General information for g1549.t19
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g1549 is located on chr_3: 11796660..11799246 (- 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 | g1549 | g1549.t19 | isoform | g1549.t19 | 11795344 | 11796529 |
| chr_3 | g1549 | g1549.t19 | exon | g1549.t19.exon1 | 11795344 | 11796529 |
| chr_3 | g1549 | g1549.t19 | cds | g1549.t19.CDS1 | 11795448 | 11796215 |
| chr_3 | g1549 | g1549.t19 | TSS | g1549.t19 | 11796736 | 11796736 |
| chr_3 | g1549 | g1549.t19 | TTS | g1549.t19 | NA | NA |
Sequences
>g1549.t19 Gene=g1549 Length=1186
CAACATTTCAAAACTCAAGCTTATCAGATGATAAATGTAATCAAGTTGTGTGTAAAAGAG
TTGAAACAGAGAGTGATGGAAGAAAATTCGCTTTAATTGCAACAAATTCAAGTGTTTATA
AAGCAGAATTAAATGATAGCAAATATGAAGATACTTACTTAGCAATTCATAATAAAACTA
CAGGCGAAATCAATTTAATTCAAGTACAAAAAGCTGATTTTCGTAATGTACTTTATGATA
ATAAAAGATCAATCTATGAAAACAATGTTGTTGATAAGAGAAAACTGTATAAAGAATTTG
GTGGAAAGAAAGCAATGGCATCGTTTGATAGGCAGAATCAAAGTCAAACACAAAATTCGA
GCATTTTAGAAAATACCGTTGATAAAGTGCTACAAAATGTTGATATAGATAAAATTTTGG
ACTCGAGCACTTTGGAAAATGAGAAGGAATTTTCAATATTTCCAGAAATCAAAGAAGACA
TTGAAGGAAAAGATGTTCGTGAAATTTTCACGCTTGATATTCTTTTTGGTGCGGAAATAG
TAGAACACATGAATGAAATTGCATTAGAAGCATTAGCATCGCCAATAGATCAATTGGATT
TTAAAAATAATCATCTTAAAAAAACAGCTGCTAGTCTTCAATTATCAAAGCAGCCAGAAA
AAAATGTCAATGAAATGATCATGCTACTCTATGCTAAAATATTGATGAAACTGATAAATT
TTCGACAAAAATATTTTGAAATTTCGAGAGAATTGAAAAATGTGTCGCCTCGATTACAAC
AAAACATTCTCTCAATTTTTTTCATAAATGGTTCAAATGAATATTCAAATTATACTAAAC
AAAAAGCGACTGTCTTTTATATAATTCTTATGCTGCTCACAACAAAGTCTTTAACAATTG
ATTTATATGATCTTCTTGATGGTGTCGTGATGTCTAAACGTGAAATATTTAAATATGCTT
CGATTATTGGTTGTAAAAAGAGTAATGGTGAAAAATTAAGTTTAACAAAAGTTGCAAAGT
TAGATAAAAATTTCAAATTTACTGTCCCTACACTGAAAGGAAAGAAAGATCGTTCTAAAT
GAATTTTTTTAAAGAAACAAAATAAAAGTTTAATATTTTATTAAGAATTAAAATGGTAAT
TGTTCTTTATTAATAATGGAATAGTTCAATAAAATTCATTTTATTT
>g1549.t19 Gene=g1549 Length=255
MASFDRQNQSQTQNSSILENTVDKVLQNVDIDKILDSSTLENEKEFSIFPEIKEDIEGKD
VREIFTLDILFGAEIVEHMNEIALEALASPIDQLDFKNNHLKKTAASLQLSKQPEKNVNE
MIMLLYAKILMKLINFRQKYFEISRELKNVSPRLQQNILSIFFINGSNEYSNYTKQKATV
FYIILMLLTTKSLTIDLYDLLDGVVMSKREIFKYASIIGCKKSNGEKLSLTKVAKLDKNF
KFTVPTLKGKKDRSK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value |
|---|---|---|---|---|---|---|
| g1549.t19 | Pfam | PF06870 | A49-like RNA polymerase I associated factor | 17 | 236 | 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:0003677 | DNA binding | MF |
| GO:0006351 | transcription, DNA-templated | 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.
