General information for g10665.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as CCR4-NOT transcription complex subunit 3.
Parent gene
- The parent gene g10665 is located on chr_1: 11244488..11245783 (- 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_1 | g10665 | g10665.t3 | TTS | g10665.t3 | 11241491 | 11241491 |
| chr_1 | g10665 | g10665.t3 | isoform | g10665.t3 | 11242093 | 11245783 |
| chr_1 | g10665 | g10665.t3 | exon | g10665.t3.exon1 | 11242093 | 11242191 |
| chr_1 | g10665 | g10665.t3 | cds | g10665.t3.CDS1 | 11242093 | 11242191 |
| chr_1 | g10665 | g10665.t3 | exon | g10665.t3.exon2 | 11242256 | 11242465 |
| chr_1 | g10665 | g10665.t3 | cds | g10665.t3.CDS2 | 11242256 | 11242465 |
| chr_1 | g10665 | g10665.t3 | exon | g10665.t3.exon3 | 11242528 | 11242638 |
| chr_1 | g10665 | g10665.t3 | cds | g10665.t3.CDS3 | 11242528 | 11242638 |
| chr_1 | g10665 | g10665.t3 | exon | g10665.t3.exon4 | 11242706 | 11243340 |
| chr_1 | g10665 | g10665.t3 | cds | g10665.t3.CDS4 | 11242706 | 11243340 |
| chr_1 | g10665 | g10665.t3 | exon | g10665.t3.exon5 | 11243760 | 11244054 |
| chr_1 | g10665 | g10665.t3 | cds | g10665.t3.CDS5 | 11243760 | 11244054 |
| chr_1 | g10665 | g10665.t3 | exon | g10665.t3.exon6 | 11244173 | 11244402 |
| chr_1 | g10665 | g10665.t3 | cds | g10665.t3.CDS6 | 11244173 | 11244402 |
| chr_1 | g10665 | g10665.t3 | exon | g10665.t3.exon7 | 11244472 | 11244937 |
| chr_1 | g10665 | g10665.t3 | cds | g10665.t3.CDS7 | 11244472 | 11244937 |
| chr_1 | g10665 | g10665.t3 | exon | g10665.t3.exon8 | 11244995 | 11245129 |
| chr_1 | g10665 | g10665.t3 | cds | g10665.t3.CDS8 | 11244995 | 11245129 |
| chr_1 | g10665 | g10665.t3 | exon | g10665.t3.exon9 | 11245258 | 11245355 |
| chr_1 | g10665 | g10665.t3 | cds | g10665.t3.CDS9 | 11245258 | 11245355 |
| chr_1 | g10665 | g10665.t3 | exon | g10665.t3.exon10 | 11245759 | 11245783 |
| chr_1 | g10665 | g10665.t3 | cds | g10665.t3.CDS10 | 11245759 | 11245783 |
| chr_1 | g10665 | g10665.t3 | TSS | g10665.t3 | 11246066 | 11246066 |
Sequences
>g10665.t3 Gene=g10665 Length=2304
ATGGCAGCCACGAGAAAACTACAAGGTGAAATTGATCGTTGTCTAAAAAAGGTGACGGAA
GGTGTTGAGACATTCGAAGATATTTGGCAAAAGGTTCATAATGCAACCAACAGCAATCAA
AAGGAAAAGTATGAAGCCGACCTCAAAAAAGAAATTAAGAAGCTGCAGAGACTTCGAGAT
