General information for g469.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g469 is located on chr_3: 3557937..3558972 (- 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_3 | g469 | g469.t1 | TTS | g469.t1 | 3557861 | 3557861 |
| chr_3 | g469 | g469.t1 | isoform | g469.t1 | 3557937 | 3558972 |
| chr_3 | g469 | g469.t1 | exon | g469.t1.exon1 | 3557937 | 3558759 |
| chr_3 | g469 | g469.t1 | cds | g469.t1.CDS1 | 3557937 | 3558759 |
| chr_3 | g469 | g469.t1 | exon | g469.t1.exon2 | 3558815 | 3558972 |
| chr_3 | g469 | g469.t1 | cds | g469.t1.CDS2 | 3558815 | 3558972 |
| chr_3 | g469 | g469.t1 | TSS | g469.t1 | 3559061 | 3559061 |
Sequences
>g469.t1 Gene=g469 Length=981
ATGGATTCAACTGTTATAACAAACCATCCTCTATTAAAGAAAGTTCCAGGCGAGCCGAAA
AAGGAAAAGGAATATGCATTAAACAAAGATTTAACAAAATTATCAAGGCGCGAATTACTC
GATTTGAAAAGTCGTCAAACAAAATTACTGGAAAATAGACATTTTATAAACAGACTTCCA
GATAAAGGTGAAAAAATAAAGAATTTGTATGATCGGATTGTTGAAGCTTTAGAATACAGA
ACTGACATTGAAAATGCTTCAAAATTACTGTCGAAACTCAATATAGGCTCAAATAATCTT
AACAATCTTGAATGGGAAGGATCAATTCAAATAAAAAAGCCACAGACTCTCGATAGCGAC
GATGAGGAACAAAACCCATTAGAAATTCTCGCCTCATCTAATAGCACTTTTAAAAATCAA
AAAATTGTCAAGAAAAGTAATGATCCAAATGAGAAACCACTAATAACAGAAGAAGATCTT
AAAGAAGCTAATGAGATAATCAATGGTGAACTTCATTTAAATCCAGTTGATGAAAAAATT
TGTGAAAGAGAGAAACTGGAATTAGAATATAGATTTCTTCCTTATAAGAGTACTGAATTT
AAAAAGAAGAAAGAAGAGGACGATAAAAAGAAGGAACCAAAAAAACGTGAAGTTACAGCA
GCAACACCGCCAGTAATTTTGAAAGGAACAGTACCTTTGACATTAAAAGAGTCTCTTGAT
ATTGAACTGCATCATCAGACAGTAATGAAACAATTATTAGAAAAACAAGCCGTTGAACGA
CTTGAGGCAAAGATGAAAGAACTTAAAGCTGCTGGTTTAGAAATTTCTTCATCACCAGAA
ATTGTGCCACGATCAAAAGTTTTAAGCATGAAAAAATATCGTTTACCTGATCCAATTATC
GATGAATGTGATCTTGTTGAAGATGAAGACGAAGATAAAAGTGATGATAGTCTTACAGAT
GAAGAAAATGAAGAGTACTAA
>g469.t1 Gene=g469 Length=326
MDSTVITNHPLLKKVPGEPKKEKEYALNKDLTKLSRRELLDLKSRQTKLLENRHFINRLP
DKGEKIKNLYDRIVEALEYRTDIENASKLLSKLNIGSNNLNNLEWEGSIQIKKPQTLDSD
DEEQNPLEILASSNSTFKNQKIVKKSNDPNEKPLITEEDLKEANEIINGELHLNPVDEKI
CEREKLELEYRFLPYKSTEFKKKKEEDDKKKEPKKREVTAATPPVILKGTVPLTLKESLD
IELHHQTVMKQLLEKQAVERLEAKMKELKAAGLEISSSPEIVPRSKVLSMKKYRLPDPII
DECDLVEDEDEDKSDDSLTDEENEEY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g469.t1 | Coils | Coil | Coil | 251 | 271 | - |
| 7 | g469.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 301 | 326 | - |
| 6 | g469.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 302 | 326 | - |
| 2 | g469.t1 | PANTHER | PTHR23171:SF13 | - | 12 | 165 | 4.1E-17 |
| 3 | g469.t1 | PANTHER | PTHR23171 | - | 12 | 165 | 4.1E-17 |
| 4 | g469.t1 | PRINTS | PR02085 | DNA-directed RNA polymerase II subunit GRINL1 signature | 30 | 47 | 3.0E-6 |
| 5 | g469.t1 | PRINTS | PR02085 | DNA-directed RNA polymerase II subunit GRINL1 signature | 49 | 72 | 3.0E-6 |
| 1 | g469.t1 | Pfam | PF15328 | Putative GRINL1B complex locus protein 2 | 42 | 172 | 4.0E-17 |
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:0016591 | RNA polymerase II, holoenzyme | CC |
KEGG
Orthology
- This transcript has been annotated with K21987 (DNA-directed RNA polymerase II subunit GRINL1A)
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.
