RetrogeneDB ID: retro_ocun_111

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 18:50800284..50801634(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023839
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000028032
• Aliases: None
• Description: None

Sequence

>retro_ocun_111
ATGCGTGAGTGCATCTCCATCCACGTCGGCCAGGCTGGTGTCCAGATCGGCAATGCCTGCTGGGAGCTCTACTGCCTGGA
ACATGGCATCCAGCCCGATGGCCAGATGCCAAGTGACAAGACCATTGGGGGAGGAGACGACTCCTTCAACACCTTCTTCA
GTGAGACGGGCGCTGGCAAGCACGTGCCCAGGGCCGTGTTTGTAGACCTGGAGCCCACGGTCATTGATGAAGTTCGCACC
GGCACCTACCGCCAGCTCTTCCACCCCGAGCAGCTCATCACGGGCAAGGAAGATGCTGCCAATAACTATGCCCGCGGGCA
CTACACCATTGGCAAGGAGATCATTGACCTCGTCCTGGACCGAATTTGCAAGCTGGCTGACCAGTGCACTGGCCTGCAGG
GCTTCTTGGTTTTCCACAGCTTTGGTGGGGGAACTGGTTCTGGGTTCACCTCCCTGCTGATGGAACGCCTCTCTGTCGAT
TACGGCAAGAAGTCCAAGCTGGAGTTCTCCATCTACCCAGCCCCCCAGGTTTCCACAGCTGTGGTGGAGCCCTACAACTC
CATCCTCACCACCCACACCACCCTGGAGCACTCTGATTGTGCCTTCATGGTAGACAACGAGGCCATCTATGACATCTGTC
GTAGAAACCTCGATATCGAGCGCCCCACCTACACTAACCTGAACCGCCTTATTAGCCAGATCGTGTCCTCCATCACGGCT
TCCCTGCAGTTTGATGGAGCCCTGAATGTTGATCTGACAGAATTCCAGACCAACCTGGTGCCCTACCCCCACATCCACTT
CCCTCTGGCCACATACGCCCCCGTCATCTCTGCTGAGAAAGCCTACCACGAGCAGCTTTCTGTAGCAGAGATCACCAATG
CCTGCTTTGAGCCGGCCAACCAGATGGTGAAATGTGACCCTCGCCACGGTAAATACATGGCTTGCTGCCTGCTGTACCAT
GGCGACGTGGTTCCCAAAGATGTCAATGCTGCCATCGCCACCATCAAGACCAAGCGCAGCATCCAGTTTGTGGATTGGTG
CCCCACTGGCTTCAAGGTTGGCATTAACTACCAGCCTCCCACGGTGGTGCCTGGTGGAGACCTGGCCAAAGTGCAGCGAG
CTGTGTGCATGCTGAGCAACACCACAGCCGTGGCCGAGGCCTGGGCTCGCCTGGACCACAAGTTTGACCTGATGTATGCC
AAGCGTGCCTTTGTTCACTGGTACATGGGGGAGGGCAGGGAGGAGGGAGAGTTTTCTGAAGCTCGTGAGGACATGGCTGC
CCTGGAGAAGGATTACGAGGAGGTTGGAGCAGACAGTGCCGAGGGAGAGGATGAGGGTGAAGAATATTAA

Alignment

ORF - retro_ocun_111 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.66 %
• Parental protein coverage: 99.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLE
          RECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLE
Retrocopy RECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLE

Parental  PTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSF
          PTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRI.KLADQCTGLQGFLVFHSF
Retrocopy PTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRICKLADQCTGLQGFLVFHSF

Parental  GGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYD
          GGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYD
Retrocopy GGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYD

Parental  ICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKA
          ICRRNLDIERPTYTNLNRLISQIVSSITASL.FDGALNVDLTEFQTNLVPYP.IHFPLATYAPVISAEKA
Retrocopy ICRRNLDIERPTYTNLNRLISQIVSSITASLQFDGALNVDLTEFQTNLVPYPHIHFPLATYAPVISAEKA

Parental  YHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGF
          YHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLY.GDVVPKDVNAAIATIKTKRSIQFVDWCPTGF
Retrocopy YHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYHGDVVPKDVNAAIATIKTKRSIQFVDWCPTGF

Parental  KVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAVAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEA
          KVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAVAEAWARLDHKFDLMYAKRAFVHWY.GEG.EEGEFSEA
Retrocopy KVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAVAEAWARLDHKFDLMYAKRAFVHWYMGEGREEGEFSEA

Parental  REDMAALEKDYEEVGADSAEGEDEGEEY
          REDMAALEKDYEEVGADSAEGEDEGEEY
Retrocopy REDMAALEKDYEEVGADSAEGEDEGEEY

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	0.72 RPM	56.40 RPM
SRP017611_kidney	4.05 RPM	60.81 RPM
SRP017611_liver	2.47 RPM	28.67 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_111 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_111 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_111 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039992	1 retrocopy	retro_btau_840,
Canis familiaris	ENSCAFG00000008661	2 retrocopies	retro_cfam_960, retro_cfam_978,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Equus caballus	ENSECAG00000009504	1 retrocopy	retro_ecab_1041,
Erinaceus europaeus	ENSEEUG00000004068	1 retrocopy	retro_eeur_669,
Felis catus	ENSFCAG00000024852	1 retrocopy	retro_fcat_361,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
Mus musculus	ENSMUSG00000043091	1 retrocopy	retro_mmus_843,
Oryctolagus cuniculus	ENSOCUG00000027812	1 retrocopy	retro_ocun_197,
Oryctolagus cuniculus	ENSOCUG00000028032	1 retrocopy	retro_ocun_111 ,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Pteropus vampyrus	ENSPVAG00000004646	1 retrocopy	retro_pvam_929,
Rattus norvegicus	ENSRNOG00000015544	3 retrocopies	retro_rnor_1193, retro_rnor_2260, retro_rnor_960,