CAAATCAAATCATGGATTGCATCAGGAGAAATTAAAGATAAAACATCACTCCTGGATAAT
AGACGACTTATAGAAACGCAAATGGAGAGATTTAAAGTAGTGGAAAGAGAGACGAAAACG
AAAGCATACTCAAAAGAAGGACTTGGAGCTGCACAAAAGCTTGATCCAGCACAGCGAGAA
AAAGAGTCTGTTAGTTGTTGGCTTCAAAATTCCATTAGTTCCCTACAAATACAAACTGAT
CAGTACGAGAGCGAAATTGAATCGCTGCTGGCGAATAAAAAAAAGCGTCTCGATAAAGAG
AAACAAGACAAAATGGACGATCTTAAGTCAAAACTTGAACGTCACAAGTTTCATATAACA
AAACTCGAAACTCTATTAAGGATGCTTGACAATGATAGTGTCGATGTAGAGCAGATAAGA
AAGATTCATGACGATGTGGAGTACTATATTGAATCATCACAAGAACCTGATTTCGAAGAG
AACGAATTCATATATGACGATATTGAAGGTCTTGATGAAGTGGAATTGAGTGGCGGTGAT
CAATGTTTACCATCAGTGGCTGGAACGACTGAGAGTAACAACAGTAATGAAACAGGGGAA
TCGCCGACAAGTACAGAGTCGACTAGTCCTATCAATTCAAATTCACCGGCACTTAACTGC
AGCGCGCCCACTACAGCGAATGTGACAAATAAACATAATCATAGTGGATCAACATCTGTG
GACTATACTGATTTGAAGAAAAATAAAGTAGTGTCTGAAAATTCCATCTCAAAGCCCTTA
AAGCCGACAGCTGTAAGAGCGAAAATTGAAAACAACATTACTTCTTCAATACCAGCAACA
ACTACTTCGCTCAACAACAACAATAATAATAACAACAACAGTAATAGTACGTCCACTGCT
TCCGTTGCTGCCTCGCATAATACTAAGCCATTGATAACGCCTAGTAAAATCCAACCTTCA
GCTGCCCAAATTTTGGCGAATAATACAAACAACAATAGCATACAATCACCTTCAACTATA
CTACCTAATCCGCCTATAGCATTTGCAGCAGTTGCTAAACAAAATCCAGATATTTTACAG
CATACGTCGTCGGTTGTGCACAGTAATAATTCTAGTAATGTGATGTCAAATAATAATAAT
GCGACAATTGAGAATCATTTGAACAATAACAACAGTTCTCTGAGTAATTGTGTTTCTCCA
ACAAGTAATAATCAGTCCGCAGCAATAAGTAGCAGTCGAACTTCTCCGACGAGTCTCATG
TCTCCACCACAGCAGCAAGTCCAAGTTCTAAACGGACCCTCACAAAAATTACAGCAAGTA
ACGTCATCATCTCAGCAGCAACAGCAGTCAAATGCAAATGCAGTGTCTCATTCTTCTGAT
CCATCCAGTGAGCCTATGTCAACATTAAAAACAATTGCACAAGAAGTGGTGAACAGAACG
AACGTAAGTTTAGTTACTCCGCCAATTATGTCTCAAAATCTTCAACAGCAGCAGCAGCAG
CAGCAACAACAACAACAACAATCTTATGTAATGGACACATCGTCAATTGATCCATCTTCA
ACTGCCAACATCAATAGTTTGATAAATGCCACCAATGCATCGGGCACAACTAAAACTGCG
GGAACTAATGAAGCTTTAATTCCTCCTCTACTCGGTGTAGCACCACTTGGCCCATCACCG
CTTCAAAAAGATCATCAAAATCAATTTCAAATGATGGAAGCAGCTTATTATCATCTCCCA
TCACCAAGCGATTCCGAACGCCTGCGGTCATATCTACAAAGGCAGCCAGTTCAAACTCCA
TTACATTATCCACAGACTCAACTTCCACATTCGGATACAATAGATTTCTTTCAACGTCTC
GCGACCGAAACTTTATTCTTTGTGTTTTATTATATGGAAGGAACAAAGGCTCAATATCTT
GCTGCAAAAGCTCTTAAAAAGCAAAGTTGGAGATTTCATACAAAATATATGATGTGGTTT
CAACGTCATGAAGAACCTAAAATTATTAATGAAGAATTTGAGCAGGGCACTTACATATAC
TTTGATTATGAAAAGTGGGGTCAACGAAAAAAAGAGGGATTTACGTTTGAGTATAAGTAC
TTAGAAGATAAAGACCTGAATTGA
>g10665.t3 Gene=g10665 Length=767
