Gene loci information

Transcript annotation

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

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.t2 isoform g5502.t2 9924828 9927314
chr_2 g5502 g5502.t2 exon g5502.t2.exon1 9924828 9924839
chr_2 g5502 g5502.t2 cds g5502.t2.CDS1 9924828 9924839
chr_2 g5502 g5502.t2 exon g5502.t2.exon2 9924911 9926026
chr_2 g5502 g5502.t2 cds g5502.t2.CDS2 9924911 9926026
chr_2 g5502 g5502.t2 exon g5502.t2.exon3 9926094 9927314
chr_2 g5502 g5502.t2 cds g5502.t2.CDS3 9926094 9927314
chr_2 g5502 g5502.t2 TSS g5502.t2 NA NA
chr_2 g5502 g5502.t2 TTS g5502.t2 NA NA

Sequences

>g5502.t2 Gene=g5502 Length=2349
ATGCAGACTAGAGGGAGGAAGAGGAGGCAACAACAACAAGCTTCAAATGGTGAGAATAGT
GAGAATTCTGAAACTGAAAATTCACACGAGGCTACAACAACAACAAAGCCAAAAAAGGCT
AAAACGCCCAAAACAAAAACGCCCAACGCAACAACAACAACGCCTATAAAGGCAGCAACA
ACAACGCCTTCAAAGGCAACAACAACAACAAGTTCTACACAGAACAACAACATCAACAAC
AGTCAGCAAGGCAAAACCAAGCCGATTTTTATTTCGACTAATTATCAAGTCGCCATCAAC
CTGCTCAAGTCATTGAGTCTCAACAACAAGCCTGTTCTAAAAATAATTAACAGCCAGCTT
GTTTCAGTCACAGCAGCAGATCTCATCAGCAAAGAGACCATCATCAAGGCTTTGTCCGAA
AAGCAGTTCCAGTACCATTCGTTCACTGAAAAAGTGAATAGGAAGTTGACCTTTGTTCTC
AAAGGGTTTTACAAGACCACTGCTGAATCACTACTTGACGTCTTGAAGGTAGCAGGTATT
CCGGCATTGAGTGTGTCCATCATCTCCCAGTCTGATGATCGTTCAGTGTACACCGTACAG
TTCCCACAGGGAACGACAACCATCCAGCAACTCAATCAGCAATTCAAAGTCATCGACTAT
TTATTGGTTCGCTGGGAGGTCATTGACAGGTCGAAGCGTCGCCATGTCCAGTGTGGCAAC
TGCAAGAGATGGGGCCATACTTCAGCCAATTGTGGACATCCTTTCCGCTGCATCAAATGC
ACAGGCAGCCATGCCAGGGGTGAGTGTCAACGCACCACGAAGGAGAGTACAGCAGATAGC
AAGGTAGCTTGCGTTAATTGCTCAGGCGAGCATCCTGCAAACAGTCGCAAGTGTCCAGCT
TTCACAGCATACGTCGCCAGGACCAAGTCCAAAGGCAGGCCGGTCTCACAGCCATCCAAG
CCGCCTAGTAGCAGCATTGCAGATCCTTCTGCATGGCCCACTCCCAGCAGTTCTGCACCA
GCAGCACAGCTTGCACAGAACTCTTCAGCACCACAGCCGAAGATCACGCCGAGAGGACGA
GCATCATACGCAGAGGCTATTAGAAGTATTAATTCACAAGCGAGTAGTTCGGGATCTTCT
TTCAATGTCCAGTCCGTTGAGTCCGAAAATCCGTTATTGGTAGAGGCTATTAAGACTCTC
CAAGCCCAAGTGCAGAGTATGTTAATGTCTTGGAATTGTCAGTCTGTCAGTAGGAAGAAA
GCGGAATTAAGCCACTTTCTTTTAGACCATAATATTGATATTGCTCTTCTCTCTGAAACT
TGGCTCAACGATGAGGCTACGTACTCTATACCAGGTTTCAATACTTTCACTGTATGTAGG
CAACATGGTGGTGTCATGATTTTGACCAAAGACTCCATTACAGTGAATGGTGTTAATAGG
ATTGCTCTGAGCTATGCTGAGGCAATCTCGATTAACATTCCATCAGCGATAGGAACAATT
AGTGTTACTTCTATATACTGCTCTCCTGCAAGCTCTAGAAGCCAAGCTTCAGAGTTTTTC
AGAAGAGTGCTTGATTTCCCAGGTTCAGTGGTCATTGCTGGTGACTTCAATGCCAAGCAC
TCGTCTTGGAACAACAGCTCTGACACACTGAAAGGTAAAGACCTATTTGGATTATGTAGG
CATGGTAACTACACGATTCATCCTCCTGATGGCCCCACTTTATATTCAAGTAGAGGAACT
CTTTCAGTAGTCGACTTTGTCATTTCAAAGGCATTACCTGGGGTAAATGGGCCAAAAGTA
ATTAATGAACTTTCATCAGACCACTTACCTTTAACCTTTTCCATACCTGTAGCTTCTTCC
CAGGTATCACAGCACACCTTTTTCCACTGGCCCAAAGCCAATTGGAAGAAGTTTAGAGCA
CAACTCAACTGCAAGGTCCCAGAACTTGCAAGTCTTGACTTGTCCTCTTGCGATGCAATT
GATTGTGCTATTGATGCAGTAACTGTGGCTATTAATGACGCAGCTTCTTCATCTATTCCG
CGTAAGGCACCATATCGATTTAGATTTCCTTTCTCGGATCATTTGCATCGTCTTACTCGC
GAAAGAAATCGCTATCGCCAACAATTCAGGGCTACACAAAGACCTGAATTTAGGAGTTTG
GTCAATCAGTTGAATCGGCTAATTAAAGACGAAACAACGAAATTGAGCCAAGCTTCTTTT
GATTCCAAGCTGAGTCAGCTGTACACACAAGACTGTTCAGCATTTCGATTCATCAAAGCA
ATCAAGAACAAGCGGAATGGCTTTTCCCCCTTGTTAAATCCAGCTACTAACCAATTGTTG
GCTGTCTAA

