RetrogeneDB ID: retro_ocun_1215

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:144102871..144103738(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RARGAMMA
• Ensembl ID: ENSOCUG00000001432
• Aliases: None
• Description: None

Sequence

>retro_ocun_1215
AAAGAGGTGAAGGAAGAAGGCTCACCCGACAGCTATGAGCTGAGCCCCCAGTTAGAGGAACTCATCAGCAAGGTCAGCAA
AGCCCACCAGGAGACCTTCCCCTCGCTCTGCCAGCTGGGCAAGTACACCACGAACTCCAGCGCAGACCACCGGGTGCAGC
TGGACCTGGGGCTGTGGGACAAGTTCAGTGAGTTGGCCACCAAGTGCATCATCAAGATCGTGGAGTTTGCCAAGCGGCTG
CCCGGCTTCACTGGGCTCAGCATCGCCGACCAGATCACTCTGCTCAAGGCCGCCTGCCTGGACATCCTGATGCTGCGGAT
CTGCACGAGGTACACTCCGGAGCAGGACACCATGACCTTCTCCGACGGGCTCACCCTGAACCGCACCCAGATGCACAACG
CAGGCTTCGGGCCCCTCACAGACCTCGTGTTTACCTTTGCCGGGCAGCTCCTGCCGCTGGAGATGGACGACACGGAGACG
GGGCTGCTCAGTGCCATCTGCCTCATCTGTGGAGATCGCATGGACCTGGAGGAGCCTGAAAAAGTGGACAAGCTGCAGGA
GCCGCTGCTGGAGGCCCTGAGGCTGTACGCCCGGCGCCGGCGGCCCAGCCAGCCCTACATGTTCCCGAGGATGCTCATGA
AAATCACCGACCTGCGGGGCATCAGCACCAAGGGAGCAGAAAGGGCCATTACCCTGAAGATGGAGATTCCAGGCCCGATA
CCCCCCCTGATCCGAGAGATGCTGGAGAACCCCGAAATGTTTGAGGACGACTCCTCGCAGCCTGACTCCCACCCGAAGGC
CTCGAGCGAGGATGAGGCTCCTGGGGGCCAGGGCAAGCGGGGTCGAAGTCCCCAGCCGGACCAGGGT

Alignment

ORF - retro_ocun_1215 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.04 %
• Parental protein coverage: 68.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KEVKEEGSPDSYELSPQLEELISKVSKAHQETFPSLCQLGKYTTNSSADHRVQLDLGLWDKFSELATKCI
          KEVKEEGSPDSYELSPQLEELISKVSKAHQETFPSLCQLGKYTTNSSADHRVQLDLGLWDKFSELATKCI
Retrocopy KEVKEEGSPDSYELSPQLEELISKVSKAHQETFPSLCQLGKYTTNSSADHRVQLDLGLWDKFSELATKCI

Parental  IKIVEFAKRLPGFTGLSIADQITLLKAVCLDILVGQALGGPVPE----AFSNFWSMKRTQMHNAGFGPLT
          IKIVEFAKRLPGFTGLSIADQITLLKA.CLDIL.........PE.....FS......RTQMHNAGFGPLT
Retrocopy IKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGPLT

Parental  DLVFAFAGQLLPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPR
          DLVF.FAGQLLPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPR
Retrocopy DLVFTFAGQLLPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPR

Parental  MLMKITDLRGISTKGAERAITLKMEIPGPMPPLIREMLENPEMFEDDSSQPDSHPKASSEDEAPGGQGKR
          MLMKITDLRGISTKGAERAITLKMEIPGP.PPLIREMLENPEMFEDDSSQPDSHPKASSEDEAPGGQGKR
Retrocopy MLMKITDLRGISTKGAERAITLKMEIPGPIPPLIREMLENPEMFEDDSSQPDSHPKASSEDEAPGGQGKR

Parental  GRSPQPDQG
          GRSPQPDQG
Retrocopy GRSPQPDQG

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	2.54 RPM	7.73 RPM
SRP017611_kidney	3.14 RPM	7.91 RPM
SRP017611_liver	0.85 RPM	2.16 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1215 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1215 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1215 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000001432	1 retrocopy	retro_ocun_1215 ,