General information for g17.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as RNA-directed DNA polymerase from mobile element jockey.
Parent gene
- The parent gene g17 is located on chr_3: 216993..220606 (- 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 | g17 | g17.t1 | isoform | g17.t1 | 216993 | 220606 |
| chr_3 | g17 | g17.t1 | exon | g17.t1.exon1 | 216993 | 218853 |
| chr_3 | g17 | g17.t1 | cds | g17.t1.CDS1 | 216993 | 218853 |
| chr_3 | g17 | g17.t1 | exon | g17.t1.exon2 | 220311 | 220606 |
| chr_3 | g17 | g17.t1 | cds | g17.t1.CDS2 | 220311 | 220606 |
| chr_3 | g17 | g17.t1 | TSS | g17.t1 | NA | NA |
| chr_3 | g17 | g17.t1 | TTS | g17.t1 | NA | NA |
Sequences
>g17.t1 Gene=g17 Length=2157
ATGGGAAATAAAAAGAATCTCCCGCATGGTTCGGGTCAACAAAACTTAAATAATTTCCTG
CTCACTCCAACTCGTTTCAAACGAGGTTTTGATCAACTTCCAGATAATGTTGAAGATTCC
GATTGTGCTCCATCTCCACTTAAAGTGAAGAAAACTCGTGATAAAAATATATCAACAAAA
GAAAAATGTCCGCCATTAGTCATAATTGGCCAGAGCATTTCCAAAATTCGCGATATCACA
GATCCACTCAAAATTAAAAATCTACAATTAAAACTTTTTAAAGAAGGAATAAAAGTCACT
TATATTCAAAGTCGACTCTTTGAACCACAACAAATTGACGATCATATACATAAACTCACT
AAAATCATCTTAGAGGCACAAGACAAAGCAATTCCACGCAAACAATGTTCATCCTATAAG
TTGAATCTTCCTGATGAATTAATAAACACAATTAAAATTAAAAATTCTATTAAGAGAGCA
TGGCAAAGATCACGTGATGACCGTTTTAAAGCACAAGTCAGACTAATGGAGAGAATTATC
AAAGAAAGAGTCAATATCATCCGAAACGATAATTGGTCACATAAACTTAGTACAATACTA
CCAAATCACACAAACATTTGGAAAGTTAGTAAGTTTCTCACGAAACAAAATTCAAAAATT
CCACCATTACAAACTGTTGATGGACTTCTGCTCACTTCCGAGCAAAAAGCAAACAAAATT
GCTGATGTCTTTCAAACAAATCACATTAACCCACTCAATGAAAGTTCACCGGATTTCTCT
TCTCATATTAAAAGTAAGGTCTCCGACCTTCGGCAACCATTGCCATCCGACCGTTCAACA
ACGCTAACAGACGAAGCCGAGATCAATGCAATAATTCGAAATTTAAAAAATCCTAAGTGT
CCAGGCCCTGACAAAATTTCAAATCGTCTTATCAAAAATCTACCACGTCGAGGAATAAAA
TATTTATCAAAAATTTTCAATTCCTGCTTATATCACAATTATTTTCCTACCACATGGAAA
TCAGCTAACGTCGTTCCTATCCCTAAACCTGGGAAGAAAAAGGCGGATCCAACCGCCTAT
AGACCTATCTCTCTGTTGAGCTCACTGAGTAAAATTCTTGAAAGAATCATTTTGATTCGT
ATACAAAACCATATCGAAATAAATAATATCATTCCGAATGAGCAACATGGTTTTAGAAGC
AATTCTTCAACGACTCACTTGCTTTACAAAATCATCAATCATGCGAATACTGGTCTTAAG
TCCAAAAAGTCTACAGGTCTTCTTTCCTTAGATGTGGAGAAAGCATTTGATCGTATCTGG
CATGAGGGACTTATAGCGAAGATGATCGACTTCAAATTCCCAAACAGTTTGATCCTAATC
