General information for g17798.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable RNA-directed DNA polymerase from transposon X-element.
Parent gene
- The parent gene g17798 is located on HiC_scaffold_370: 1410..4070 (+ 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 |
|---|---|---|---|---|---|---|
| HiC_scaffold_370 | g17798 | g17798.t1 | isoform | g17798.t1 | 1410 | 4070 |
| HiC_scaffold_370 | g17798 | g17798.t1 | exon | g17798.t1.exon1 | 1410 | 4070 |
| HiC_scaffold_370 | g17798 | g17798.t1 | cds | g17798.t1.CDS1 | 1410 | 4070 |
| HiC_scaffold_370 | g17798 | g17798.t1 | TSS | g17798.t1 | NA | NA |
| HiC_scaffold_370 | g17798 | g17798.t1 | TTS | g17798.t1 | NA | NA |
Sequences
>g17798.t1 Gene=g17798 Length=2661
ATGAATAATTTAATTAATTCAATTCGAGTCCTATTCTGGAATAGCAATGGTATTCAACCG
AAAATTCACGAATTATATCTATATGCAAATACGAATTTTATTGATGTTATTTGTCTCAGT
GAGACATTTCTCAAGAATCATATGAAATTGGCTCGTGATCCAAACTACTTAATTTATCGA
TTGGACAGAGCTGAACAAAATAAAGGTGGTGTTGCAATTCTTATCAAGAAGAACCTCAAA
CATCAAATTTTACCGACCGCTCATACTGAAATTATTGAAAATATCGGTATATCAATTCCG
CTCGCAAACGGCTCAAATGTCTGCATCTATAGCGTCTACCTTCCTGGTGGTACAAAAAAC
AATGAGATAAATAATCACTTTGTCAAGGACATTCGTACCTTAATGTCCTCTTCACGAAAT
TCTCTCTTCTGTGGTGATTTAAACGCTAAGCATCGTTTCTGGAATTGTAAAATGGCAAAT
AGAGCTGGTACTTTGTTATACAATGAATATTGCTCGAATAATTTCAACATTTATTTTCCA
CAAGAAAGCACATATATTCCTCCAGACATAAACCGACAACCATCCACTCTCGATCTGGTC
CTTACAAATAACAATTTTAATATAGTCCCGGAAATATGTAATGATTTGCTTAGTGACCAC
ACAGCAATCAGTTTTAACATTAAATTTCAATCCACTGCCGAATTACTTGAAAATAGGGGA
CAATTCGATTACAGCAACGCAAATTGGAAAAAATACAGAAGATTATTGAACGGAACATTT
CATGAACAAGTAGGTACACCAACATTTACAACAACTTCTGATATTGATACACATATTGAG
AAACTTACTACTGCGATCATAAACGCAAGAGATGCTTCAATACCAAAAGTCATCCATAAC
CAATACAAAATCAACCTCCCTGACTCGCTCATTGGGATGATTAAGGTTAAAAATGCACTG
AAATGTACTTGGAGAAGAAACAGAATACCTTCACTCAAATCAGAAATAAATAGGATGGAG
AACAAAATTAAATATGAGATTAGTCAAATACGCAATTCAAACTGGAGTCACAAACTAAAG
AGTATTACTCCTGGTAATCAGTCCTTATGGAAAACCGCTCGCATGATGAAAATCGGCAGC
AAAATTATTCCACCATTGAAGACAGCAACTGGACTGGCAACTTGTAATGTTGATAAAGCT
AACGTTATAGCTAATACATTCAAAAATAACCATGTCAATCCTATAAATAGAGTTCCAGCT
GTTTATGATTACACAGTAAACGCGACAGTTACAAATTTCTTGAACAATAACTCACAAACA
GATGCATCGGACTCACTTCTGCTCCCAACAATGGACGAACTGAAAGAAGCAGTCAACAGG
CTCCCAAATAATAAGGAACCTGGAAAAGATGGCATTAAGAATTGTCTAATTAAAAATCTT
CCAGTATACGGATTTGAACTACTTCTTCTTATCTTTATAGCTTGTTTAAGGCTTGGTTAC
TTTCCTATGACTTGGAAACACGCCAAAGTCTTTCCCATAGGTAAGCCTAACAAAGACCCA
TCATTGCCTACAAGTTATAGGCCTATTAGTTTATTAAGTTCAATTAGTAAACTACTAGAG
AGGCTCATCCTCAATCGAGTGAACAAGCACTGTGATATAAATAAGATTATACCAGATACG
CAGCATGGCTTTCGTTCTGGATTTTCAACTGTGCATCAATTAAAAAGAGTAATTGATTAT
GCAAAACAAGGTTTGCGCAACAAAAATTCAATAGGACTGATCACTTTAGATGTTGAGAAG
GCGTTCGATCGAGTATGGTATAATGGAATAATTTTCAAAATGATTAAACTTAATTTCAAC
ACGAATATCATCAAAATTGTCAATTCATTTTTGAGAAACAGAAGCTTTCATGTCGCGATA
TCCAATAAAGTGTCACAAACACACCAAATTGATATTGGAGTTCCACAAGGTGCAGTATTG
