RetrogeneDB ID: retro_ogla_14

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 1:31950702..31951770(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORGLA01G0385900
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA01G0385600
• Aliases: None
• Description: None

Sequence

>retro_ogla_14
GGCGTCCGCCGGTTTGCTGCTGCCGGTTTGCTGCTGCTCGCCGCCGCGGCCGCGCTGGTGTGCAGCTCGGCGGCGGCGAG
GATGCCGCCGTTGGCGAAGGGGTTGTCGCTGGGCTACTACGATGAGAGATGCCCGCAGGCGGAGGCCGTCGTGTTCGAGT
TCCTGCAGGACGCCATCGGCAAGGACGTCGGCCTCGCCGCAGCGCTGATCCGGCTCCACTTCCACGACTGCTTCGTCCAG
GGCTGCGACGCCTCCATCCTGCTCGACAGCACACCCACCGAGAAGAGCGAGAAGTTGGCGCCGCCGAACAAGACCCTCCG
CAAGTCGGCGTTCGACGCCATCGACGATCTCCGCGACCTGCTCGACAGGGAATGCGGCGACACCGTCGTGTCCTGCTCCG
ACATCGTCACCCTCGCCGCCCGCGATTCCGTCCTCCTCGCCGGTGGCCCGTGGTACGATGTTCCCCTCGGCCGCCACGAC
GGCTCCAGTTTCGCGTCTGAGGACGCCGTCCTGAGCGCGCTCCCGTCGCCGGACTCCAACGTCACCACGCTCCTCGAAGC
GCTGGGCAAGCTCAAGCTCGACGCCCACGACCTCGTCGCCCTCTCCGGCGCGCACACCGTCGGCATCGCGCACTGCACTT
CCTTCGACAAGCGCCTCTTCCCTCAAGTCGACCCCACCATGGACAAGTGGTTCGCCGGCCACCTCAAGGTCACCTGCCCG
GTGCTGAACACCAACGACACCACCGTCAACGACATCCGGACGCCCAACACCTTCGACAACAAGTACTACGTCGACCTGCA
AAACCGCCAGGGCCTCTTCACCTCCGACCAGGGCCTCTTCTTCAACGCAACCACCAAGCCGATCGTCACCAAGTTCGCCG
TCGACCAGTCGGCCTTCTTCGACCAGTACGTCTACTCCGTCGTCAAGATGGGCATGATCGAGGTGCTCACCGGCTCGCAG
GGGCAGATCCGCAAGCGCTGTTCGGTGTCCAACGCCGCCGCCGCCGGCGACCGTGCTTGGTCCGTCGTGGAGACCGTCGC
TGAGGCCGCCGAGAGCTTGGTGCTGTAG

Alignment

ORF - retro_ogla_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.73 %
• Parental protein coverage: 95.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVVAVCLLVCSAPAAAAAKKPSYPPVAKGLSFDHYKKSCPQAEAIVFNFLHDAIARDVGLAAALIRLHFH
          A.....LL...A...........PP.AKGLS...Y...CPQAEA.VF.FL.DAI..DVGLAAALIRLHFH
Retrocopy AAAGLLLLAAAAALVCSSAAARMPPLAKGLSLGYYDERCPQAEAVVFEFLQDAIGKDVGLAAALIRLHFH

Parental  DCFVQGCDGSILLTKTPGGPDSEQEAVPNLTLRPAAFKAVNDIRALLDKACG-RVVSCSDIVTLAARDSV
          DCFVQGCD.SILL..TP....SE..A.PN.TLR..AF.A..D.R.LLD..CG..VVSCSDIVTLAARDSV
Retrocopy DCFVQGCDASILLDSTPT-EKSEKLAPPNKTLRKSAFDAIDDLRDLLDRECGDTVVSCSDIVTLAARDSV

Parental  KLAGGPEYKVPLGRRDGFTSATTKQVGDALPPPFSHVPELIAALAKLNLDATDLIALSGAHTVGIAHCTS
          .LAGGP.Y.VPLGR.DG...A....V..ALP.P.S.V..L..AL.KL.LDA.DL.ALSGAHTVGIAHCTS
Retrocopy LLAGGPWYDVPLGRHDGSSFASEDAVLSALPSPDSNVTTLLEALGKLKLDAHDLVALSGAHTVGIAHCTS

Parental  FDDRLFPQVDATMDKWFAGHLKLSCPVKNTANTTVNDIRTPNVFDNKYYVDLQNRQGLFTSDQDLFVNAT
          FD.RLFPQVD.TMDKWFAGHLK..CPV.NT..TTVNDIRTPN.FDNKYYVDLQNRQGLFTSDQ.LF.NAT
Retrocopy FDKRLFPQVDPTMDKWFAGHLKVTCPVLNTNDTTVNDIRTPNTFDNKYYVDLQNRQGLFTSDQGLFFNAT

Parental  TRPLVAEFAVDQSAFFHQFVFSVVKMGQIQVLTGSQGQIRANCSVRNPGAAAADEELPWSAAVETVVEAA
          T.P.V..FAVDQSAFF.Q.V.SVVKMG.I.VLTGSQGQIR..CSV.N...AAA.....WS..VETV.EAA
Retrocopy TKPIVTKFAVDQSAFFDQYVYSVVKMGMIEVLTGSQGQIRKRCSVSN---AAAAGDRAWS-VVETVAEAA

Parental  ESIVL
          ES.VL
Retrocopy ESLVL

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_14 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza glaberrima	ORGLA01G0385600	1 retrocopy	retro_ogla_14 ,