General information for g13648.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Probable RNA-directed DNA polymerase from transposon X-element.
Parent gene
- The parent gene g13648 is located on chr_1: 31407964..31409487 (- 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 | g13648 | g13648.t1 | isoform | g13648.t1 | 31407964 | 31409487 |
| chr_1 | g13648 | g13648.t1 | exon | g13648.t1.exon1 | 31407964 | 31408768 |
| chr_1 | g13648 | g13648.t1 | cds | g13648.t1.CDS1 | 31407964 | 31408768 |
| chr_1 | g13648 | g13648.t1 | exon | g13648.t1.exon2 | 31409483 | 31409487 |
| chr_1 | g13648 | g13648.t1 | cds | g13648.t1.CDS2 | 31409483 | 31409487 |
| chr_1 | g13648 | g13648.t1 | TSS | g13648.t1 | 31409916 | 31409916 |
| chr_1 | g13648 | g13648.t1 | TTS | g13648.t1 | NA | NA |
Sequences
>g13648.t1 Gene=g13648 Length=810
ATGAATGCTGGTGTTCCTCAAGGCAGTTTACTTGCTCCTCATTTATTTAACATATTCATC
AACGATATCCCAATACCTAAAGGTGCTAAATTGTCACTATTTGCAGATGACACTGCTTTG
GCAGTTGAAGTTAATTGGAAGAATCTCAAATTAGCGAAAAAGAAAGTTCTAAGTTCTTTG
GATTTGATAGTTAGGTTCTTCGACAAATGGAACATCAAAATTAATGAATCAAAAACTAAA
TTTATCATGTTCAGTAAGTCAAGAGTGATGCTAAACAGAACTGAAGTTGATCAAATTAAC
TTTGGTAACTCTATTTCCAAATGGGAGAAATCAGTTAAATATCTAGGAATTAATCTTGAT
CAGAAACTCTTGTTTAAAGATCATATTAATAAATCACTTACTATTGCTAAGTCCATCGCT
TTTTCTACCTTATACTGTTTTTTTAAGAAAAATAATGTTGTCAAGGAGCATCAAAAAGTT
CACTTATACAAGACAGTCATAAGACCTATATTGACATATGGTTGTCAAGTATTTAATAAT
TGTGCCAAGAGTCACTTTAACAAACTCCAAATTTTTCAAAACAAAATGTTAAGACTCTGT
TTTAATATTAATTGGGATGATTTTATCAACAATGAAAAACTTCATGAATTAGCTAATATT
CCAACAATCAGAGAATTTGTTAATAAATTAACTTCTCGCTTTTATGACGATTGTCATTCG
CATGACAATAACCTTATATCAAATTTAGGAAACTACGATCACGAGACATTCATGAATGGC
TTTAAGCATAGATTACCCCTTGCTGTTTGA
>g13648.t1 Gene=g13648 Length=269
MNAGVPQGSLLAPHLFNIFINDIPIPKGAKLSLFADDTALAVEVNWKNLKLAKKKVLSSL
DLIVRFFDKWNIKINESKTKFIMFSKSRVMLNRTEVDQINFGNSISKWEKSVKYLGINLD
QKLLFKDHINKSLTIAKSIAFSTLYCFFKKNNVVKEHQKVHLYKTVIRPILTYGCQVFNN
CAKSHFNKLQIFQNKMLRLCFNINWDDFINNEKLHELANIPTIREFVNKLTSRFYDDCHS
HDNNLISNLGNYDHETFMNGFKHRLPLAV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g13648.t1 | PANTHER | PTHR33332 | - | 2 | 256 | 0.0000000 |
| 1 | g13648.t1 | Pfam | PF00078 | Reverse transcriptase (RNA-dependent DNA polymerase) | 2 | 119 | 0.0000000 |
| 4 | g13648.t1 | ProSiteProfiles | PS50878 | Reverse transcriptase (RT) catalytic domain profile. | 1 | 119 | 16.6860000 |
| 3 | g13648.t1 | SUPERFAMILY | SSF56672 | DNA/RNA polymerases | 5 | 132 | 0.0000031 |
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.
