RetrogeneDB ID: retro_osat_20

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 3:8369346..8370978(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OS03G0258500
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OS01G0681400
• Aliases: None
• Description: None

Sequence

>retro_osat_20
ATGTCAGTGACTGTTTGCTCCTGCGACGACGAATCTGTGCCGACCTTGTTTCACCGCCTCCGCCTCCGATTCGACCTCCG
CGGCCGCCATGAAATTGGAGCTTCCGGGAGGAGGAAATCTCGAGAAGTAGAGAGAGAAGACCACAGCGTGGGCGAGCGCG
TCGGCGTCATTGATTCCGGCGACATGAAGCCCCCCGCCGCGGCCGCGGCCGGCAACAGGGCTGGTGGGGTGGATCCGTCG
ATACCGCGGTTCAAGTGCCAGGAGTGCCACCGCGCGCTCGTCGTCGTCGGCGTGGACTCCTTCGCCGCCGATAAGCTCCC
GGCTCAGGCCACCTCTGGGCATGTATCCTCTGTTCATGGAAGTATTATGGGAGCTAGCAGGATGGATAATTCTTATGTCG
TGCTATCCAAGCAAAACAAATCTCATGGCCATGGAATTCCCCCACGCCCACCGAGTGCAGCAGCCCCACATATCGAACCT
AACCAGCCAACAAGAGCGATGGAGGGTTCATATATAGTGCTTCCACCTGCTGCTGCTTCCATATACAAGACATCTACTTC
TGAAGGAGGTGGTGCGCAGTTGCCACCACCAAGTATCAATTCCAGCAGTTTGTTAACAGGAAATAGTTTTCACTCTAACG
TGACTGTATTAAAACGGGCATTTGAGATTGCTACGTCACAAACTCAGGTTGAGCAGCCAATGTGTCTGGGCTGTATGAGG
TTGCTCTCTGATAAGATGGATAAGGAGATTGAAGATGTTAATGCTGACATTAAAGCTCATGAAGTTTGTCTTCAACATTT
GGAGCAGGAATCCTACAATGTCCTCAGCGATGCTGGTTTTCAGGAGGAGAAACTGAAGATTGAAGAAGAAGAAAAGAAGC
TTAACGCTGCTATTGAAGAAGCTGAAAAGCAATATTCAGAAATTAGTTCTGAGATGAAGGATCTTGAAATAAAATCTAAA
GAATTTGAAGAATTGGAAGAAAGGTATTGGCATGAATTCAATAGCTTTCAGTTTCAGTTGACATCTCACCAGGAAGAAAG
AGAAGCAATTTTGGCAAAAATAGAAGTTTCACAGGTTCATCTGGAATTGCTGAAGCGAAGAAATGTTCTCAATGATGCAT
TCTATATTTCACATGATGGAGTAATTGGAACAATAAACAACTTCCGACTCGGACGCCTTCCTAATGTACAGGTTGAATGG
GATGAGATAAATGCTGCTTGGGGTCAGGCTGCTCTTCTTTTGCATACCATGGCTCAGTACTTCACCCCAAAATTTGAGTA
CCGGATTAAGATTCATCCTATGGGTAGCTACGCAAGAGTCACAGATATCCACAAAAATACATATGAACTTTATATCATGC
TAACCAGGTTTGGTCCCGTGGATTTATTCTGGAGCACACGTTTTGACAAAGCCATGACATGGTTTCTGACCTGCCTGCAA
GATTTTGCTGAGTTCGCTATTAGCTTGGATAAAGAGAACAATGTACCACCTGAGAAGTCATTAAAGCTCCCATACAAGAT
TGATGGTGACAAGGTAGGGAGCCACACAATCTTCTTAAGTTTTAATAAAGTGGAGAACTGGACGAAAGCACTAAAATACA
CGTTGTGCAACTTGAAGTGGGTCCTCTACTGA

Alignment

ORF - retro_osat_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.66 %
• Parental protein coverage: 78.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKAPAAAAAAVGNRAGGVDPSIPRFKCQECHRALVVVGVDSFA-DKLPAQATSAHASSVHGSIMGASRMD
          MK.PAAAAA..GNRAGGVDPSIPRFKCQECHRALVVVGVDSFA.DKLPAQATS.H.SSVHGSIMGASRMD
Retrocopy MKPPAAAAA--GNRAGGVDPSIPRFKCQECHRALVVVGVDSFAADKLPAQATSGHVSSVHGSIMGASRMD

Parental  NSYVVLSKQNKSHGHGIPPRPPSAAAPHIEPNQPTRAMEGSYIVLPPAAASIYKTSTSEGGGAQLPPPSI
          NSYVVLSKQNKSHGHGIPPRPPSAAAPHIEPNQPTRAMEGSYIVLPPAAASIYKTSTSEGGGAQLPPPSI
Retrocopy NSYVVLSKQNKSHGHGIPPRPPSAAAPHIEPNQPTRAMEGSYIVLPPAAASIYKTSTSEGGGAQLPPPSI

Parental  NSSSLLPGNSFHSNVTVLKRAFEIATSQTQVEQPMCLDCMRLLSDKMDKEIEDVNADIKAYEVCLQHLEQ
          NSSSLL.GNSFHSNVTVLKRAFEIATSQTQVEQPMCL.CMRLLSDKMDKEIEDVNADIKA.EVCLQHLEQ
Retrocopy NSSSLLTGNSFHSNVTVLKRAFEIATSQTQVEQPMCLGCMRLLSDKMDKEIEDVNADIKAHEVCLQHLEQ

Parental  ESHTVLSDAGFQKEKLKIEEEEKKLNAAIEEAEKQYSEISSEMKDLEIKSKEFEELEERYWHEFNSFQFQ
          ES..VLSDAGFQ.EKLKIEEEEKKLNAAIEEAEKQYSEISSEMKDLEIKSKEFEELEERYWHEFNSFQFQ
Retrocopy ESYNVLSDAGFQEEKLKIEEEEKKLNAAIEEAEKQYSEISSEMKDLEIKSKEFEELEERYWHEFNSFQFQ

Parental  LTSHQEERDAILAKIEVSQVHLELLKQTNVLNDAFYISHDGVIGTINNFRLGRLPNVQVEWDEINAAWGQ
          LTSHQEER.AILAKIEVSQVHLELLK..NVLNDAFYISHDGVIGTINNFRLGRLPNVQVEWDEINAAWGQ
Retrocopy LTSHQEEREAILAKIEVSQVHLELLKRRNVLNDAFYISHDGVIGTINNFRLGRLPNVQVEWDEINAAWGQ

Parental  AALLLHTMAQYFTPKFEYRIKIHPMGSYPRVTDIHKNTYELF
          AALLLHTMAQYFTPKFEYRIKIHPMGSY.RVTDIHKNTYEL.
Retrocopy AALLLHTMAQYFTPKFEYRIKIHPMGSYARVTDIHKNTYELY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryza sativa japonica was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza sativa japonica was not studied using ChIP-Seq data.

EST

Oryza sativa japonica was not studied using EST data.

TSS

Oryza sativa japonica was not studied using FANTOM5 data.

Lab

retro_osat_20 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza sativa japonica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza glumaepatula	OGLUM01G30530	1 retrocopy	retro_oglu_35,
Oryza glaberrima	ORGLA01G0218200	1 retrocopy	retro_ogla_19,
Oryza sativa japonica	OS01G0681400	1 retrocopy	retro_osat_20 ,