General information for g1549.t1
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.t1 | TTS | g1549.t1 | 11795401 | 11795401 |
| chr_3 | g1549 | g1549.t1 | isoform | g1549.t1 | 11795448 | 11796660 |
| chr_3 | g1549 | g1549.t1 | exon | g1549.t1.exon1 | 11795448 | 11796529 |
| chr_3 | g1549 | g1549.t1 | cds | g1549.t1.CDS1 | 11795448 | 11796529 |
| chr_3 | g1549 | g1549.t1 | exon | g1549.t1.exon2 | 11796588 | 11796660 |
| chr_3 | g1549 | g1549.t1 | cds | g1549.t1.CDS2 | 11796588 | 11796660 |
| chr_3 | g1549 | g1549.t1 | TSS | g1549.t1 | 11796736 | 11796736 |
Sequences
>g1549.t1 Gene=g1549 Length=1155
ATGGAAGGCTTAATAAATAGTAAAATAGTCTCAGTTGATAAAATTAATAGTAAAAAAGCA
TCACCAATTTTGGCAACATTTCAAAACTCAAGCTTATCAGATGATAAATGTAATCAAGTT
GTGTGTAAAAGAGTTGAAACAGAGAGTGATGGAAGAAAATTCGCTTTAATTGCAACAAAT
TCAAGTGTTTATAAAGCAGAATTAAATGATAGCAAATATGAAGATACTTACTTAGCAATT
CATAATAAAACTACAGGCGAAATCAATTTAATTCAAGTACAAAAAGCTGATTTTCGTAAT
GTACTTTATGATAATAAAAGATCAATCTATGAAAACAATGTTGTTGATAAGAGAAAACTG
TATAAAGAATTTGGTGGAAAGAAAGCAATGGCATCGTTTGATAGGCAGAATCAAAGTCAA
ACACAAAATTCGAGCATTTTAGAAAATACCGTTGATAAAGTGCTACAAAATGTTGATATA
GATAAAATTTTGGACTCGAGCACTTTGGAAAATGAGAAGGAATTTTCAATATTTCCAGAA
ATCAAAGAAGACATTGAAGGAAAAGATGTTCGTGAAATTTTCACGCTTGATATTCTTTTT
GGTGCGGAAATAGTAGAACACATGAATGAAATTGCATTAGAAGCATTAGCATCGCCAATA
GATCAATTGGATTTTAAAAATAATCATCTTAAAAAAACAGCTGCTAGTCTTCAATTATCA
AAGCAGCCAGAAAAAAATGTCAATGAAATGATCATGCTACTCTATGCTAAAATATTGATG
AAACTGATAAATTTTCGACAAAAATATTTTGAAATTTCGAGAGAATTGAAAAATGTGTCG
CCTCGATTACAACAAAACATTCTCTCAATTTTTTTCATAAATGGTTCAAATGAATATTCA
AATTATACTAAACAAAAAGCGACTGTCTTTTATATAATTCTTATGCTGCTCACAACAAAG
TCTTTAACAATTGATTTATATGATCTTCTTGATGGTGTCGTGATGTCTAAACGTGAAATA
TTTAAATATGCTTCGATTATTGGTTGTAAAAAGAGTAATGGTGAAAAATTAAGTTTAACA
AAAGTTGCAAAGTTAGATAAAAATTTCAAATTTACTGTCCCTACACTGAAAGGAAAGAAA
GATCGTTCTAAATGA
>g1549.t1 Gene=g1549 Length=384
MEGLINSKIVSVDKINSKKASPILATFQNSSLSDDKCNQVVCKRVETESDGRKFALIATN
SSVYKAELNDSKYEDTYLAIHNKTTGEINLIQVQKADFRNVLYDNKRSIYENNVVDKRKL
YKEFGGKKAMASFDRQNQSQTQNSSILENTVDKVLQNVDIDKILDSSTLENEKEFSIFPE
IKEDIEGKDVREIFTLDILFGAEIVEHMNEIALEALASPIDQLDFKNNHLKKTAASLQLS
KQPEKNVNEMIMLLYAKILMKLINFRQKYFEISRELKNVSPRLQQNILSIFFINGSNEYS
NYTKQKATVFYIILMLLTTKSLTIDLYDLLDGVVMSKREIFKYASIIGCKKSNGEKLSLT
KVAKLDKNFKFTVPTLKGKKDRSK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g1549.t1 | PANTHER | PTHR14440 | DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49 | 11 | 382 | 3.1E-21 |
| 1 | g1549.t1 | Pfam | PF06870 | A49-like RNA polymerase I associated factor | 71 | 365 | 1.1E-17 |
| 4 | g1549.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 308 | - |
| 5 | g1549.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 309 | 330 | - |
| 3 | g1549.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 331 | 384 | - |
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 transcript has been annotated with K03005 (DNA-directed RNA polymerase I subunit RPA49)
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.