ACCAAATCGTTCTTGTCAGAAAGAACATTCAAGGTGATTTGCGATGGCTCACATTCAACC
ATTCGTTCAATTCCAGCTGGTGTTCCGCAGGGTGCAGTCCTCAGTCCGACGCTATACAAT
ATCTACACAGCTGATGTCCCAATCAGTTCCTATTATGAAACTGCACTTTTTGCAGACGAT
ACTTCGTTCTACAAAACTGCTACAAATTTTTCAATCATTTCGTCACAACTCAAATTAGCA
TCCAGGAAGATCGCATCATACATGGAAAAGTGGAAAATCTTAATCAACACTACCAAAACA
TCAGCGATTTATGTAACAAATGGTAAGAAAAAAGAAATCCCTATCGGTCCAATTGAAGTT
TTCGATACAAATGTTGAATGGCAAGATTCAATCAAGTTATTAGGCATACATATTGACAAA
AGACTTACTTTTAAACAACACATTGATAGTGTGATAACTAAAGCAAATTTAGCAATTAGA
ATGCTCTATCCATTGATATGTCGAAAATCAAAACTCCATGTTGAAAACAAACTCCTCATA
TACAAACTTGCTATACGACCTATCCTGACTTATGGATACCCAGCATTCCATGGTTTCATC
GCCGATACACACACACGCAAATTACAAACGCTACAAAATCGTTCGCTGAAGATGATTCTA
GATCGACCTTGGTGGGAAAGCACTCAACAAATTCACGCAGATACAAATCTACCTCTGATC
AACAGCTACTTATACAAAATCACAACAAAATTTAGAAACAAACTGACCCAGTCTTAG
>g17.t1 Gene=g17 Length=718
MGNKKNLPHGSGQQNLNNFLLTPTRFKRGFDQLPDNVEDSDCAPSPLKVKKTRDKNISTK
EKCPPLVIIGQSISKIRDITDPLKIKNLQLKLFKEGIKVTYIQSRLFEPQQIDDHIHKLT
KIILEAQDKAIPRKQCSSYKLNLPDELINTIKIKNSIKRAWQRSRDDRFKAQVRLMERII
KERVNIIRNDNWSHKLSTILPNHTNIWKVSKFLTKQNSKIPPLQTVDGLLLTSEQKANKI
ADVFQTNHINPLNESSPDFSSHIKSKVSDLRQPLPSDRSTTLTDEAEINAIIRNLKNPKC
PGPDKISNRLIKNLPRRGIKYLSKIFNSCLYHNYFPTTWKSANVVPIPKPGKKKADPTAY
RPISLLSSLSKILERIILIRIQNHIEINNIIPNEQHGFRSNSSTTHLLYKIINHANTGLK
SKKSTGLLSLDVEKAFDRIWHEGLIAKMIDFKFPNSLILITKSFLSERTFKVICDGSHST
IRSIPAGVPQGAVLSPTLYNIYTADVPISSYYETALFADDTSFYKTATNFSIISSQLKLA
SRKIASYMEKWKILINTTKTSAIYVTNGKKKEIPIGPIEVFDTNVEWQDSIKLLGIHIDK
RLTFKQHIDSVITKANLAIRMLYPLICRKSKLHVENKLLIYKLAIRPILTYGYPAFHGFI
ADTHTRKLQTLQNRSLKMILDRPWWESTQQIHADTNLPLINSYLYKITTKFRNKLTQS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g17.t1 | CDD | cd01650 | RT_nLTR_like | 342 | 598 | 0.000 |
| 2 | g17.t1 | PANTHER | PTHR33332 | - | 285 | 682 | 0.000 |
| 1 | g17.t1 | Pfam | PF00078 | Reverse transcriptase (RNA-dependent DNA polymerase) | 347 | 598 | 0.000 |
| 4 | g17.t1 | ProSiteProfiles | PS50878 | Reverse transcriptase (RT) catalytic domain profile. | 328 | 598 | 22.774 |
| 3 | g17.t1 | SUPERFAMILY | SSF56672 | DNA/RNA polymerases | 251 | 568 | 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.
