General information for g4941.t1
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.t1 | TTS | g4941.t1 | 6113719 | 6113719 |
| chr_2 | g4941 | g4941.t1 | isoform | g4941.t1 | 6114616 | 6118994 |
| chr_2 | g4941 | g4941.t1 | exon | g4941.t1.exon1 | 6114616 | 6114777 |
| chr_2 | g4941 | g4941.t1 | cds | g4941.t1.CDS1 | 6114616 | 6114777 |
| chr_2 | g4941 | g4941.t1 | exon | g4941.t1.exon2 | 6114892 | 6114962 |
| chr_2 | g4941 | g4941.t1 | cds | g4941.t1.CDS2 | 6114892 | 6114962 |
| chr_2 | g4941 | g4941.t1 | exon | g4941.t1.exon3 | 6115164 | 6115295 |
| chr_2 | g4941 | g4941.t1 | cds | g4941.t1.CDS3 | 6115164 | 6115295 |
| chr_2 | g4941 | g4941.t1 | exon | g4941.t1.exon4 | 6115447 | 6115572 |
| chr_2 | g4941 | g4941.t1 | cds | g4941.t1.CDS4 | 6115447 | 6115572 |
| chr_2 | g4941 | g4941.t1 | exon | g4941.t1.exon5 | 6115630 | 6115809 |
| chr_2 | g4941 | g4941.t1 | cds | g4941.t1.CDS5 | 6115630 | 6115809 |
| chr_2 | g4941 | g4941.t1 | exon | g4941.t1.exon6 | 6115882 | 6116022 |
| chr_2 | g4941 | g4941.t1 | cds | g4941.t1.CDS6 | 6115882 | 6116022 |
| chr_2 | g4941 | g4941.t1 | exon | g4941.t1.exon7 | 6116103 | 6116396 |
| chr_2 | g4941 | g4941.t1 | cds | g4941.t1.CDS7 | 6116103 | 6116396 |
| chr_2 | g4941 | g4941.t1 | exon | g4941.t1.exon8 | 6116618 | 6117013 |
| chr_2 | g4941 | g4941.t1 | cds | g4941.t1.CDS8 | 6116618 | 6117013 |
| chr_2 | g4941 | g4941.t1 | exon | g4941.t1.exon9 | 6117164 | 6117700 |
| chr_2 | g4941 | g4941.t1 | cds | g4941.t1.CDS9 | 6117164 | 6117700 |
| chr_2 | g4941 | g4941.t1 | exon | g4941.t1.exon10 | 6117922 | 6118711 |
| chr_2 | g4941 | g4941.t1 | cds | g4941.t1.CDS10 | 6117922 | 6118711 |
| chr_2 | g4941 | g4941.t1 | exon | g4941.t1.exon11 | 6118773 | 6118994 |
| chr_2 | g4941 | g4941.t1 | cds | g4941.t1.CDS11 | 6118773 | 6118994 |
| chr_2 | g4941 | g4941.t1 | TSS | g4941.t1 | NA | NA |
Sequences
>g4941.t1 Gene=g4941 Length=3051
ATGAACGTCTTGAATACAAGCGGAGATGAATTACCTGAATGTCCATTGTGCATGGAGCCT
TTAGAAGTTGACGACTTAAGTTTCTATCCGTGTACTTGTGGTTATCAAATCTGTCGATTC
TGTTGGCATCGGATTAGAACGGATGAGAATGAACTGTGTCCTGCATGCAGGAAAGCTTAT
CCTGAAAATCCAGCTGATTTTAAGCCTCTTACTCAAGAGCAAATTTCTGCTCTGAAAGCT
GAGAAGCGTCAGCGCGATCAACAACGTAAGCAGAAGATTACGGAAAACCGAAAGCATTTA
GCGAATGTTCGTGTTGTCCAGAAGAATCTGGTGTTTGTTGTTGGTCTTCCTCCTAGACTA
GCTGACGCTGAAATTCTTAAGAAGCACGAGTATTTCGGAAAGTATGGAAAAATTCATAAA
GTCGTCATAAATCCAAGTACAACGTATGCGGGTGTGCAAGGTCCATCGGCATCGGCGTAC
GTGACTTATGTACATAATAATGATGCGCTCCGGGCAATTCAGAGTGTGAATAATATTACA
ATTGACGGACGGTCGATAAAAACAAGTTTAGGAACCACAAAGTATTGTTCTCATTTTATG
AAGAATCAAGTTTGTCCCAAACCGGATTGTATGTATCTTCATGAATTGGGAGATCCGGAA
GCTAGTTTTACGAAGGAGGAAATGCATCAAGGAAAACATCAAGAATATGAAAAACGACTG
