Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable RNA-directed DNA polymerase from transposon BS.

Parent gene

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 g124 g124.t1 isoform g124.t1 1181857 1184517
chr_3 g124 g124.t1 exon g124.t1.exon1 1181857 1184517
chr_3 g124 g124.t1 cds g124.t1.CDS1 1181857 1184517
chr_3 g124 g124.t1 TSS g124.t1 NA NA
chr_3 g124 g124.t1 TTS g124.t1 NA NA

Sequences

>g124.t1 Gene=g124 Length=2661
ATGTCTAGATTCGTTGGCAATATAAAAGTCTTTCAATGGAACGCAAATGGCGTCAAAGAA
AAATTATTCGAAATTTTCCAACATCTCAACAAATATAATATTCACGTCGCATGCATATGC
GAAACAAATTTAAATTATCAATCTAAATTGAAATCCGATCCCAATTACAGAATTCATAGA
CTCGATAGACAGGACCAAAGCAAAAGAGGAGGAGTTGCAATCCTTGTCCGAAAGGATGTA
GCTTATGAATTGCTACCCTTGGTAAGCACCAAATTAATTGAAAGCATCGGTGTAGCAATT
AAACTTGAAAATGGTAGTAAAATAAATATCTTCTCATGCTATGTACCTGGAAGTACAACG
TCTCAACAAATAAATAATCTCTTTATATATGATATAAGGAAGCTCTCAAATACAAGCAAT
AAATACTATCTGGTAGGAGATTTTTACTGCAAGCATAGATCATGGAACTGCTTTCAAGCA
AATCGTGCAGGCACACTACTCTATGAAGAGTCTTGTTCAAAAGAGCTCTTCATAGATCAT
CCACCAAGCCACACACATTATCCTGGTGATTTAAGTCGTAGGCCCTCAACCATCGATCTG
ATTTTATCCAATGCATCACACACTATCACGAAGTTACGTACTGCAGAACTAATGAGCGAC
CATATATCCATCACCTTCAAAATTTGCACAAATGCAACAATCAGTGCAGCAAACGCTGGA
ACAAGGTTGGATTACGCAAATGCAAATTGGGATAAATATAAGAGAATTATCAATTATCAT
CTCTTGAACAATTTTAATGAACCCCAATTGGATTCTGCACAACAAATTGATACAACAGTT
AAAAATTTATCCGAATTGATACTGCATGCAAGAAACAGAGCAGTGCCATTGACAATCAAT
AAAAGCTTCTGTCTGGTAATTGATGAGAATCTAAAGGCGAAAATAAAAGTTAAAAATCAA
CTTAGAAGATTGTGGATGAGAACAAGACTGCCCCATTTCAAATCTCAAGTAAATGCTCTT
GAATGCCAAATCAAACAAGAGATAAACTCTATTAGAAATGCAAACTGGAATCATAAATTG
GCGGATATCAAGCCAAACAACCAAACAATTTGGCGAACAGCTCGTTACCTCAAACTAGGA
AAACGACAATTGCCTCCTATCAACAATAGTGGTCAATTGGCTATTACTGATATAGAAAAA
GCCAATATGATTGCAGTTCAGTTTAATGAAAACTTTTCAAACACTCTTACCAGCAGTATC
AATCAATCTCAAATTATAACTCGCACAATAAATAATTTTACCACGCAATTTTCAACAAAC
AATCAAACTGAAGAAACTCTTCTACCAACATTAGATGAAGTGACCCAGATAATCAAGAGA
CTTCCTAACAAGAAAGCACCAGGTCCCGACCAAATTAAAAATTGTCTAATCAAAAATCTT
CCTACAAAAGGTTATTTATTTATTACTAGCATTCTTATTGCTTGCTACAAAAACTGCTAT
TTCCCTGATGCATGGAAAACAGCTGACATAACTCCTATCGCCAAGCCAAACAAAAATCCA
TCACACGCCTCAAGCTATCGACCTATCAGCCTACTTAATACTTTGGGAAAAATCCTTGAG
CACACAATTCTTTCACGACTCAATAAGCACTGCATTGAGAAAAGTATAATTCCTTCTATA
CAACACGGTTTTAGAGCGGGCTTTTCTACCGTGCATCAATTAAAAAGAGTTATATCGCAT
ATGAAGAAGGAAATTGAACACAAAAGATCCACAGCCTTGATAACTCTCGACGTTGAAAAA
GCATTCGACAGAGTATGCCACAAAGGACTATTGTTCAAGCTCATATCTGGTAATTTTCCT
CCCTTATTAATTAAATTAATAAGTTCGTTTTTGTCAAATAGATCATTCAGAGTAGTAATC
AATGGCAAGAGGTCTGAACCTTACCAACTACTAGCGGGTGTACCTCAGGGCGCTGTCATG
AGTCCTACACTGTTTAATGTGTTCACTGCAGATTTCCCACAAGAAGACTTTTACGACACA
GCACTTTTTGCGGACGACGTGGCGATTTTTAAGTCACATAGATGCTCCAAACCAATAACA
AATGGTATTTCAAAAGCAGCTAAGTCTATCTCATCATACTACAAAAAATGGCGAATAGGA
TTAAATGCCCAGAAGACCACAGCCATGTTTGTAACTCGTAGACGAAAGAAACAATTACCA
TCTCAAAGACTTCGCATATTCAATGCAAATATTGAATGGACAAACCAAACCAAATATCTT
GGCTTGATTATAGACAAGAACTTATCATTTAAACCTCATATCGACTATATAATACAACGA
GCGAATAATGCGATTCGACTCCTATATCCTATGTTAGCTCGAAATTCCAAGCTAGACATT
AGAAACAAGATAATTATATATAAAATGGCGATTAGACCTATTTTAACCTACGGTTTCCCT
GCTATTCCAGCGATAGCAAAAACTCATATAAAGAAACTACAGGTCCTACAAAATAAAGCC
TTAAAAATGATAATGAACAAGCCTTGGTATACTAGCACAACTCAAATACATCAAATGTGT
AACATCAAACCGATTGACGAATATTTGAAGGATCTCAATATTAAATTCAACAATAGACTT
CCTAGTTCTCATATCTCATAA

