Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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 g4036 g4036.t1 isoform g4036.t1 29892902 29894973
chr_3 g4036 g4036.t1 exon g4036.t1.exon1 29892902 29893013
chr_3 g4036 g4036.t1 cds g4036.t1.CDS1 29892902 29893013
chr_3 g4036 g4036.t1 exon g4036.t1.exon2 29893859 29894368
chr_3 g4036 g4036.t1 cds g4036.t1.CDS2 29893859 29894368
chr_3 g4036 g4036.t1 exon g4036.t1.exon3 29894447 29894973
chr_3 g4036 g4036.t1 cds g4036.t1.CDS3 29894447 29894973
chr_3 g4036 g4036.t1 TSS g4036.t1 NA NA
chr_3 g4036 g4036.t1 TTS g4036.t1 NA NA

Sequences

>g4036.t1 Gene=g4036 Length=1149
ATGTTCAAAATTTTTATAGATATTACAACACAACTTTCTGGTGCTAGAACAAAGCATGAG
CAAATTCAAATCATAATGTCGGTTGCCATCAAATATGCAGTGCCTTACAATGATGACCTT
ATCGATGAGAGAAAGTCGATGAAGAAAAGATGGCAAAGATCTCGTGACGTCACTTTAAAA
GCTCAGGTCAGATTCCTGGAAAGATTGATCAAAGAGAGAGTCAACTTAATCAGAAATGAG
AGCTGGTCACATAAACTCAGTACTATAAAACCAAATCACACCAATGTTTGGAAATTAACA
AAATTTTTAAAGAAGCGCGATTCAAATATTCCTCCAATTAAAACTGCAGATGGTATTCTA
AATACTCCTGAAGAAAAAGCCAACAAGTTAGCGGAAGTTTTCGAATCAAATGATCTAAAC
CCACTTGAAAGAAGTTGTCCGGACTTCACTTACCTAATTAAAAATAAGGTCTCCGGTCTT
AGGCAACCACTGCCAGCAAACGAATTGTCAACTTTTACTGATGCCGATGAAATATTTTCA
ATCATTCAAAACGTGAAAAATCTCAAATGTCCTGGTGCTGATCAAATCTCAAATCGACTC
ATAAAGAAACTACCACGTCGCGTTATCCAAATTCCAAAACCAAGAAAAGTAAAATCAGAT
CCTCCATCGTACAGACCAATTTCGCTCCTCAGTTCTCTGAGTAAAATACTTGAAAAAGTT
ATTCTTGTTCGTTTACAATATCACATTGAAGTTAATAACATCATCTCAGAGGAACAATTT
GGCTTTAGAAGTAACTCTTCCACTACTCATCAACTCTACAAAATCATCAAGCATGCTCAT
AAGGGATTAAAGTTCAAAAAGTCTACAGGACTGCTTTCACTAGATGAGAAAGCATTCGAT
CGTATTTGGAATGATGAACTTATTGCAAAGACGATTGATTTCGATTTTCCATCTAATTTG
ATCTTAATCACAAAATCGTTCTTGTCCGAGAGAACGTTTAAAGTGATTTGTAATGGCTCA
ACCATCCGCTTAATTCGAGCCGGGGTTCCACAAGGTGCAGTCCTGAGTCCAACTCTCTAC
AACATTTACACGGCGGATATCCCATTAAATAGCTTTTACGAGATAACCATGTTTGCAGAC
GACACTTGA

>g4036.t1 Gene=g4036 Length=382
MFKIFIDITTQLSGARTKHEQIQIIMSVAIKYAVPYNDDLIDERKSMKKRWQRSRDVTLK
AQVRFLERLIKERVNLIRNESWSHKLSTIKPNHTNVWKLTKFLKKRDSNIPPIKTADGIL
NTPEEKANKLAEVFESNDLNPLERSCPDFTYLIKNKVSGLRQPLPANELSTFTDADEIFS
IIQNVKNLKCPGADQISNRLIKKLPRRVIQIPKPRKVKSDPPSYRPISLLSSLSKILEKV
ILVRLQYHIEVNNIISEEQFGFRSNSSTTHQLYKIIKHAHKGLKFKKSTGLLSLDEKAFD
RIWNDELIAKTIDFDFPSNLILITKSFLSERTFKVICNGSTIRLIRAGVPQGAVLSPTLY
NIYTADIPLNSFYEITMFADDT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g4036.t1 PANTHER PTHR19446:SF438 RNA-DIRECTED DNA POLYMERASE FROM TRANSPOSON X-ELEMENT-LIKE PROTEIN-RELATED 150 382 0.000
3 g4036.t1 PANTHER PTHR19446 REVERSE TRANSCRIPTASES 150 382 0.000
1 g4036.t1 Pfam PF00078 Reverse transcriptase (RNA-dependent DNA polymerase) 211 382 0.000
5 g4036.t1 ProSiteProfiles PS50878 Reverse transcriptase (RT) catalytic domain profile. 192 382 15.784
4 g4036.t1 SUPERFAMILY SSF56672 DNA/RNA polymerases 96 369 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