CATGACGCACTTATTGCTCAAATGCAACAGCAGGCTCAAACGCCAACGAGCAATGGTGGA
AGTAGCAATCCAGCTTCGACAAGTCCTGTAAATGCAACAACCACAATTTCAGGAATTGGC
ACTTCAAGTAATGGCTTAGTGAAACCGAATAGTGCAGAAACAAAGGAACTAACTGCTAGT
GGAAGCAATAATGGAACGGTAAATAATGGACAAATTCAAAAAGAGGAGGCATGGCCAAGC
TTATCTACATCACCCGTAACAATAAAGGAAAATAAGACGAGTGTGAAAGGAAATGCTAAT
CATAAGGAAAATCTAAAGAACGAAGCAAACAGAAAACACGAGAAGGTGAAAGGAGAAAAA
TCAAAATCAAATTCGAAAAGTCAAAAGACTCTATCTTCGTCATCTTCCTCTTCAACCACA
AACAGTACTGCACGGGATAAAAATAAAAATAGTCTACATCTACAGTCAAATAATAATTTC
GAGGATGATTTAGGTGAAACAGACGAAAGCGACGACACTCCGTCTATCAGTAGCATGACT
GATAGCGGTACTGTTAGTGAAAGTGATAGCGGCAAAAGCTCGCCACCAAGTTCATTCCCT
GATCATCCACATAATGCACTTCAAAATAGCAGTAACCTCGTGACGGCAACATCACCAGAT
CAAATAACGAAGAGTCTACAAAATGAACAGCAAACTAAATCGATTATATCATCATCCAGT
AGTATTATCGATACGAACGATATAACGTCTCTATATAGTAGTAATAACAATAATGATAAA
GTGAATAATAGCATTCTCAAAGACAGTGTAAATTTAGCGGACACGTCAACACGCCTTGGG
AAACTTAATTTATTTGATGACAACTCAAGTTTCTTCTCAAGAAATTCATTCAATCCATTC
TCAAAACTCGATGGTAGTTCTGATCTTAGAATGAGCAATGCACAATTACCGGACTTATTG
AATGGAACTACTGTTAATAATAACAATAGTATGGGATTAGATCCAAAACAATTACTCAAA
AATTTGGGAAGTTTTGGAAATGAAACACATGATGATTGGGAAAATGCGTTTAAATTAATT
ATTTCAAAAAATTCCTTTAATAAACATTATGATGAACAGCAACATCAACATGAAGATTGG
CTGCGTTTCCAAGAGATAAGAAAACTCCCAAATATGTCAAGTGGTAGTGGACTTGGATTG
AATCAATTCAACAACATGTTCAATAATGATAATAATATTGATAGCATGCTTACGCAAAAT
GAAATCAATCGAATGATGTTCAATAATCAATTTTCTCAACAACAACAGCAGCAGCAGCAA
CAACAGAGGATTAATCATAATAATTCAGATTTGAATCTTGTACATCCAAATATGTCAAAA
TTCTTTGATTTCCACAAACAACAGCAGCAACAAAATCAATTCATGATGAATTCAAATCCA
GTAACAGATCAACTTAATATGGCAAATCTATTAGATAATCATCATCGTATGAATCCCAAT
TTTATGGATCAATCAAATGGATTATCACATTTACAAAAGCAAAGATTAATGAATATGAGT
AACAAGTACGATGGTAACAGCGGTATGCCTTTTAGTTCAAATCCACAGAGTCGTATGCAT
ACAAATAATTCAGCACAATTTTCTGTTGAAGATGATTTAGGTTTTGATCCAATTAAAGAA
AGTCATAAGGGATTATCGGAACTAATAAATGATGAGCAGCAACAAATGATTAATAATGGA
CAACGGTCAACATCAAGAATGCCACCGCCACCAGGTTTCAACCATTTGCAATCTCAATCT
GGATTTAATAATTATGGTGCTGCATCACCAAGAACACAAAGTGGAAGTAAATTTCCATTT
GTCAACATGCAAGGGACATCACAAAATAACTGGCCAATGCACATGGGTTTTCAAAACAAT
TCAGATGCATTCTCGCATCAACAGAATAGCCAGCACAAATCAGCAGATTGGACATCAATG
GATCCAGCTATAGTTTCGTTCAGACAGTTTTCACAATTTAATCCTCAGCAGCAGCAACAA
ACTCAAAATCAACCAAACAATAATGATTTGTTCCAAATGTCTCAAATGAATCAACAAGGT
TTCGGTCATCATCACGGTATGAATATGAATATGCAAAACAACATGCAGTCTCAAACTTCG
CCAGCACAGGTCTTTTCTCATTCAAATTTAATGAACAACTATCACATGAATAATATGGCA
AATGGCTTTCCCAACAATAGTTATGACAAATTTTCCATGTCAAATATTCCTCCACCTGGT
TTCCAACAAAGCAACAACACTAACAATAAAAAGACAGAATGCATTAATTAA
>g4941.t1 Gene=g4941 Length=1016
MNVLNTSGDELPECPLCMEPLEVDDLSFYPCTCGYQICRFCWHRIRTDENELCPACRKAY
PENPADFKPLTQEQISALKAEKRQRDQQRKQKITENRKHLANVRVVQKNLVFVVGLPPRL
ADAEILKKHEYFGKYGKIHKVVINPSTTYAGVQGPSASAYVTYVHNNDALRAIQSVNNIT
IDGRSIKTSLGTTKYCSHFMKNQVCPKPDCMYLHELGDPEASFTKEEMHQGKHQEYEKRL
