General information for g3263.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 g3263 is located on chr_3: 24086028..24088586 (- 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 | g3263 | g3263.t1 | isoform | g3263.t1 | 24086028 | 24088586 |
| chr_3 | g3263 | g3263.t1 | exon | g3263.t1.exon1 | 24086028 | 24088586 |
| chr_3 | g3263 | g3263.t1 | cds | g3263.t1.CDS1 | 24086028 | 24088586 |
| chr_3 | g3263 | g3263.t1 | TSS | g3263.t1 | NA | NA |
| chr_3 | g3263 | g3263.t1 | TTS | g3263.t1 | NA | NA |
Sequences
>g3263.t1 Gene=g3263 Length=2559
ATGGAAACAAATCACATACATGTATGTTGCTTGAGTGAGACCTTTTTAAAAGATGACATA
AAATTACCAGCTCATCCTAAATTTATAACATATAGGCTTGATCGTCCTGAAAAAAGAAAG
GGTGGAGTTGCTATAGTTGTTAGAAAGACAATAAAACACAGACTATTGCCTTCTTTAGGA
ATGAAATATGTAGAACAAATAGGAATTCAAGTTTATTTAATAAATTCTCAAAATATTAGC
ATTTACTCTCTTTATGTGCCAGGAACAAATGACATTGACAGTGTTAATCATTTCCTTGTA
AAGGATCTGAGAAAACTGTCTAAATATCAAAATAGTTTCTTTGCTTGCGGTGATTTGAAT
GCACACCATCGTGCATGGAATTGCGTCAGAGCAAACAGAGCAGGTACATTGCTCTACGAT
GAAATGTGTCGAGGCACTTTTTTCATTGAATCACCTGATGAACCAACTCACTATCCTGTG
GATAAAAATAAAAAACCATCAACTATTGACCTATTATTAACAAATAAATTACACCAACAT
AGTGAACTTACATTATCAAAGGGATTAATTAGCGACCATAATGCTGTGGAATTCACAATT
GATACAAAACCAGAAAAATCTAATCAAACTTCAGACTTCTTTGATTACAAAAATGCCGAA
TGGGAAAAATATTGCGCTGTAATAAATCAGAAGTTAAGCATCATAGCAAATGCACCAACC
TTACCTCAAGAATGTCAACAAATTGACGAGAGTATAGCGATGTTCACAAATTTAATATTG
GAAGCACAGGACATTTCTGTCCCCAAAAAAAGAAGAAACAGCTATAAGTTAGACCTTCCT
GATAAATTACTAAAAGCGATAAAGATTAAAAACACATTAAAGCGTAAATGGCAACGTACC
AGAGATTCTCAATTGAAGTCAATGGTTAATTATTATGAAAGACTAATCAAAGAATCGGTA
AACAGTATTAAAAATGAAAACTGGTCCTACAAATTAAGCCAAATTGATCCTGATAATGTG
AAAGTTTGGAAAACAGCAAAAATCCTGAAAAAGAAAAATATAATACCACCTCTAAAAATT
CAAGAAAAAATTTTACTCACGACGCATGAAAAAGCTGAAGCCATTGCAGAAAGTTTCGAA
AACAATCACATAAATCCTTTGATGGAGTCCGATCCAACATTTACATTGTCAGTAAATAAC
AACGTCCGAGTTATTATAACCGACAAATGTGATGAAGACATACTGCTTACTAATTATGAC
GAAATTTCATTGATTATTCGACGACTCAAAAACAACAAATGCCCTGGTGAAGATAAAATT
ACTAATCGTCTCCTAAAACAATTACCACCAAAAGGAGTGAAATTTTTAGTTAAAATAATC
AATAATTGCTTAATTTCAAGATACTTCCCTTGTAAATGGAAATGTGCTAACGTCGTACCT
ATCGCTAAGCCTGGTAAAAAGAAAAATGATCCAACTGGTTATAGACCAATATCGCTTCTC
AGCTCTGTAAGCAAAATTTTAGAAAGAATAATTTTATCAAGATTAGAAACTCACATTGAT
AATAATAACATCATACCTGACATTCAACATGGATTCAGAAAAAATTACTCTACGACTCAT
CAAATTCACAGGGTAATTAAAAGAGCTAGGGATGCATTGAGGAGAAAGGAATCAACTGGA
TTGATTGCCTTGGACATTGAAAAGGCGTTCGACAGAGTATGGATCGAAGGCCTAATTTCA
AAGATGATCGCTCTCAATTTCCCTACAAACTTGGTCCAAATCACTCATTCGTTCTTATCC
GAAAGAACTTTTAGAGTGACCATAAATGGAACCTTTTCATCTCTAAAGAGACTTGAAGCT
GGATTACCACAGGGCGCAGTTCTAAGTCCAACGCTTTATAATTTATACACGCATGATATT
