Gene loci information

Transcript annotation

  • This transcript has been annotated as RNA-directed DNA polymerase from mobile element jockey.

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_2 g5502 g5502.t1 isoform g5502.t1 9923357 9926038
chr_2 g5502 g5502.t1 exon g5502.t1.exon1 9923357 9926038
chr_2 g5502 g5502.t1 cds g5502.t1.CDS1 9923357 9926038
chr_2 g5502 g5502.t1 TSS g5502.t1 NA NA
chr_2 g5502 g5502.t1 TTS g5502.t1 NA NA

Sequences

>g5502.t1 Gene=g5502 Length=2682
ATGGCTCTTAAGTTAATGTCTTGGAATTGTCAGTCTGTCAGTAGGAAGAAAGCGGAATTA
AGCCACTTTCTTTTAGACCATAATATTGATATTGCTCTTCTCTCTGAAACTTGGCTCAAC
GATGAGGCTACGTACTCTATACCAGGTTTCAATACTTTCACTGTATGTAGGCAACATGGT
GGTGTCATGATTTTGACCAAAGACTCCATTACAGTGAATGGTGTTAATAGGATTGCTCTG
AGCTATGCTGAGGCAATCTCGATTAACATTCCATCAGCGATAGGAACAATTAGTGTTACT
TCTATATACTGCTCTCCTGCAAGCTCTAGAAGCCAAGCTTCAGAGTTTTTCAGAAGAGTG
CTTGATTTCCCAGGTTCAGTGGTCATTGCTGGTGACTTCAATGCCAAGCACTCGTCTTGG
AACAACAGCTCTGACACACTGAAAGGTAAAGACCTATTTGGATTATGTAGGCATGGTAAC
TACACGATTCATCCTCCTGATGGCCCCACTTTATATTCAAGTAGAGGAACTCTTTCAGTA
GTCGACTTTGTCATTTCAAAGGCATTACCTGGGGTAAATGGGCCAAAAGTAATTAATGAA
CTTTCATCAGACCACTTACCTTTAACCTTTTCCATACCTGTAGCTTCTTCCCAGGTATCA
CAGCACACCTTTTTCCACTGGCCCAAAGCCAATTGGAAGAAGTTTAGAGCACAACTCAAC
TGCAAGGTCCCAGAACTTGCAAGTCTTGACTTGTCCTCTTGCGATGCAATTGATTGTGCT
ATTGATGCAGTAACTGTGGCTATTAATGACGCAGCTTCTTCATCTATTCCGCGTAAGGCA
CCATATCGATTTAGATTTCCTTTCTCGGATCATTTGCATCGTCTTACTCGCGAAAGAAAT
CGCTATCGCCAACAATTCAGGGCTACACAAAGACCTGAATTTAGGAGTTTGGTCAATCAG
TTGAATCGGCTAATTAAAGACGAAACAACGAAATTGAGCCAAGCTTCTTTTGATTCCAAG
CTGAGTCAGCTGTACACACAAGACTGTTCAGCATTTCGATTCATCAAAGCAATCAAGAAC
AAGCGGAATGGCTTTTCCCCCTTGTTAAATCCAGCTACTAACCAATTGGTCTATACTGAT
TCTGCTAAGGCTTCTGTACTTTCAGATTCTTTTTTGACTAATCATTGTATTACCACCAGT
TGGCTGTCTAATAAAGACGCACTGGTAAGTAATGTAGTTAATACATTCAGAAGGAGCCAA
ATTGCTGTTTCTGAAAGTATCACTGATCATGAGTCTCTTACTCTGATCATTAAATCTTTG
AGAGTACGGAAGGCTGAAGGCTTAGATGGCATTGCCACTAGGTTTCTCAAAAACCTACCA
AAATCTCTACTTAAGGTAGTAACTATGATTTTTAATCAAAGTTACAAGTTGGGCTACTTC
CCAAGTGCCTGGAAGCGAGCTAAAGTTATCGCTATCCCGAAAAAGGACAAGCCAACGGAC
AAACCTAGTAACTTTCGTCCAATTTCATTGCTATCTACTCTAGGAAAGCTTTATGAGAAG
GTTATTCTGGATAAAGTTTCTCGTTTTGAAGAGGCCAATGAACTCATCAAACCCCAGCAA
TTTGGGTTTCGTAGTAGGCATTCGACTACTCACCAAGTTCTGAGAATTATTGAAGAAGCC
ACAATAGGCTTCAACAACAAGAAAAGCACGGGCATTGTACTTCTCGATCTCGAGAAGGCT
TTTGATACCGTGTGGCACGAGGGCCTCATTTATAAGCTTATAAAGCTCAAATTCCCTCCC
GAACAGATCAGAGTCATTGACTCTTTTCTAACTGGAAGACAGGCGTCAGTATATGTCAAT
GGACACGCTTCGCCATTCTTCACGCTTCCAGCTGGAGTACCACAGGGCTCTACCTTGTCT
CCATTTCTGTTCAATGTGTTTATCAATGACATTCCACGTTTGAAGCACTGCAAGCTTGCA
CAGTTCGCAGATGATACCGCGCTATATACTGTTAACTCCTGGAAGAATCTTGGCCTTATT
AAAACCAGACTTTTAGGAGATTTAAGCACATTGGCGTCTTTCTATCGTGATTGGAAGGTC
AAGATGAATGATAGTAAAACTGAGTTTTCTATCTTCACTAGATCATACAACATGCGCAGG
AAGGCAGAAGCTGATACAATTTCATTCGGTACCAACACTTATAAGTGGCAAAAAGAGGTC
CGATATCTAGGTGTTACACTAGATACTCGTTTGAGCTTCCAAGCCCATATAAAGAGTGTG
CTAGCAAAGGCTAGCGGCGTTGGACGCAGCATTTACTGCATTTTCAAGAAGCATAACACT
GTTCCTATCCGTACTAAAATCAATCTCTACAAAGTTTGCATAAGGCCATTACTGACTTAT
GCTGCGCCAGTTTTTGCAAACTGCCCAGTTACCTACTCGCGTAAGCTCCAAATTACGCAA
AACAAATTCTTGAGAATGTGTCTCAACGCAAGCTATTATACTAGGACTGCGGACCTTCAT
GAAGAGGGCCAAGTACCTCTTATCTCAGACTTCATTAAAAAGTTAACTACTAACTTCTAC
GACAGGGCTAATAACCATACCAACTCTCTTATTTGCGCATTAGGTAACTATTCATCCAGA
CTGAGAGGTCGCAGAATCAGGCATAAACTGCCTCGTCCTTAA