AGCCCAATATTGTATAATATATATACTCACGACTTGCCTACTAATGATTCCTATGAATCC
GCACTCTTCGCCGATGATGTTGCCAAATTCTCTGCGAACTCGACTCTATTAAGAGTGAAC
AAATCGATCACACTTGCTGCTAAGGAAACCTATGAATATATGCGTAAGTGGAAAATAAAT
ATCAATGGCGCAAAGACGAATGCTATTTTTATAACAAAAAGAATTTCGCGACAAATACCT
GATACTCCATTACCAATCTTTGAAACTAGTGTAAATTGGTGTGATGAATTGAAATATCTC
GGAATAGTAATTGACAAACGGTTGACATTTGGAAAACATATCGATTATGTTATAGCTAAA
ACGAATATAGCAATTAAAATTTTATATCCACTATTAAGTAGAAATTCAAAACTCGATACA
AAAAACAAGCTACTCATCTATAAACTCGCAATCCGACCAATTTTCACTTATGGCATGCCA
GCATTGAAAGGAATTGCCGATACTCATTTAAAGAAACTCCAGATTACACAAAACAAAGCA
TTGAAGATGATTCTCAACAGAAGCCACTTTGAAAACACGTCCAAATTGCATAAAGATGCC
GATATTCCTCTGGTTAAGGAATACATTGAGAAAATAACAAGAAAATTCGATGAGAAATTA
ATATTATCACAAGAATTATAA
>g17798.t1 Gene=g17798 Length=886
MNNLINSIRVLFWNSNGIQPKIHELYLYANTNFIDVICLSETFLKNHMKLARDPNYLIYR
LDRAEQNKGGVAILIKKNLKHQILPTAHTEIIENIGISIPLANGSNVCIYSVYLPGGTKN
NEINNHFVKDIRTLMSSSRNSLFCGDLNAKHRFWNCKMANRAGTLLYNEYCSNNFNIYFP
QESTYIPPDINRQPSTLDLVLTNNNFNIVPEICNDLLSDHTAISFNIKFQSTAELLENRG
QFDYSNANWKKYRRLLNGTFHEQVGTPTFTTTSDIDTHIEKLTTAIINARDASIPKVIHN
QYKINLPDSLIGMIKVKNALKCTWRRNRIPSLKSEINRMENKIKYEISQIRNSNWSHKLK
SITPGNQSLWKTARMMKIGSKIIPPLKTATGLATCNVDKANVIANTFKNNHVNPINRVPA
VYDYTVNATVTNFLNNNSQTDASDSLLLPTMDELKEAVNRLPNNKEPGKDGIKNCLIKNL
PVYGFELLLLIFIACLRLGYFPMTWKHAKVFPIGKPNKDPSLPTSYRPISLLSSISKLLE
RLILNRVNKHCDINKIIPDTQHGFRSGFSTVHQLKRVIDYAKQGLRNKNSIGLITLDVEK
AFDRVWYNGIIFKMIKLNFNTNIIKIVNSFLRNRSFHVAISNKVSQTHQIDIGVPQGAVL
SPILYNIYTHDLPTNDSYESALFADDVAKFSANSTLLRVNKSITLAAKETYEYMRKWKIN
INGAKTNAIFITKRISRQIPDTPLPIFETSVNWCDELKYLGIVIDKRLTFGKHIDYVIAK
TNIAIKILYPLLSRNSKLDTKNKLLIYKLAIRPIFTYGMPALKGIADTHLKKLQITQNKA
LKMILNRSHFENTSKLHKDADIPLVKEYIEKITRKFDEKLILSQEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g17798.t1 | CDD | cd01650 | RT_nLTR_like | 507 | 764 | 2.16121E-32 |
| 7 | g17798.t1 | Gene3D | G3DSA:3.60.10.10 | - | 7 | 230 | 6.1E-36 |
| 3 | g17798.t1 | PANTHER | PTHR33332:SF29 | - | 398 | 857 | 3.2E-52 |
| 4 | g17798.t1 | PANTHER | PTHR33332 | - | 398 | 857 | 3.2E-52 |
| 2 | g17798.t1 | Pfam | PF14529 | Endonuclease-reverse transcriptase | 108 | 223 | 1.1E-13 |
| 1 | g17798.t1 | Pfam | PF00078 | Reverse transcriptase (RNA-dependent DNA polymerase) | 516 | 763 | 3.7E-44 |
| 10 | g17798.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 479 | - |
| 11 | g17798.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 480 | 500 | - |
| 9 | g17798.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 501 | 886 | - |
| 8 | g17798.t1 | ProSiteProfiles | PS50878 | Reverse transcriptase (RT) catalytic domain profile. | 494 | 764 | 22.015 |
| 6 | g17798.t1 | SUPERFAMILY | SSF56219 | DNase I-like | 7 | 229 | 1.02E-33 |
| 5 | g17798.t1 | SUPERFAMILY | SSF56672 | DNA/RNA polymerases | 453 | 731 | 1.47E-14 |
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. There were no conditions that were differentially expressed