HDALIAQMQQQAQTPTSNGGSSNPASTSPVNATTTISGIGTSSNGLVKPNSAETKELTAS
GSNNGTVNNGQIQKEEAWPSLSTSPVTIKENKTSVKGNANHKENLKNEANRKHEKVKGEK
SKSNSKSQKTLSSSSSSSTTNSTARDKNKNSLHLQSNNNFEDDLGETDESDDTPSISSMT
DSGTVSESDSGKSSPPSSFPDHPHNALQNSSNLVTATSPDQITKSLQNEQQTKSIISSSS
SIIDTNDITSLYSSNNNNDKVNNSILKDSVNLADTSTRLGKLNLFDDNSSFFSRNSFNPF
SKLDGSSDLRMSNAQLPDLLNGTTVNNNNSMGLDPKQLLKNLGSFGNETHDDWENAFKLI
ISKNSFNKHYDEQQHQHEDWLRFQEIRKLPNMSSGSGLGLNQFNNMFNNDNNIDSMLTQN
EINRMMFNNQFSQQQQQQQQQQRINHNNSDLNLVHPNMSKFFDFHKQQQQQNQFMMNSNP
VTDQLNMANLLDNHHRMNPNFMDQSNGLSHLQKQRLMNMSNKYDGNSGMPFSSNPQSRMH
TNNSAQFSVEDDLGFDPIKESHKGLSELINDEQQQMINNGQRSTSRMPPPPGFNHLQSQS
GFNNYGAASPRTQSGSKFPFVNMQGTSQNNWPMHMGFQNNSDAFSHQQNSQHKSADWTSM
DPAIVSFRQFSQFNPQQQQQTQNQPNNNDLFQMSQMNQQGFGHHHGMNMNMQNNMQSQTS
PAQVFSHSNLMNNYHMNNMANGFPNNSYDKFSMSNIPPPGFQQSNNTNNKKTECIN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g4941.t1 | CDD | cd16618 | mRING-HC-C4C4_CNOT4 | 14 | 58 | 4.8719E-31 |
| 11 | g4941.t1 | CDD | cd12438 | RRM_CNOT4 | 104 | 201 | 4.07982E-58 |
| 9 | g4941.t1 | Coils | Coil | Coil | 339 | 362 | - |
| 8 | g4941.t1 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 3 | 78 | 7.6E-27 |
| 7 | g4941.t1 | Gene3D | G3DSA:3.30.70.330 | - | 110 | 190 | 5.0E-27 |
| 18 | g4941.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 249 | 269 | - |
| 16 | g4941.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 295 | 441 | - |
| 17 | g4941.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 295 | 334 | - |
| 13 | g4941.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 335 | 364 | - |
| 15 | g4941.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 365 | 401 | - |
| 14 | g4941.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 411 | 441 | - |
| 3 | g4941.t1 | PANTHER | PTHR12603:SF0 | CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 4 | 9 | 1005 | 2.7E-136 |
| 4 | g4941.t1 | PANTHER | PTHR12603 | CCR4-NOT TRANSCRIPTION COMPLEX RELATED | 9 | 1005 | 2.7E-136 |
| 1 | g4941.t1 | Pfam | PF14570 | RING/Ubox like zinc-binding domain | 14 | 60 | 4.4E-19 |
| 2 | g4941.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 111 | 187 | 1.9E-5 |
| 20 | g4941.t1 | ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 14 | 57 | 10.129 |
| 21 | g4941.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 109 | 193 | 11.094 |
| 19 | g4941.t1 | ProSiteProfiles | PS50103 | Zinc finger C3H1-type profile. | 190 | 217 | 9.516 |
| 12 | g4941.t1 | SMART | SM00361 | rrm2_1 | 110 | 189 | 7.7E-17 |
| 6 | g4941.t1 | SUPERFAMILY | SSF57850 | RING/U-box | 9 | 73 | 2.36E-16 |
| 5 | g4941.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 103 | 187 | 6.45E-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.