MAATRKLQGEIDRCLKKVTEGVETFEDIWQKVHNATNSNQKEKYEADLKKEIKKLQRLRD
QIKSWIASGEIKDKTSLLDNRRLIETQMERFKVVERETKTKAYSKEGLGAAQKLDPAQRE
KESVSCWLQNSISSLQIQTDQYESEIESLLANKKKRLDKEKQDKMDDLKSKLERHKFHIT
KLETLLRMLDNDSVDVEQIRKIHDDVEYYIESSQEPDFEENEFIYDDIEGLDEVELSGGD
QCLPSVAGTTESNNSNETGESPTSTESTSPINSNSPALNCSAPTTANVTNKHNHSGSTSV
DYTDLKKNKVVSENSISKPLKPTAVRAKIENNITSSIPATTTSLNNNNNNNNNSNSTSTA
SVAASHNTKPLITPSKIQPSAAQILANNTNNNSIQSPSTILPNPPIAFAAVAKQNPDILQ
HTSSVVHSNNSSNVMSNNNNATIENHLNNNNSSLSNCVSPTSNNQSAAISSSRTSPTSLM
SPPQQQVQVLNGPSQKLQQVTSSSQQQQQSNANAVSHSSDPSSEPMSTLKTIAQEVVNRT
NVSLVTPPIMSQNLQQQQQQQQQQQQQSYVMDTSSIDPSSTANINSLINATNASGTTKTA
GTNEALIPPLLGVAPLGPSPLQKDHQNQFQMMEAAYYHLPSPSDSERLRSYLQRQPVQTP
LHYPQTQLPHSDTIDFFQRLATETLFFVFYYMEGTKAQYLAAKALKKQSWRFHTKYMMWF
QRHEEPKIINEEFEQGTYIYFDYEKWGQRKKEGFTFEYKYLEDKDLN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g10665.t3 | Coils | Coil | Coil | 41 | 68 | - |
| 13 | g10665.t3 | Coils | Coil | Coil | 132 | 152 | - |
| 11 | g10665.t3 | Coils | Coil | Coil | 154 | 174 | - |
| 10 | g10665.t3 | Gene3D | G3DSA:2.30.30.1020 | - | 618 | 762 | 7.6E-62 |
| 7 | g10665.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 245 | 275 | - |
| 9 | g10665.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 456 | 527 | - |
| 8 | g10665.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 553 | 578 | - |
| 4 | g10665.t3 | PANTHER | PTHR23326 | CCR4 NOT-RELATED | 5 | 432 | 5.4E-218 |
| 6 | g10665.t3 | PANTHER | PTHR23326:SF24 | CCR4-NOT TRANSCRIPTION COMPLEX, SUBUNIT 3A | 5 | 432 | 5.4E-218 |
| 3 | g10665.t3 | PANTHER | PTHR23326 | CCR4 NOT-RELATED | 592 | 766 | 5.4E-218 |
| 5 | g10665.t3 | PANTHER | PTHR23326:SF24 | CCR4-NOT TRANSCRIPTION COMPLEX, SUBUNIT 3A | 592 | 766 | 5.4E-218 |
| 15 | g10665.t3 | PIRSF | PIRSF005290 | NOT_su_3_5 | 1 | 586 | 1.6E-143 |
| 14 | g10665.t3 | PIRSF | PIRSF005290 | NOT_su_3_5 | 245 | 767 | 2.7E-87 |
| 1 | g10665.t3 | Pfam | PF04065 | Not1 N-terminal domain, CCR4-Not complex component | 4 | 229 | 3.9E-91 |
| 2 | g10665.t3 | Pfam | PF04153 | NOT2 / NOT3 / NOT5 family | 636 | 761 | 1.8E-39 |
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
- This transcript has been annotated with K12580 (CCR4-NOT transcription complex subunit 3)
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.
