General information for g14288.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 BS.
Parent gene
- The parent gene g14288 is located on chr_1: 36319193..36320745 (- 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 | g14288 | g14288.t1 | isoform | g14288.t1 | 36319193 | 36320745 |
| chr_1 | g14288 | g14288.t1 | exon | g14288.t1.exon1 | 36319193 | 36320343 |
| chr_1 | g14288 | g14288.t1 | cds | g14288.t1.CDS1 | 36319193 | 36320343 |
| chr_1 | g14288 | g14288.t1 | exon | g14288.t1.exon2 | 36320403 | 36320745 |
| chr_1 | g14288 | g14288.t1 | cds | g14288.t1.CDS2 | 36320403 | 36320745 |
| chr_1 | g14288 | g14288.t1 | TSS | g14288.t1 | NA | NA |
| chr_1 | g14288 | g14288.t1 | TTS | g14288.t1 | NA | NA |
Sequences
>g14288.t1 Gene=g14288 Length=1494
ATGTCTGATGTAGAGAAAGCCCAAGCTCTTGCTGATACCTTTAAAGAAAGTCATAACATA
TCATCGGATAGAAGTCCTGAGGTGGAAAATTCTATTAATAGAATAATTAATTCTCAGGTT
GGTGCATTTGATATCATTGAAAGTTCTGAAATTACTTCCATTCTTAGCTCACTCAATCAT
AAAAAGGCAACAGGTTTAGATAATATTCCAAATTGTATACTCTCAGGCTTAGCGAAATCC
AGACCTTTTGTTGATTTGTTAGTTATTTTGTTTAATGAGTGCATTCATAGATGTTACTTT
CCGAAAGATTGGAAAAAGGCAAAAATTGTTGCCATTCCTAAAAGTAAAATTTTTGAAAAA
ATTTTATTATCTAGACTTAAGGAATTTGAAAAGAATCACAATATTTTCATTAATGAGCAA
TTTGGCTTTAAAAATGGACATTCAACAACGCAGCAAATTTTAAGATTAACTAAACAAATT
TCATTAGGATTCAACAAAAGGAAAAGCACAGCACTCATTTTGTTTGATTTTAAAAAAGCC
TTCGATACTGTTTGGCATGATGGTCTGCTGCATAAGCTTCTGTTGAATAATTATCCAGTC
TATTTGATTAAGTTGCTTTTTTCCTACCTATCTGATAGAGTTGCTGCAGTTTACCTTAAT
CAGTCTTATTCTAATTTTTATAAAGTTAAAGCAGGCGTGCCACAAGGAAGCTTACTTGCT
CCTCATCTATTTAATGTTTACATTAACGATGTGCCAAAGCCCAAACATGGAAATATTGCT
CTATTTGCTGATGATACGGCTATGTATTTTGAAGTCAGTTGGAAAAATCTTAATCTTGCC
AAAAAAAGAATTCAGGAGAATTTTAATTGTCTCATCCATTATATTGATAAATGGAAAATC
AAACTTAATGAAAATAAAACTAAAATTATTATGTTTTCTAAATCCAATGTCATGCTCAAA
AAAGTTGAAAATGACTTAGTAATGCTAGGGAATTCAAACTTTGAATGGCAAGAATCGGTT
AAATATCTAGGAGTAATACTAGATCGTAAGCTCCTATTTAAAAAGCACATTGACAGATCA
ATTGCTATTGCCAATGGTGTCACATTTTCCTCATTTTACTGTTTATTTAAAAGAAACAAT
TCATTAGACTCTGCTGAAAAAGTGTTTCTATACAAGGCATATGTTAGGCCTATCTTGACT
TATGCTTGTCAGATTTTTAATAATTGTGCCAAAACGCATCTTATAAAAATTCAAGTGTTT
CAGAATAAAATTCTTAGATTATGTTACAACACGAATTGGGATGATTTCATTAGTAATGAG
ACACTCCACTCAAGAGCAGATTTACCATTGATTCGTGATTTTGTTGACAAATTGGTCAAT
CGATTTTATAACATTTGTCAGACTCATGATAATGTACTTATTTCTTCTTTAGGAATATAC
AATAATAACTTGTTCACAACTAGATTCAAACATAGACTTCCGATTGCCATATAA
>g14288.t1 Gene=g14288 Length=497
MSDVEKAQALADTFKESHNISSDRSPEVENSINRIINSQVGAFDIIESSEITSILSSLNH
KKATGLDNIPNCILSGLAKSRPFVDLLVILFNECIHRCYFPKDWKKAKIVAIPKSKIFEK
ILLSRLKEFEKNHNIFINEQFGFKNGHSTTQQILRLTKQISLGFNKRKSTALILFDFKKA
FDTVWHDGLLHKLLLNNYPVYLIKLLFSYLSDRVAAVYLNQSYSNFYKVKAGVPQGSLLA
PHLFNVYINDVPKPKHGNIALFADDTAMYFEVSWKNLNLAKKRIQENFNCLIHYIDKWKI
KLNENKTKIIMFSKSNVMLKKVENDLVMLGNSNFEWQESVKYLGVILDRKLLFKKHIDRS
IAIANGVTFSSFYCLFKRNNSLDSAEKVFLYKAYVRPILTYACQIFNNCAKTHLIKIQVF
QNKILRLCYNTNWDDFISNETLHSRADLPLIRDFVDKLVNRFYNICQTHDNVLISSLGIY
NNNLFTTRFKHRLPIAI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g14288.t1 | CDD | cd01650 | RT_nLTR_like | 106 | 347 | 0.000 |
| 2 | g14288.t1 | PANTHER | PTHR33332:SF29 | - | 12 | 452 | 0.000 |
| 3 | g14288.t1 | PANTHER | PTHR33332 | - | 12 | 452 | 0.000 |
| 1 | g14288.t1 | Pfam | PF00078 | Reverse transcriptase (RNA-dependent DNA polymerase) | 113 | 347 | 0.000 |
| 5 | g14288.t1 | ProSiteProfiles | PS50878 | Reverse transcriptase (RT) catalytic domain profile. | 93 | 347 | 20.622 |
| 4 | g14288.t1 | SUPERFAMILY | SSF56672 | DNA/RNA polymerases | 51 | 314 | 0.000 |
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.
