RetrogeneDB ID: retro_ogla_60

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 2:16798362..16799469(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA09G0122500
• Aliases: None
• Description: None

Sequence

>retro_ogla_60
GTAGCTCTCAACTCCCTCTTTTTGACTAAAGGCCGGGGATTTTCCTCCCTTAATGATGCTCTCATCTCCCTTCTGCCAAA
GAAGGATGTGGTCGTTGACGTCAAGGATTTTCGACCGATTAGCCTCATCCACAGCTTTGGGAAGTTGTTCTCCAAGATCC
TGGCTTCCCGTCTCTCTCCCCACCTTGACGGGCTTATGGCGGCCAATCAAAGTGCCTTCGTCAAAGGTCGATCCCTCCAC
GACAACTTTCGCTATGTCCAACTCGCGGCAAGGGCCCTCCATGCCAGGCGCACTCCCCGCCTCCTTCTCAAGGTGGACAT
CGCAAAGGCCTTTGACACGGTCAGTTGGCCATTCTTGCTTCAGGTGCTTGCTCATCTCGGGTTCAGTTAAGCGTTGGCGG
GATTGGATCTCCCTCATCCTCAGTGCCTCCTCTTCCCGAGTGTTGATCAATGGGGTGCCTGGTCCACGCTTCCCTCACCG
AAGGGGTCTTCGGCAAGGAGATCCTCTATCCCCTATACTCTTCATTCTAGTCATGGATGTGCTCAATGTGATGCTCTGTA
AGGCCTCTGACTCGGGCGGGTTCCTTCAGCTTAACGATCGTGCCTTGCGACCTCACGCCTCCCTCTATGCTGATGATCTA
GTTCTCTTCCTCTCCCCGGTTCGACAGGATCTTGGGTTCATCCAGTGCTTCCTTTCTGTCTTTGGTGCAGCTTTCGAGCT
GCGCACCAATTTTGCCAAATGCTCGATTACTTTGATCTGTTGCTCGGCCGAGGACCTAGAGCTAGTTCAATCCTGCTTCC
CCTGCACGATTTCTGATTTTGCTTGCACCTACCTCGACATTCCGCTGTCTGTTCGCAAGTTGCCGAAGGTGGCCCTGCAA
CCGCTTGTTGACAAAGTCTCCCATCGGCTTCCCCCTGGAAGGGACGTCTCACCACGCTGGCCGGCCGCTTTGTGCTGGTC
CAGTCTGTCCTCTCCTCCATTTCGGTCCATGTGTCTATGGCGATCGGCCTTCCTGTCTGGGTTATTAAAGCCATTAACAA
GAAGCGTCGAGCCTTCCTGTGGACGGGTACGGACTCAGCTCATGGGGGGCAGTGCCGGGTATCTTGG

Alignment

ORF - retro_ogla_60 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.84 %
• Parental protein coverage: 57.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IAITEVLVKKHKGFSSLNDALISLLPKKDEAVDVRDFRPISLIHSFGKLFSKILASHLSPLLDGLVEANQ
          .A.......K..GFSSLNDALISLLPKKD..VDV.DFRPISLIHSFGKLFSKILAS.LSP.LDGL..ANQ
Retrocopy VALNSLFLTKGRGFSSLNDALISLLPKKDVVVDVKDFRPISLIHSFGKLFSKILASRLSPHLDGLMAANQ

Parental  SAFVKGRSLHDNFCYVQLAARALHARRTPRLLLKVDIAKAFDTVSWPFLLEVLAHLGFS-QRWRDWISLI
          SAFVKGRSLHDNF.YVQLAARALHARRTPRLLLKVDIAKAFDTVSWPFLL.VLAHLGFS..RWRDWISLI
Retrocopy SAFVKGRSLHDNFRYVQLAARALHARRTPRLLLKVDIAKAFDTVSWPFLLQVLAHLGFS>KRWRDWISLI

Parental  ISASSSRVLINGVPGPRFLHRRGLRQGDPLSPMLFILVMEVLNAMLRKASDSGGFLPLNDRALRHRASLY
          .SASSSRVLINGVPGPRF.HRRGLRQGDPLSP.LFILVM.VLN.ML.KASDSGGFL.LNDRALR..ASLY
Retrocopy LSASSSRVLINGVPGPRFPHRRGLRQGDPLSPILFILVMDVLNVMLCKASDSGGFLQLNDRALRPHASLY

Parental  ADDLVLFLSPVRQDLEFIQGILSVFGAASELRTNFAKCSITPIRSSDEDLELVHSCFPCSISDFPCTYLG
          ADDLVLFLSPVRQDL.FIQ..LSVFGAA.ELRTNFAKCSIT.I..S.EDLELV.SCFPC.ISDF.CTYL.
Retrocopy ADDLVLFLSPVRQDLGFIQCFLSVFGAAFELRTNFAKCSITLICCSAEDLELVQSCFPCTISDFACTYLD

Parental  IPLSIRKLPKAALQPLVDRVAHRLP-PWKGRLTTLAGRSVLVQSVLSSIPVHVSMAIGLPAWVVKAIDKK
          IPLS.RKLPK.ALQPLVD.V.HRLP.PWKGRLTTLAGR.VLVQSVLSSI.VHVSMAIGLP.WV.KAI.KK
Retrocopy IPLSVRKLPKVALQPLVDKVSHRLP<PWKGRLTTLAGRFVLVQSVLSSISVHVSMAIGLPVWVIKAINKK

Parental  RRAFLWTGIPNLRLAGFALRIRW
          RRAFLWTG.......G...R..W
Retrocopy RRAFLWTGTDSAH--GGQCRVSW

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_60 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza glaberrima	ORGLA09G0122500	1 retrocopy	retro_ogla_60 ,