RetrogeneDB ID: retro_ogla_19

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 3:7740723..7742421(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORGLA03G0107800
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA01G0218200
• Aliases: None
• Description: None

Sequence

>retro_ogla_19
ATGTCAGTGACTGTTTGCTCCTGCGACGACGAATCTGTGCCGACCTTGTTTCACCGCCTCCGCCTCCGATTCGACCTCCG
CGGCCGCCATGAAATTGGAGCTTCCGGGAGGAGGAAATCTCGAGAAGTAGAGAGAGAAGACCACAGCGTGGGCGAGCGCG
TCGGCGTCATTGATTCCGGCGACATGAAGCCCCCCGCCGCGGCCGCGGCCGGCAACAGGGCTGGTGGGGTGGATCCGTCG
ATACCGCGGTTCAAGTGCCAGGAGTGCCACCGCGCGCTCGTCGTCGTCGGCGTGGACTCCTTCGCCGCCGATAAGCTCCC
GGCTCAGGCCACCTCTGGGCATGTATCCTCTGTTCATGGAAGTATTATGGGAGCTAGCAGGATGGATAATTCTTATGTCG
TGCTATCCAAGCAAAACAAATCTCATGGCCATGGAATTCCCCCACGCCCACCGAGTGCAGCAGCCCCACATATCGAACCT
AACCAGCCAACAAGAGCGATGGAGGGTTCATATATAGTGCTTCCACCTGCTGCTGCTTCCATATACAAGACATCTACTTC
TGAAGGAGGTGGTGCGCAGTTGCCACCACCAAGTATCAATTCCGGCAGTTTGTTAACAGGAAATAGTTTTCACTCTAACG
TGACTGTATTAAAACGGGCATTTGAGATTGCTACGTCACAAACTCAGGTTGAGCAGCCAATGTGTCTGGGCTGTATGAGG
TTGCTCTCTGATAAGATGGATAAGGAGATTGAAGATGTTAATGCTGACATTAAAGCTCATGAAGTTTGTCTTCAACATTT
GGAGCAGGAATCCTACAATGTCCTCAGCGATGCTGGTTTTCAGGAGGAGAAACTGAAGATTGAAGAAGAAGAAAAGAAGC
TTAACGCTGCTATTGAAGAAGCTGAAAAGCAATATTCAGAAATTAGTTCTGAGATGAAGGATCTTGAAATAAAATCTAAA
GAATTTGAAGAATTGGAAGAAAGGTATTGGCATGAATTCAATAGCTTTCAGTTTCAGTTGACATCTCACCAGGAAGAAAG
AGAAGCAATTTTGGCCAAAATAGAAGTTTCACAGGTTCATCTGGAATTGCTGAAGCGAAGAAATGTTCTCAATGATGCAT
TCTATATTTCACATGATGGAGTAATTGGAACAATAAACAACTTCCGACTCGGACGCCTTCCTAATGTACAGGTTGAATGG
GATGAGATAAATGCTGCTTGGGGTAAGGCTGCTCTTCTTTTGCATACCATGGCTCAGTACTTCACCCCAAAATTTGAGTA
CCGGATTAAGATTCATCCTATGGGTAGCTACGCAAGAGTCACAGATATCCACAGAAATCCATATGAACTTTATATCATGC
TAACCAGGTTTGGTCCCGTGGATTTATTCTGGAGCACACGTTTTGACAAAGCCATGACATGGTTTCTGACCTGCCTGCAA
GATTTTGCTGAGTTCGCTATTAGCTTGGATAAAGAGAACAATGTACCACCTGAGAAGTCATTAAAGCTCCCATACAAGAT
TGATGGTGACAAGGTAGGGAGCCACACAATCTTCTTAAGTTTTAATAAAGTGGAGAACTGGACGAAAGCACTAAAATACA
CGTTGTGCAACTTGAAGTGGGTCCTCTACTGGTTTATCGGCAATACGAGTTTCGCACCACCCTCTGGATCTTTGTGTGCA
GCGCAATCATCTAAGAGA

Alignment

ORF - retro_ogla_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.66 %
• Parental protein coverage: 78.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKAPAAAAAAVGNRAGGVDPSIPRFKCQECHRALVVVGVDSFA-DKLPAQATSGTHASSVHGSIMGASRM
          MK.PAAAAA..GNRAGGVDPSIPRFKCQECHRALVVVGVDSFA.DKLPAQATSG.H.SSVHGSIMGASRM
Retrocopy MKPPAAAAA--GNRAGGVDPSIPRFKCQECHRALVVVGVDSFAADKLPAQATSG-HVSSVHGSIMGASRM

Parental  DNSYVVLSKQNKSHGHGIPPRPPSAAAPHIEPNQPTRAMEGSYIVLPPAAASIYKTSTSEGGGAQLPPPS
          DNSYVVLSKQNKSHGHGIPPRPPSAAAPHIEPNQPTRAMEGSYIVLPPAAASIYKTSTSEGGGAQLPPPS
Retrocopy DNSYVVLSKQNKSHGHGIPPRPPSAAAPHIEPNQPTRAMEGSYIVLPPAAASIYKTSTSEGGGAQLPPPS

Parental  INSSSLLPGNSFHSNVTVLKRAFEIATSQTQVEQPMCLDCMRLLSDKMDKEIEDVNADIKAYEVCLQHLE
          INS.SLL.GNSFHSNVTVLKRAFEIATSQTQVEQPMCL.CMRLLSDKMDKEIEDVNADIKA.EVCLQHLE
Retrocopy INSGSLLTGNSFHSNVTVLKRAFEIATSQTQVEQPMCLGCMRLLSDKMDKEIEDVNADIKAHEVCLQHLE

Parental  QESHTVLSDAGFQKEKLKIEEEEKKLNAAIEEAEKQYSEISSEMKDLEIKSKKFEELEERYWHEFNSFQF
          QES..VLSDAGFQ.EKLKIEEEEKKLNAAIEEAEKQYSEISSEMKDLEIKSK.FEELEERYWHEFNSFQF
Retrocopy QESYNVLSDAGFQEEKLKIEEEEKKLNAAIEEAEKQYSEISSEMKDLEIKSKEFEELEERYWHEFNSFQF

Parental  QLTSHQEERDAILAKIEVSQVHLELLKRTNVLNDAFYISHDGVIGTINNFRLGRLPNVQVEWDEINAAWG
          QLTSHQEER.AILAKIEVSQVHLELLKR.NVLNDAFYISHDGVIGTINNFRLGRLPNVQVEWDEINAAWG
Retrocopy QLTSHQEEREAILAKIEVSQVHLELLKRRNVLNDAFYISHDGVIGTINNFRLGRLPNVQVEWDEINAAWG

Parental  QAALLLHTMAQYFTPKFEYRIKIHPMGSYPRVTDIHKNTYELF
          .AALLLHTMAQYFTPKFEYRIKIHPMGSY.RVTDIH.N.YEL.
Retrocopy KAALLLHTMAQYFTPKFEYRIKIHPMGSYARVTDIHRNPYELY

Legend:

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

Expression

RNA-Seq

Oryza glaberrima was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza glaberrima was not studied using ChIP-Seq data.

EST

Oryza glaberrima was not studied using EST data.

TSS

Oryza glaberrima was not studied using FANTOM5 data.

Lab

retro_ogla_19 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza glaberrima 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,