General information for g17508.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g17508 is located on chr_4: 13716272..13718297 (+ 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_4 | g17508 | g17508.t1 | isoform | g17508.t1 | 13716272 | 13718297 |
| chr_4 | g17508 | g17508.t1 | exon | g17508.t1.exon1 | 13716272 | 13716693 |
| chr_4 | g17508 | g17508.t1 | cds | g17508.t1.CDS1 | 13716272 | 13716693 |
| chr_4 | g17508 | g17508.t1 | exon | g17508.t1.exon2 | 13717398 | 13717594 |
| chr_4 | g17508 | g17508.t1 | cds | g17508.t1.CDS2 | 13717398 | 13717594 |
| chr_4 | g17508 | g17508.t1 | exon | g17508.t1.exon3 | 13718149 | 13718297 |
| chr_4 | g17508 | g17508.t1 | cds | g17508.t1.CDS3 | 13718149 | 13718297 |
| chr_4 | g17508 | g17508.t1 | TTS | g17508.t1 | 13719249 | 13719249 |
| chr_4 | g17508 | g17508.t1 | TSS | g17508.t1 | NA | NA |
Sequences
>g17508.t1 Gene=g17508 Length=768
ATGGCACTTAAAACTGCTATTTGGAATGCACACTCAGTTTGCAACAAAATCAATGAACTT
TCAGTATTTTTAAATGATTATAATATAGATTTAATCTTATTATCTGAAACTTGGACTAAT
GTCAACTCAAGAGTTGATATTATAGGCTATAATTATTATAGAGTTGATCGTGTTCATGGA
GGTGTCTTAATTTATATTAAATCATCTATACCACATAAATTTCATTCTTCTTTGGTTTTG
AATTATGCAGAATCAGTAACTATCTCGATTGATAATAAATTTTTAATTTCGTCAATTTAT
TGTTCACCGTCTGTGACTAGATTAGAAGCCCGTAATTTTTTCAATAAAATTTCTTCTATT
CAAGGACCTCACTTTATTGGAGGTGATTTCAATGCTAAACATATAGCTTGGAATAATCCT
ACTGATAGTGATAAAGCTGAGCTTCTTGCTCAATCTTTTCAAAAAAATCATGTTATCCCT
CAATCAAGATCTTTAGAAGTTGAATCATCTGTCAATATGATTGATGATTTTAATGATAAT
ACATTCGCAATAATTGAAAGTTCTGAAGTAGTTGAAGTATTAGAATCACTAAATATTAAG
AAAGCTCCTGGATTAGATGGAGTTCCGCAAGGAAGCATTCTTGCACCTCATCTTTTTAAC
TTGTACATCAATGACATTCCAAAACCTATTAATGGTGATATTTCATTATACGCTGATGAT
ACAGCGTTGTCATTTGGGGTCAGCTGGAAAAATCTAAAACTTTGCTAG
>g17508.t1 Gene=g17508 Length=255
MALKTAIWNAHSVCNKINELSVFLNDYNIDLILLSETWTNVNSRVDIIGYNYYRVDRVHG
GVLIYIKSSIPHKFHSSLVLNYAESVTISIDNKFLISSIYCSPSVTRLEARNFFNKISSI
QGPHFIGGDFNAKHIAWNNPTDSDKAELLAQSFQKNHVIPQSRSLEVESSVNMIDDFNDN
TFAIIESSEVVEVLESLNIKKAPGLDGVPQGSILAPHLFNLYINDIPKPINGDISLYADD
TALSFGVSWKNLKLC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g17508.t1 | Gene3D | G3DSA:3.60.10.10 | - | 3 | 182 | 0 |
| 2 | g17508.t1 | Pfam | PF14529 | Endonuclease-reverse transcriptase | 95 | 161 | 0 |
| 1 | g17508.t1 | Pfam | PF00078 | Reverse transcriptase (RNA-dependent DNA polymerase) | 190 | 244 | 0 |
| 3 | g17508.t1 | SUPERFAMILY | SSF56219 | DNase I-like | 2 | 156 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