>g124.t1 Gene=g124 Length=886
MSRFVGNIKVFQWNANGVKEKLFEIFQHLNKYNIHVACICETNLNYQSKLKSDPNYRIHR
LDRQDQSKRGGVAILVRKDVAYELLPLVSTKLIESIGVAIKLENGSKINIFSCYVPGSTT
SQQINNLFIYDIRKLSNTSNKYYLVGDFYCKHRSWNCFQANRAGTLLYEESCSKELFIDH
PPSHTHYPGDLSRRPSTIDLILSNASHTITKLRTAELMSDHISITFKICTNATISAANAG
TRLDYANANWDKYKRIINYHLLNNFNEPQLDSAQQIDTTVKNLSELILHARNRAVPLTIN
KSFCLVIDENLKAKIKVKNQLRRLWMRTRLPHFKSQVNALECQIKQEINSIRNANWNHKL
ADIKPNNQTIWRTARYLKLGKRQLPPINNSGQLAITDIEKANMIAVQFNENFSNTLTSSI
NQSQIITRTINNFTTQFSTNNQTEETLLPTLDEVTQIIKRLPNKKAPGPDQIKNCLIKNL
PTKGYLFITSILIACYKNCYFPDAWKTADITPIAKPNKNPSHASSYRPISLLNTLGKILE
HTILSRLNKHCIEKSIIPSIQHGFRAGFSTVHQLKRVISHMKKEIEHKRSTALITLDVEK
AFDRVCHKGLLFKLISGNFPPLLIKLISSFLSNRSFRVVINGKRSEPYQLLAGVPQGAVM
SPTLFNVFTADFPQEDFYDTALFADDVAIFKSHRCSKPITNGISKAAKSISSYYKKWRIG
LNAQKTTAMFVTRRRKKQLPSQRLRIFNANIEWTNQTKYLGLIIDKNLSFKPHIDYIIQR
ANNAIRLLYPMLARNSKLDIRNKIIIYKMAIRPILTYGFPAIPAIAKTHIKKLQVLQNKA
LKMIMNKPWYTSTTQIHQMCNIKPIDEYLKDLNIKFNNRLPSSHIS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g124.t1 CDD cd01650 RT_nLTR_like 510 764 0.000
7 g124.t1 Gene3D G3DSA:3.60.10.10 - 7 229 0.000
3 g124.t1 PANTHER PTHR33332:SF23 - 450 847 0.000
4 g124.t1 PANTHER PTHR33332 - 450 847 0.000
2 g124.t1 Pfam PF14529 Endonuclease-reverse transcriptase 108 224 0.000
1 g124.t1 Pfam PF00078 Reverse transcriptase (RNA-dependent DNA polymerase) 517 764 0.000
8 g124.t1 ProSiteProfiles PS50878 Reverse transcriptase (RT) catalytic domain profile. 494 764 22.077
6 g124.t1 SUPERFAMILY SSF56219 DNase I-like 8 229 0.000
5 g124.t1 SUPERFAMILY SSF56672 DNA/RNA polymerases 446 734 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