RetrogeneDB ID: retro_ocun_258

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018719:2541941..2542688(+)
• Located in intron of: ENSOCUG00000001137

Retrocopy information

• Ensembl ID: ENSOCUG00000024009
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000002186
• Aliases: None
• Description: None

Sequence

>retro_ocun_258
ATGCAGAAATCAGAGTGCCCTGGAGGTGTACAGCTGAAAAACAAAGTAACAGGTAACTGTAATCAAAGAACTTCATCAAA
TACACAAATAAATCACAGGAGTGCAGTTCAGCGAAGCAAATCCTCATCATCAACCCGTTCTCCAGAGTCTGTCAGAAAGC
TTCATCCTCGACCAAGTGATAAACTTAACCCTAAAACAATTAATCCTTTTGGTGAACAGTCACGAGCCCCTACTGCATTT
GCAGCTATTTACTCTAAAGGAGGTATTCCTTGCAGGTTGGTGCATGGCTCAGTAAAACATAGATTACAGTGGGAATGTCC
TCCTGAAAACCTTGCATTTGATCCTCTTCTTATTACTTTAGCTGAGGGTCTGAGAGAGACTAAACATCCATATACCTTTG
TGTCCAAGGAGGGTTTTAAAGAATTACTTTTGGTCAAAGGTGCATCTGAGAAAGCCATGCCTTTGTTGCCTAGACTGATT
CCGGTGCTAAAGGCGGCTCTGGTCCATTCAGATGATGAAGTATTTGAAAGAGGATTGACTGCTCTGGTACAGTTAAGTGT
CATTGTTGGGCCTTCTCTAAATGACCATCTGAAACATCTGCTTACAAGTCTTTCCAAGAGACTGATGGACAAGAAGTTTA
AAGAGCCAATCACCAGTGCATTACAAAAGCTAGAACAGCATGGTGGAAGTGGAAGTCTTACGATCATCAAATCTAAAATC
CCAACATACTGCTCCATATGCTGTTAA

Alignment

ORF - retro_ocun_258 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.6 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQKSECPGGVQLRNKVTGNCNQRTSSNTQINHRSAVQRSKSSSSTRSPESVRKLHPRPSDKLNPKTINPF
          MQKSECPGGVQL.NKVTGNCNQRTSSNTQINHRSAVQRSKSSSSTRSPESVRKLHPRPSDKLNPKTINPF
Retrocopy MQKSECPGGVQLKNKVTGNCNQRTSSNTQINHRSAVQRSKSSSSTRSPESVRKLHPRPSDKLNPKTINPF

Parental  GEQSRAPTAFAAIYSKGGIPCRLVHGSVKHRLQWECPPENLAFDPLLITLAEGLRETKHPYTFVSKEGFK
          GEQSRAPTAFAAIYSKGGIPCRLVHGSVKHRLQWECPPENLAFDPLLITLAEGLRETKHPYTFVSKEGFK
Retrocopy GEQSRAPTAFAAIYSKGGIPCRLVHGSVKHRLQWECPPENLAFDPLLITLAEGLRETKHPYTFVSKEGFK

Parental  ELLLVKGASEKAMPLLPRLIPVLKAALVHSDDEVFERGLTALVQLSVIVGPSLNDHLKHLLTSLSKRLMD
          ELLLVKGASEKAMPLLPRLIPVLKAALVHSDDEVFERGLTALVQLSVIVGPSLNDHLKHLLTSLSKRLMD
Retrocopy ELLLVKGASEKAMPLLPRLIPVLKAALVHSDDEVFERGLTALVQLSVIVGPSLNDHLKHLLTSLSKRLMD

Parental  KKFKEPITSALQKLEQHGGSGSLTIIKSKIPTYCSICC
          KKFKEPITSALQKLEQHGGSGSLTIIKSKIPTYCSICC
Retrocopy KKFKEPITSALQKLEQHGGSGSLTIIKSKIPTYCSICC

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	0.06 RPM	1.32 RPM
SRP017611_kidney	0.51 RPM	2.43 RPM
SRP017611_liver	0.08 RPM	0.92 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_258 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_258 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_258 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000015625	1 retrocopy	retro_dord_96,
Homo sapiens	ENSG00000163138	1 retrocopy	retro_hsap_488,
Gorilla gorilla	ENSGGOG00000012603	1 retrocopy	retro_ggor_458,
Macropus eugenii	ENSMEUG00000009937	2 retrocopies	retro_meug_1836, retro_meug_1954,
Monodelphis domestica	ENSMODG00000000641	2 retrocopies	retro_mdom_1541, retro_mdom_1646,
Oryctolagus cuniculus	ENSOCUG00000002186	1 retrocopy	retro_ocun_258 ,
Pan troglodytes	ENSPTRG00000015945	1 retrocopy	retro_ptro_368,
Rattus norvegicus	ENSRNOG00000004140	1 retrocopy	retro_rnor_1543,
Tarsius syrichta	ENSTSYG00000001584	1 retrocopy	retro_tsyr_1866,