGAAAAACGACTGCATGACGCACTTATTGCTCAAATGCAACAGCAGGCTCAAAC
GCCAACGAGCAATGGTGGAAGTAGCAATCCAGCTTCGACAAGTCCTGTAAATGCAACAAC
CACAATTTCAGGAATTGGCACTTCAAGTAATGGCTTAGTGAAACCGAATAGTGCAGAAAC
AAAGGAACTAACTGCTAGTGGAAGCAATAATGGAACGGTAAATAATGGACAAATTCAAAA
AGAGGAGGCATGGCCAAGCTTATCTACATCACCCGTAACAATAAAGGAAAATAAGACGAG
TGTGA
>g4941.t12 Gene=g4941 Length=335
MNVLNTSGDELPECPLCMEPLEVDDLSFYPCTCGYQICRFCWHRIRTDENELCPACRKAY
PENPADFKPLTQEQISALKAEKRQRDQQRKQKITENRKHLANVRVVQKNLVFVVGLPPRL
ADAEILKKHEYFGKYGKIHKVVINPSTTYAGVQGPSASAYVTYVHNNDALRAIQSVNNIT
IDGRSIKTSLGTTKYCSHFMKNQVCPKPDCMYLHELGDPEASFTKEEMHQGKHQEYEKRL
HDALIAQMQQQAQTPTSNGGSSNPASTSPVNATTTISGIGTSSNGLVKPNSAETKELTAS
GSNNGTVNNGQIQKEEAWPSLSTSPVTIKENKTSV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g4941.t12 | CDD | cd16618 | mRING-HC-C4C4_CNOT4 | 14 | 58 | 5.90461E-30 |
| 10 | g4941.t12 | CDD | cd12438 | RRM_CNOT4 | 104 | 201 | 8.96059E-61 |
| 8 | g4941.t12 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 3 | 78 | 1.5E-27 |
| 7 | g4941.t12 | Gene3D | G3DSA:3.30.70.330 | - | 110 | 190 | 9.7E-28 |
| 12 | g4941.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 249 | 335 | - |
| 3 | g4941.t12 | PANTHER | PTHR12603:SF0 | CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 4 | 9 | 324 | 5.8E-136 |
| 4 | g4941.t12 | PANTHER | PTHR12603 | CCR4-NOT TRANSCRIPTION COMPLEX RELATED | 9 | 324 | 5.8E-136 |
| 1 | g4941.t12 | Pfam | PF14570 | RING/Ubox like zinc-binding domain | 14 | 60 | 1.0E-19 |
| 2 | g4941.t12 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 111 | 187 | 3.7E-6 |
| 14 | g4941.t12 | ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 14 | 57 | 10.129 |
| 15 | g4941.t12 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 109 | 193 | 11.094 |
| 13 | g4941.t12 | ProSiteProfiles | PS50103 | Zinc finger C3H1-type profile. | 190 | 217 | 9.516 |
| 11 | g4941.t12 | SMART | SM00361 | rrm2_1 | 110 | 189 | 7.7E-17 |
| 6 | g4941.t12 | SUPERFAMILY | SSF57850 | RING/U-box | 9 | 73 | 4.71E-17 |
| 5 | g4941.t12 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 103 | 187 | 1.17E-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
- This transcript has been annotated with K10643 (CCR4-NOT transcription complex subunit 4)
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.
