General information for g12500.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative PHD finger-like domain-containing protein 5A.
Parent gene
- The parent gene g12500 is located on chr_1: 24016445..24016830 (- 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 | g12500 | g12500.t3 | isoform | g12500.t3 | 24016328 | 24016830 |
| chr_1 | g12500 | g12500.t3 | exon | g12500.t3.exon1 | 24016328 | 24016830 |
| chr_1 | g12500 | g12500.t3 | TTS | g12500.t3 | 24016356 | 24016356 |
| chr_1 | g12500 | g12500.t3 | cds | g12500.t3.CDS1 | 24016445 | 24016765 |
| chr_1 | g12500 | g12500.t3 | TSS | g12500.t3 | 24016893 | 24016893 |
Sequences
>g12500.t3 Gene=g12500 Length=503
ATGGCAAAGCATCATCCAGATTTAATATTTTGTAGAAAACAGCCAGGTGTTGGTAAGTAA
TTTTAATGAACGTAGAGTATCGATTTAAAATTAATGCTTTTTTAGCGATTGGACGATTAT
GTGAAAAATGTGATGGAAAATGCGTTATTTGTGATTCTTATGTGCGTCCATGTACATTAG
TTCGAATTTGTGATGAATGCAATTATGGAAGTTTTCAAGGAAGATGTGTGATCTGTGGTG
GTGCTGGTGTTTCTGATGCTTATTATTGCAAAGAGTGTACAATTCAAGAAAAAGATCGAG
ATGGATGTCCGAAAATTGTCAACTTGGGATCAAGCAAAACAGATCTATTTTATGAGAGAA
AGAAATATGGCTTTAAACAGCGATAATTTCTTAAAGTTTTGCCTAATTCATTCATTCTAC
TGAAAAATCCAATTACTTTCACAAATTTAATAAAACAATCCAATTCTTTTTAAACAAACT
TTTGTTGTTTTATTTTTTTGATG
>g12500.t3 Gene=g12500 Length=106
MNVEYRFKINAFLAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSFQGRCVICGGA
GVSDAYYCKECTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKQR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g12500.t3 | PANTHER | PTHR13120 | PHD FINGER-LIKE DOMAIN-CONTAINING PROTEIN 5A | 13 | 106 | 0 |
| 3 | g12500.t3 | PANTHER | PTHR13120:SF5 | BNAC03G71910D PROTEIN | 13 | 106 | 0 |
| 4 | g12500.t3 | PIRSF | PIRSF016468 | RDS3p | 6 | 106 | 0 |
| 1 | g12500.t3 | Pfam | PF03660 | PHF5-like protein | 14 | 100 | 0 |
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:0000398 | mRNA splicing, via spliceosome | BP |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
