General information for g13356.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as REST corepressor.
Parent gene
- The parent gene g13356 is located on chr_1: 29491829..29492140 (+ 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 | g13356 | g13356.t1 | TSS | g13356.t1 | 29488425 | 29488425 |
| chr_1 | g13356 | g13356.t1 | isoform | g13356.t1 | 29488573 | 29492140 |
| chr_1 | g13356 | g13356.t1 | exon | g13356.t1.exon1 | 29488573 | 29488726 |
| chr_1 | g13356 | g13356.t1 | cds | g13356.t1.CDS1 | 29488573 | 29488726 |
| chr_1 | g13356 | g13356.t1 | exon | g13356.t1.exon2 | 29488814 | 29488864 |
| chr_1 | g13356 | g13356.t1 | cds | g13356.t1.CDS2 | 29488814 | 29488864 |
| chr_1 | g13356 | g13356.t1 | exon | g13356.t1.exon3 | 29489164 | 29489504 |
| chr_1 | g13356 | g13356.t1 | cds | g13356.t1.CDS3 | 29489164 | 29489504 |
| chr_1 | g13356 | g13356.t1 | exon | g13356.t1.exon4 | 29489566 | 29489727 |
| chr_1 | g13356 | g13356.t1 | cds | g13356.t1.CDS4 | 29489566 | 29489727 |
| chr_1 | g13356 | g13356.t1 | exon | g13356.t1.exon5 | 29490579 | 29490769 |
| chr_1 | g13356 | g13356.t1 | cds | g13356.t1.CDS5 | 29490579 | 29490769 |
| chr_1 | g13356 | g13356.t1 | exon | g13356.t1.exon6 | 29490973 | 29491243 |
| chr_1 | g13356 | g13356.t1 | cds | g13356.t1.CDS6 | 29490973 | 29491243 |
| chr_1 | g13356 | g13356.t1 | exon | g13356.t1.exon7 | 29491328 | 29491495 |
| chr_1 | g13356 | g13356.t1 | cds | g13356.t1.CDS7 | 29491328 | 29491495 |
| chr_1 | g13356 | g13356.t1 | exon | g13356.t1.exon8 | 29491567 | 29491746 |
| chr_1 | g13356 | g13356.t1 | cds | g13356.t1.CDS8 | 29491567 | 29491746 |
| chr_1 | g13356 | g13356.t1 | exon | g13356.t1.exon9 | 29491829 | 29492140 |
| chr_1 | g13356 | g13356.t1 | cds | g13356.t1.CDS9 | 29491829 | 29492140 |
| chr_1 | g13356 | g13356.t1 | TTS | g13356.t1 | 29492439 | 29492439 |
Sequences
>g13356.t1 Gene=g13356 Length=1830
ATGAATGTGGATACTAAGGAAGTAAACAAGAACGGAAGAAAGTCGTCAAACACAAACTCA
GCGCCATTGCCTTCACCTACAGCACCTTCAGAAAAGGCTAACAACAAAAATATTCTTGAT
GATCTCACACCAGAAACTTCAGACGACGATAGTAACTCGAGAAAGAATCTCAAACAACAA
AAAAATGGCAAAAGCGAATATGAGGAAAAAATTCGCGTTGGAAAGGACTATCAAGCTATT
GTTCCCGAATATAATCCAAAATTAGAAAATATTACTGAAAAAGCGTTACTTGTATGGTCT
CCAAATACAAAAGACATTCCTGATAGCAGAATTGAAGAATATATACAATTAGCTAAAGAG
CGATATGGTTATAATGCAGAACAAGCGCTTGGTATGTTGTTCTGGCATAAACATGACTTA
GAAAAGGCTGTAATTGATCTAGCAAATTTCACACCGTTTCCTGAAGAATGGACAAAAGAA
GATAAAATTCTGTTTGAACAGGCTTTTCAATTTCATGGTAAATGTTTTCATCGAATACGT
CAAATGCTTCCTGATAAATCAATTGCAAGTTTGGTAAAACATTATTATTCATGGAAAAAG
ACAAGAAGTCGTACAAGCTTAATGGATCGCCAAGAAAAAAGAAAAAATGAAGGCGGTTCT
GAAAATGGCAGTGATGATACCCCCGACAATTCAGATGCCGAAGATAAGGACGTTAAAAGA
ATGACTGGTATAAATAGAATTGAAAATAAACACGATACTGGATATTCATCATCCTCATCT
TCTTCAAATGGAATTTCCAAGCTGTTATCGTTAAATTGTCAAAACTGTAAGGTCTTATGC
AATGAACTTAATCAAACAACAGTTGGAAGCTTTTGTTCGAGTTGCTTTCAGCATTGGAGA
CGCACTGGAGAATTACGACCTGTGCAAGGACCAAATGTTCAGCGACCTCGATCAAAAACC
AATAAACTTTATTACTATCAGGGATATCATGATGGAAGTAGCAAATATAAAAGAAAACCT
CCAAAAGGAATGTATATTAATCATGATGATGTCTTAAAGTTAGCTGCACAAGATTTAAAT
GAATCTGTGACACCTCGAAAGCAACCAGTTCCACATAAATTTGATCTCTTGGCTGAGACT
GATCGCGAAATCAATGTATTGTATAGTCAAATTCAAGCAAACAAACAAAAAATTAGTTCC
GTAAAAGCAGAAAATGAATCGTTTCGTGAAAGTCGCCTACCTGAAGAAATTGCAATGAGT
CGTGTTAATATTCGATGGACAAAAGATGAATTATCTCTTGCCATTCTTGGATTTAGAAAA
TTCGGTCAAAATTTCAAGGCAATTTCTGAAGTAATTTCAACTAAAACTGAATCACATGTT
CGTAAATTTTTCACAAAATATCGTAAAAGTCGCGATTTGGACACAGTGTGTCAAGAGTCA
