RetrogeneDB ID: retro_ocun_155

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 6:4472235..4473534(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021942
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000006144
• Aliases: None
• Description: None

Sequence

>retro_ocun_155
ATGGACGAGGCCGTGGGCGACCTGAAGCAGGCATTGCCCTGCGTGGCCGAAGCGCCCACGGTCCACGTGGAGGTGCACCA
GCGGAGCGGCAGCACCGCGAAGAGGGAAGACGTGAAGCTGGCTGTCAGAAAGCTGCTCGACAGACACAACATTGTGTTCG
GCGACTACAAGTGGACTGAGTTTGATGACCCTTTTCTGAGCAGGAACGTGCAGTCTGTGGCGCTCGTTGACACCGAGCTG
AAGGTGAAAGCCCCGCAGCCCATTGATTTGAGTGCATGCACTATTGCACTTCACATCTTCCAGCTGAATGAAGATGGCCC
CAGCAGTGAAAATTTGGAAGAAGAGACAGAAAACATAATTGCAGCCAATCACTGGGTTCTGCCTGCAGCTGAATTCCACG
GAGTCGGGGACAGCCTGGTGTACGATGCGGAAGTGAAGTCACACCTCCTCGATTACGTGATGACAACCTTACTGTTCTCG
GACAAGAACGTGGACAGCAACCTCATCACCTGGAACCGCGTGGTGCTGCTGCACGGTCCTCCAGGGACTGGGAAAACATC
GCTGTGCAAAGCGTTGGCCCAGAAACTGACCATTAGACTGTCAAGCAGGTACCGGTATGGTCAATTAATTGAAATAAACA
GCCACAGTCTGTTTTCCAAGTGGTTTTCTGAAAGTGGCAAGCTGGTAACTAGGATGTTGCAGAAGATTCAAGATTTGATT
GACGACAAAGAAGCGCTGGTGTTTGTGCTGATTGACGAGGTGGAGAGTCTCACGGCCGCCCGCAGCGCCTGCAGGGCAGG
CACCGAGCCCTCGGACGCCATCCGTGTGGTCAACGCCGTCTTGACCCAGATTGACCAGATTAAAAGGCATTCCAATGTGG
TGATCCTGACCACTTCCAACATCACTGAGAAGATCGACGTGGCCTTCGTGGACAGAGCTGATCTCAAGCAGTACATCGGG
CCCCCCTCGGCAGCAGCCATCTTTAAAATCTACCTCTCTTGCTTGGAAGAACTCATGAAGTGTCAGATCATCTACCCGCG
CCAGCAGCTGCTGACCCTGCGAGAGCTCGAGATGATCGGCTTCATTGAAAACAACGTGTCCAAGCTCAGCCTCCTTTTGA
GTGAGATTTCAAGGAAGAGCGAGGGCCTCAGCAGCCGGGTCCTGAGGAAGCTGCCTTTCCTGGCTCACGCGCTGTACGTG
CAGGCCCCCACCATCACCATAGAGGGCTTCCTGCAGGCGCTGTCGCTGGCAGTGGACAAGCAGTTTGAAGAGAGAAAGAA
GCTCTCAGCTTATGTTTGA

Alignment

ORF - retro_ocun_155 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STAKREDVKLAVRKLLDRHNIVFGDYKWTEFDDPFLSRNVRSVALVDTELKVKAPQPIDLSACTIALHIF
          STAKREDVKLAVRKLLDRHNIVFGDYKWTEFDDPFLSRNV.SVALVDTELKVKAPQPIDLSACTIALHIF
Retrocopy STAKREDVKLAVRKLLDRHNIVFGDYKWTEFDDPFLSRNVQSVALVDTELKVKAPQPIDLSACTIALHIF

Parental  QLNEDGPSSENLEEETENIIAANHWVLPAAEFHGLWDSLVYDAEVKSHLLDYVMTTLLFSDKNVDSNLIT
          QLNEDGPSSENLEEETENIIAANHWVLPAAEFHG..DSLVYDAEVKSHLLDYVMTTLLFSDKNVDSNLIT
Retrocopy QLNEDGPSSENLEEETENIIAANHWVLPAAEFHGVGDSLVYDAEVKSHLLDYVMTTLLFSDKNVDSNLIT

Parental  WNRVVLLHGPPGTGKTSLCKALAQKLTIRLSSRYRYGQLIEINSHSLFSKWFSESGKLVTRMFQKIQDLI
          WNRVVLLHGPPGTGKTSLCKALAQKLTIRLSSRYRYGQLIEINSHSLFSKWFSESGKLVTRM.QKIQDLI
Retrocopy WNRVVLLHGPPGTGKTSLCKALAQKLTIRLSSRYRYGQLIEINSHSLFSKWFSESGKLVTRMLQKIQDLI

Parental  DDKEALVFVLIDEVESLTAARSACRAGTEPSDAIRVVNAVLTQIDQIKRHSNVVILTTSNITEKIDVAFV
          DDKEALVFVLIDEVESLTAARSACRAGTEPSDAIRVVNAVLTQIDQIKRHSNVVILTTSNITEKIDVAFV
Retrocopy DDKEALVFVLIDEVESLTAARSACRAGTEPSDAIRVVNAVLTQIDQIKRHSNVVILTTSNITEKIDVAFV

Parental  DRADLKQYIGPPSAAAIFKIYLSCLEELMKCQIIYPRQQLLTLRELEMIGFIENNVSKLSLLLSEISRKS
          DRADLKQYIGPPSAAAIFKIYLSCLEELMKCQIIYPRQQLLTLRELEMIGFIENNVSKLSLLLSEISRKS
Retrocopy DRADLKQYIGPPSAAAIFKIYLSCLEELMKCQIIYPRQQLLTLRELEMIGFIENNVSKLSLLLSEISRKS

Parental  EGLSGRVLRKLPFLAHALYVQAPTVTIEGFLQALSLAVDKQFEERKKLSAYV
          EGLS.RVLRKLPFLAHALYVQAPT.TIEGFLQALSLAVDKQFEERKKLSAYV
Retrocopy EGLSSRVLRKLPFLAHALYVQAPTITIEGFLQALSLAVDKQFEERKKLSAYV

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	0.11 RPM	0.55 RPM
SRP017611_kidney	0.10 RPM	0.30 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_155 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_155 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_155 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007439	1 retrocopy	retro_chof_2003,
Callithrix jacchus	ENSCJAG00000003849	1 retrocopy	retro_cjac_1987,
Dasypus novemcinctus	ENSDNOG00000015202	1 retrocopy	retro_dnov_2464,
Oryctolagus cuniculus	ENSOCUG00000006144	1 retrocopy	retro_ocun_155 ,
Pongo abelii	ENSPPYG00000015309	1 retrocopy	retro_pabe_1358,