General information for g8044.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Retinoblastoma-like protein 1.
Parent gene
- The parent gene g8044 is located on chr_2: 28204570..28205041 (+ 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 | g8044 | g8044.t3 | isoform | g8044.t3 | 28203930 | 28204728 |
| chr_2 | g8044 | g8044.t3 | exon | g8044.t3.exon1 | 28203930 | 28203995 |
| chr_2 | g8044 | g8044.t3 | cds | g8044.t3.CDS1 | 28203933 | 28203995 |
| chr_2 | g8044 | g8044.t3 | exon | g8044.t3.exon2 | 28204063 | 28204509 |
| chr_2 | g8044 | g8044.t3 | cds | g8044.t3.CDS2 | 28204063 | 28204509 |
| chr_2 | g8044 | g8044.t3 | exon | g8044.t3.exon3 | 28204567 | 28204728 |
| chr_2 | g8044 | g8044.t3 | cds | g8044.t3.CDS3 | 28204567 | 28204728 |
| chr_2 | g8044 | g8044.t3 | TSS | g8044.t3 | NA | NA |
| chr_2 | g8044 | g8044.t3 | TTS | g8044.t3 | NA | NA |
Sequences
>g8044.t3 Gene=g8044 Length=675
TTAATGAAAGATCGTCATTTAGATCAAATTTTGATGTGTTGTGTTTATGTCCTTTGTAAG
ATTAGGCCAAATGAAAATCGTCACACATTTGCAGACATCATGAAGTTTTACAGAAATCAG
CCACAATCTGACTCGCATATCTATCGTAGTGTCTTCATAGAATATGTTCAAACGGATAAA
GCTAATGAGATGCAAGAACCGAAGGCAAGTGCTGCTGAGCCAGAAGTCGTTAATGGTAGA
AACACTATATATGGAACTGAAAGTCGAGGAGACATCATTTATTTTTACAACAAAATATTT
GTTCCAAAAATGCAACAATTTGCGATGAGATTTTCAACTTCTTCACAAAATAATCTTCTT
CTATCACCATTGCCACAGTCACGTCCTCTGATCTCACCTAGAAAAAAAATTTCACCTTAT
CATGATGTATATGTACAACCGTTGACAAAACAAAGCATTCTTTCACCTTCAGCACGTACT
CTTACTTTTACAATTGAACAAAGCCCCTCAAAGGATCTCCAGAAAATAAATTCCATGATT
AATCAGAATAAGAAGGCAAGCGTTGCAAAGCGTTTTATGATGGATACTGAAGATGATTTC
CGTCCTGCAAAAGTTTCAAAGGACTCTTCTTTACAACTTCGACTTTTAATTGACCGTGAA
GAGATTAGCAATTAG
>g8044.t3 Gene=g8044 Length=223
MKDRHLDQILMCCVYVLCKIRPNENRHTFADIMKFYRNQPQSDSHIYRSVFIEYVQTDKA
NEMQEPKASAAEPEVVNGRNTIYGTESRGDIIYFYNKIFVPKMQQFAMRFSTSSQNNLLL
SPLPQSRPLISPRKKISPYHDVYVQPLTKQSILSPSARTLTFTIEQSPSKDLQKINSMIN
QNKKASVAKRFMMDTEDDFRPAKVSKDSSLQLRLLIDREEISN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g8044.t3 | Gene3D | G3DSA:1.10.472.10 | - | 1 | 128 | 0 |
| 2 | g8044.t3 | PANTHER | PTHR13742 | RETINOBLASTOMA-ASSOCIATED PROTEIN RB -RELATED | 1 | 198 | 0 |
| 1 | g8044.t3 | Pfam | PF01857 | Retinoblastoma-associated protein B domain | 1 | 104 | 0 |
| 3 | g8044.t3 | SUPERFAMILY | SSF47954 | Cyclin-like | 1 | 125 | 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:0006357 | regulation of transcription by RNA polymerase II | BP |
| GO:0005634 | nucleus | CC |
| GO:0051726 | regulation of cell cycle | 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.