>g5502.t1 Gene=g5502 Length=893
MALKLMSWNCQSVSRKKAELSHFLLDHNIDIALLSETWLNDEATYSIPGFNTFTVCRQHG
GVMILTKDSITVNGVNRIALSYAEAISINIPSAIGTISVTSIYCSPASSRSQASEFFRRV
LDFPGSVVIAGDFNAKHSSWNNSSDTLKGKDLFGLCRHGNYTIHPPDGPTLYSSRGTLSV
VDFVISKALPGVNGPKVINELSSDHLPLTFSIPVASSQVSQHTFFHWPKANWKKFRAQLN
CKVPELASLDLSSCDAIDCAIDAVTVAINDAASSSIPRKAPYRFRFPFSDHLHRLTRERN
RYRQQFRATQRPEFRSLVNQLNRLIKDETTKLSQASFDSKLSQLYTQDCSAFRFIKAIKN
KRNGFSPLLNPATNQLVYTDSAKASVLSDSFLTNHCITTSWLSNKDALVSNVVNTFRRSQ
IAVSESITDHESLTLIIKSLRVRKAEGLDGIATRFLKNLPKSLLKVVTMIFNQSYKLGYF
PSAWKRAKVIAIPKKDKPTDKPSNFRPISLLSTLGKLYEKVILDKVSRFEEANELIKPQQ
FGFRSRHSTTHQVLRIIEEATIGFNNKKSTGIVLLDLEKAFDTVWHEGLIYKLIKLKFPP
EQIRVIDSFLTGRQASVYVNGHASPFFTLPAGVPQGSTLSPFLFNVFINDIPRLKHCKLA
QFADDTALYTVNSWKNLGLIKTRLLGDLSTLASFYRDWKVKMNDSKTEFSIFTRSYNMRR
KAEADTISFGTNTYKWQKEVRYLGVTLDTRLSFQAHIKSVLAKASGVGRSIYCIFKKHNT
VPIRTKINLYKVCIRPLLTYAAPVFANCPVTYSRKLQITQNKFLRMCLNASYYTRTADLH
EEGQVPLISDFIKKLTTNFYDRANNHTNSLICALGNYSSRLRGRRIRHKLPRP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g5502.t1 CDD cd01650 RT_nLTR_like 486 747 0.000
7 g5502.t1 Gene3D G3DSA:3.60.10.10 - 2 214 0.000
3 g5502.t1 PANTHER PTHR33332:SF29 - 395 835 0.000
4 g5502.t1 PANTHER PTHR33332 - 395 835 0.000
2 g5502.t1 Pfam PF14529 Endonuclease-reverse transcriptase 98 208 0.000
1 g5502.t1 Pfam PF00078 Reverse transcriptase (RNA-dependent DNA polymerase) 492 747 0.000
8 g5502.t1 ProSiteProfiles PS50878 Reverse transcriptase (RT) catalytic domain profile. 473 747 28.329
6 g5502.t1 SUPERFAMILY SSF56219 DNase I-like 1 213 0.000
5 g5502.t1 SUPERFAMILY SSF56672 DNA/RNA polymerases 407 714 0.000

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5502/g5502.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5502.t1.fa.iupred3.txt does not exist

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