CCAACAAACGGCAGTCACCAAGTAGCTCAGTATGCTGATGATACACTCCTATTCAAATCT
GCTCCATCCTACTTTGAAATAACTCAAAGTCTTAAATACGCCGCTTCAAATTTAATTGAT
TATCTGAAACGATGGAAAATAAATGTAAATAATAATAAAACAAATGCAGTGTACATCACC
AAAAGAAGAAAACTGGAATTGCCGAGTGGTCCTATCAATATTTTTGGCTCTGAAATAGAA
TGGACAAGTTCTATAAAATATTTAGGTGTTGAATTAGATTCTGGACTCACCTATAAAACT
CATGTTGAGAAAGTCATCGCAAAGGCCAATACAGCAATTAAAATCCTATATCCTTTAATA
AATAGATATTCAAAGTTACATGTCAACAACAAAATAACAATTTACAAACTTGCAATTCGA
CCAATATTAACTTATGCAATGCCAGCACTCACAGAAATGGCTCCATCACATATTAGGAAG
ATACAAACAATCCAAAATAAAGTGATTAAAATGATTCTGAATCGTCCTTGGTTTGAGAGT
ACCGATGAAATCCATAGAGTTACAAATTTACCTAGAATAGATTGCTTTATAGAAAAATTA
ACTAAAAATTTCCACTCTAAATTAATTAATCTTACCTAA
>g3263.t1 Gene=g3263 Length=852
METNHIHVCCLSETFLKDDIKLPAHPKFITYRLDRPEKRKGGVAIVVRKTIKHRLLPSLG
MKYVEQIGIQVYLINSQNISIYSLYVPGTNDIDSVNHFLVKDLRKLSKYQNSFFACGDLN
AHHRAWNCVRANRAGTLLYDEMCRGTFFIESPDEPTHYPVDKNKKPSTIDLLLTNKLHQH
SELTLSKGLISDHNAVEFTIDTKPEKSNQTSDFFDYKNAEWEKYCAVINQKLSIIANAPT
LPQECQQIDESIAMFTNLILEAQDISVPKKRRNSYKLDLPDKLLKAIKIKNTLKRKWQRT
RDSQLKSMVNYYERLIKESVNSIKNENWSYKLSQIDPDNVKVWKTAKILKKKNIIPPLKI
QEKILLTTHEKAEAIAESFENNHINPLMESDPTFTLSVNNNVRVIITDKCDEDILLTNYD
EISLIIRRLKNNKCPGEDKITNRLLKQLPPKGVKFLVKIINNCLISRYFPCKWKCANVVP
IAKPGKKKNDPTGYRPISLLSSVSKILERIILSRLETHIDNNNIIPDIQHGFRKNYSTTH
QIHRVIKRARDALRRKESTGLIALDIEKAFDRVWIEGLISKMIALNFPTNLVQITHSFLS
ERTFRVTINGTFSSLKRLEAGLPQGAVLSPTLYNLYTHDIPTNGSHQVAQYADDTLLFKS
APSYFEITQSLKYAASNLIDYLKRWKINVNNNKTNAVYITKRRKLELPSGPINIFGSEIE
WTSSIKYLGVELDSGLTYKTHVEKVIAKANTAIKILYPLINRYSKLHVNNKITIYKLAIR
PILTYAMPALTEMAPSHIRKIQTIQNKVIKMILNRPWFESTDEIHRVTNLPRIDCFIEKL
TKNFHSKLINLT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g3263.t1 | CDD | cd01650 | RT_nLTR_like | 475 | 732 | 0.000 |
| 7 | g3263.t1 | Gene3D | G3DSA:3.60.10.10 | - | 1 | 202 | 0.000 |
| 3 | g3263.t1 | PANTHER | PTHR33332:SF23 | - | 412 | 814 | 0.000 |
| 4 | g3263.t1 | PANTHER | PTHR33332 | - | 412 | 814 | 0.000 |
| 2 | g3263.t1 | Pfam | PF14529 | Endonuclease-reverse transcriptase | 79 | 196 | 0.000 |
| 1 | g3263.t1 | Pfam | PF00078 | Reverse transcriptase (RNA-dependent DNA polymerase) | 487 | 732 | 0.000 |
| 8 | g3263.t1 | ProSiteProfiles | PS50878 | Reverse transcriptase (RT) catalytic domain profile. | 462 | 732 | 23.717 |
| 6 | g3263.t1 | SUPERFAMILY | SSF56219 | DNase I-like | 4 | 203 | 0.000 |
| 5 | g3263.t1 | SUPERFAMILY | SSF56672 | DNA/RNA polymerases | 400 | 704 | 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. There were no conditions that were differentially expressed