>g5502.t2 Gene=g5502 Length=782
MQTRGRKRRQQQQASNGENSENSETENSHEATTTTKPKKAKTPKTKTPNATTTTPIKAAT
TTPSKATTTTSSTQNNNINNSQQGKTKPIFISTNYQVAINLLKSLSLNNKPVLKIINSQL
VSVTAADLISKETIIKALSEKQFQYHSFTEKVNRKLTFVLKGFYKTTAESLLDVLKVAGI
PALSVSIISQSDDRSVYTVQFPQGTTTIQQLNQQFKVIDYLLVRWEVIDRSKRRHVQCGN
CKRWGHTSANCGHPFRCIKCTGSHARGECQRTTKESTADSKVACVNCSGEHPANSRKCPA
FTAYVARTKSKGRPVSQPSKPPSSSIADPSAWPTPSSSAPAAQLAQNSSAPQPKITPRGR
ASYAEAIRSINSQASSSGSSFNVQSVESENPLLVEAIKTLQAQVQSMLMSWNCQSVSRKK
AELSHFLLDHNIDIALLSETWLNDEATYSIPGFNTFTVCRQHGGVMILTKDSITVNGVNR
IALSYAEAISINIPSAIGTISVTSIYCSPASSRSQASEFFRRVLDFPGSVVIAGDFNAKH
SSWNNSSDTLKGKDLFGLCRHGNYTIHPPDGPTLYSSRGTLSVVDFVISKALPGVNGPKV
INELSSDHLPLTFSIPVASSQVSQHTFFHWPKANWKKFRAQLNCKVPELASLDLSSCDAI
DCAIDAVTVAINDAASSSIPRKAPYRFRFPFSDHLHRLTRERNRYRQQFRATQRPEFRSL
VNQLNRLIKDETTKLSQASFDSKLSQLYTQDCSAFRFIKAIKNKRNGFSPLLNPATNQLL
AV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g5502.t2 Gene3D G3DSA:3.60.10.10 - 407 617 2.9E-37
3 g5502.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 81 -
4 g5502.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 30 -
5 g5502.t2 MobiDBLite mobidb-lite consensus disorder prediction 44 81 -
7 g5502.t2 MobiDBLite mobidb-lite consensus disorder prediction 309 360 -
6 g5502.t2 MobiDBLite mobidb-lite consensus disorder prediction 312 355 -
1 g5502.t2 Pfam PF14529 Endonuclease-reverse transcriptase 501 611 9.3E-16
2 g5502.t2 SUPERFAMILY SSF56219 DNase I-like 408 616 3.8E-32

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5502/g5502.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5502.t2.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