RetrogeneDB ID: retro_ocun_1138

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 20:31481890..31482441(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF115
• Ensembl ID: ENSOCUG00000003055
• Aliases: None
• Description: ring finger protein 115 [Source:HGNC Symbol;Acc:18154]

Sequence

>retro_ocun_1138
CTCCAGCTGCCAGTGAGATACAGATCTCGGGGAAGTACTCGTCCTGACAGATCACCAGCTATTGAAGGAATAATGCAACA
GATCTTTGCAGGATTCTTCTCAACTTCTGCGATTCCTGGGTCCCCACACCCTTTTTCCTGGAGCAGGATGCTGCACTCCA
ACCCTGGGGACTATGCCTGGGGTCAGACAGGGCCTGATGCCATTGTAACCCAGCTTTTAGGACAACTGGGAAACACAGGG
CCTCCCCCAGCTGACAGGGAGAAGATTACATCTCTTCCAACAGCGTCAGTAACTCAGGAACAAGTTGATAGGGGTTTAGA
GTGTCCAGTGTGCAAAGAAGATCACACAGTTAGAGAGGAAGTCCGGCAGTTGCCCGGCAATCACTTCTTTTACAGCAGTT
GTATTGTGCCATGGTTAGAACTGCATGACACTTGTCCTGTATGTAGCAGGAGCCTAAACGGTGAGGACTCTACGCAGCAA
TCCCAGAGCTCTGAGCTTCTGCAAACAACAGATTTACCAGTGACGGCCAACTACATGACCGATGGACTTTC

Alignment

ORF - retro_ocun_1138 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.11 %
• Parental protein coverage: 60.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LPMTRRYRSRGSTRPDRSPAIEGIMQQIFAGFFANSAIPGSPHPFSWSGMLHSNPGDYAWGQTGLDAIVT
          L....RYRSRGSTRPDRSPAIEGIMQQIFAGFF..SAIPGSPHPFSWS.MLHSNPGDYAWGQTG.DAIVT
Retrocopy LQLPVRYRSRGSTRPDRSPAIEGIMQQIFAGFFSTSAIPGSPHPFSWSRMLHSNPGDYAWGQTGPDAIVT

Parental  QLLGQLENTGPPPADKEKITSLPTVSVTQEQVDMGLECPVCKEDYTVREEVRQLPCNHFFHSSCIVPWLE
          QLLGQL.NTGPPPAD.EKITSLPT.SVTQEQVD.GLECPVCKED.TVREEVRQLP.NHFF.SSCIVPWLE
Retrocopy QLLGQLGNTGPPPADREKITSLPTASVTQEQVDRGLECPVCKEDHTVREEVRQLPGNHFFYSSCIVPWLE

Parental  LHDTCPVCRKSLNGEDSTRQSQSSE-ASASNRFSSDSQLHDRWTF
          LHDTCPVC..SLNGEDST.QSQSSE.ASA.NRF.SD.QLHDRWTF
Retrocopy LHDTCPVCSRSLNGEDSTQQSQSSE<ASANNRFTSDGQLHDRWTF

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	0.00 RPM	33.83 RPM
SRP017611_kidney	0.10 RPM	35.88 RPM
SRP017611_liver	0.00 RPM	19.58 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1138 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1138 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1138 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000009030	1 retrocopy	retro_ecab_459,
Macropus eugenii	ENSMEUG00000002500	1 retrocopy	retro_meug_1546,
Oryctolagus cuniculus	ENSOCUG00000003055	1 retrocopy	retro_ocun_1138 ,
Pteropus vampyrus	ENSPVAG00000014487	13 retrocopies	retro_pvam_1039, retro_pvam_1096, retro_pvam_1111, retro_pvam_1293, retro_pvam_1295, retro_pvam_1442, retro_pvam_730, retro_pvam_733, retro_pvam_759, retro_pvam_796, retro_pvam_806, retro_pvam_849, retro_pvam_964,
Tarsius syrichta	ENSTSYG00000004867	2 retrocopies	retro_tsyr_1734, retro_tsyr_1870,