CAAGCGACAACGTCTGTTATAAATGCACAACAAAAGAGCAATAGTAATGATGGAATGAAA
GATATTGAAGTCATGGAGATTGACTCTGATGATGATTCAAAAAGTGAAAAAAACAATGGA
AACACAGATGAAGCTGGGACAAAGAAAAATAGTGTGAAAGTTCAAAGTAAAGCTAATATT
GTTGTGGTTTCGACTTCAAAGCCATTAAAACGTAAATTGGACTTTTCTGGGAAAGGCAAT
GATGATGTATGTATCATCGATGATGATAATAATCTTGATAAAAAATTTGCACCAATGTTA
TTGAACGATAACAGTGAAATTTCAATTGTTCCGATCAGGAAATCATCAGCTGATGGGAAG
CAAAATGGAAAAGATGCAACTTTTGCATAA
>g13356.t1 Gene=g13356 Length=609
MNVDTKEVNKNGRKSSNTNSAPLPSPTAPSEKANNKNILDDLTPETSDDDSNSRKNLKQQ
KNGKSEYEEKIRVGKDYQAIVPEYNPKLENITEKALLVWSPNTKDIPDSRIEEYIQLAKE
RYGYNAEQALGMLFWHKHDLEKAVIDLANFTPFPEEWTKEDKILFEQAFQFHGKCFHRIR
QMLPDKSIASLVKHYYSWKKTRSRTSLMDRQEKRKNEGGSENGSDDTPDNSDAEDKDVKR
MTGINRIENKHDTGYSSSSSSSNGISKLLSLNCQNCKVLCNELNQTTVGSFCSSCFQHWR
RTGELRPVQGPNVQRPRSKTNKLYYYQGYHDGSSKYKRKPPKGMYINHDDVLKLAAQDLN
ESVTPRKQPVPHKFDLLAETDREINVLYSQIQANKQKISSVKAENESFRESRLPEEIAMS
RVNIRWTKDELSLAILGFRKFGQNFKAISEVISTKTESHVRKFFTKYRKSRDLDTVCQES
QATTSVINAQQKSNSNDGMKDIEVMEIDSDDDSKSEKNNGNTDEAGTKKNSVKVQSKANI
VVVSTSKPLKRKLDFSGKGNDDVCIIDDDNNLDKKFAPMLLNDNSEISIVPIRKSSADGK
QNGKDATFA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g13356.t1 | CDD | cd00167 | SANT | 425 | 467 | 3.72707E-4 |
| 10 | g13356.t1 | Gene3D | G3DSA:1.10.10.60 | - | 155 | 202 | 2.7E-21 |
| 11 | g13356.t1 | Gene3D | G3DSA:1.20.58.1880 | - | 338 | 483 | 9.5E-41 |
| 22 | g13356.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 69 | - |
| 18 | g13356.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 12 | 41 | - |
| 20 | g13356.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 47 | 69 | - |
| 17 | g13356.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 206 | 261 | - |
| 21 | g13356.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 206 | 222 | - |
| 19 | g13356.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 232 | 247 | - |
| 16 | g13356.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 507 | 532 | - |
| 5 | g13356.t1 | PANTHER | PTHR16089:SF13 | REST COREPRESSOR 3 | 56 | 240 | 2.3E-101 |
| 7 | g13356.t1 | PANTHER | PTHR16089 | REST COREPRESSOR COREST PROTEIN-RELATED | 56 | 240 | 2.3E-101 |
| 4 | g13356.t1 | PANTHER | PTHR16089:SF13 | REST COREPRESSOR 3 | 330 | 535 | 2.3E-101 |
| 6 | g13356.t1 | PANTHER | PTHR16089 | REST COREPRESSOR COREST PROTEIN-RELATED | 330 | 535 | 2.3E-101 |
| 1 | g13356.t1 | Pfam | PF01448 | ELM2 domain | 71 | 119 | 2.7E-10 |
| 2 | g13356.t1 | Pfam | PF00249 | Myb-like DNA-binding domain | 156 | 199 | 3.5E-6 |
| 3 | g13356.t1 | Pfam | PF00249 | Myb-like DNA-binding domain | 425 | 468 | 7.0E-6 |
| 23 | g13356.t1 | ProSiteProfiles | PS51156 | ELM2 domain profile. | 69 | 151 | 24.681 |
| 25 | g13356.t1 | ProSiteProfiles | PS51293 | SANT domain profile. | 152 | 203 | 13.216 |
| 24 | g13356.t1 | ProSiteProfiles | PS51293 | SANT domain profile. | 421 | 472 | 10.678 |
| 13 | g13356.t1 | SMART | SM01189 | ELM2_2 | 71 | 122 | 1.0E-13 |
| 14 | g13356.t1 | SMART | SM00717 | sant | 153 | 201 | 8.1E-9 |
| 15 | g13356.t1 | SMART | SM00717 | sant | 422 | 470 | 0.0052 |
| 9 | g13356.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 142 | 201 | 4.04E-12 |
| 8 | g13356.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 425 | 472 | 2.32E-7 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K11829 (REST corepressor 1)
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.
