RetrogeneDB ID: retro_ocun_1176

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:124816100..124816762(+)
• Located in intron of: ENSOCUG00000004673

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM60A
• Ensembl ID: ENSOCUG00000008618
• Aliases: None
• Description: family with sequence similarity 60, member A [Source:HGNC Symbol;Acc:30702]

Sequence

>retro_ocun_1176
ATGTTTGGTTTCCATAAGCCAAAGATGTACCAAAGCATAGAGGGCTGCTGCATCTGCCAGGCCAAGTCCTCTAGCTCCCA
CTTCACCGACAGTAAGCTCTACGGGAAGGACTTCCAGAGCTGTTTTGGGTTACACGAGTTGCGTTCTGGAGACATCTGCA
ATGCCTGTGTCCTGCTGGTGAAAAGATGGAAGAAGCTACTGGCAGGATCCAAAAAAAAAAAAAAACCTGGAAATCATGTG
GTAGATGCAAGGGCAGGACCCAGTCTAAAGACCACACTGAAACCAAAGAAAGTGAAGACTGGAAACAGGATGAAAAGCAA
CCAGATCGGCAAACTGCAGAAGGAATTTAAACGCCATAATTCTGATGCTCACAGTACCACCTCAGTGCCCCTCCAGCTCA
GTCCCCTTGTTACAGTAACCAGTCAGATGATGGCTCAGATACAGAGATGGCTTCCGGCTCCAGCAGAACACCGGTCTTCT
TTTTAGATCTCACCTACTGGAAAAGGCAGAAGATCTGCTGTGGGATCATCTACAGAGGGTGTTTGGGGGAAGTGCTCATC
GACACGCACCTCTTCAAGCCTTGCTGCAACAGCAAGAAGCTGGCTGCCAAGCCGCCAGCACCCCAGGGCCCCGAGCCGCT
GCCCATGGCCCCTCAGGAGTGG

Alignment

ORF - retro_ocun_1176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.5 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFGFHKPKMYRSIEGCCICRAKSSSSRFTDSKRYEKDFQSCFGLHETRSGDICNACVLLVKRWKKLPAGS
          MFGFHKPKMY.SIEGCCIC.AKSSSS.FTDSK.Y.KDFQSCFGLHE.RSGDICNACVLLVKRWKKL.AGS
Retrocopy MFGFHKPKMYQSIEGCCICQAKSSSSHFTDSKLYGKDFQSCFGLHELRSGDICNACVLLVKRWKKLLAGS

Parental  KKN---WNHVVDARAGPSLKTTLKPKKVKTLSGSRMKSNQISKLQKEFKRHNSDAHSTTS-SASPAQSPC
          KK.....NHVVDARAGPSLKTTLKPKKVKT..G.RMKSNQI.KLQKEFKRHNSDAHSTTS.SA.PAQSPC
Retrocopy KKKKKPGNHVVDARAGPSLKTTLKPKKVKT--GNRMKSNQIGKLQKEFKRHNSDAHSTTS<SAPPAQSPC

Parental  YSNQSDDGSDTEMASGSSRTPVFSFLDLTYWKRQKICCGIIYKGRFGEVLIDTHLFKPCCNSKKPAAEPS
          YSNQSDDGSDTEMASGSSRTPVF.FLDLTYWKRQKICCGIIY.G..GEVLIDTHLFKPCCNSKK.AA.P.
Retrocopy YSNQSDDGSDTEMASGSSRTPVF-FLDLTYWKRQKICCGIIYRGCLGEVLIDTHLFKPCCNSKKLAAKP-

Parental  PAPQGPEPLPRAPQEW
          PAPQGPEPLP.APQEW
Retrocopy PAPQGPEPLPMAPQEW

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	2.87 RPM
SRP017611_kidney	0.00 RPM	17.53 RPM
SRP017611_liver	0.00 RPM	3.39 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1176 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1176 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1176 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010685	4 retrocopies	retro_cfam_1120, retro_cfam_1552, retro_cfam_1692, retro_cfam_1837,
Choloepus hoffmanni	ENSCHOG00000007193	17 retrocopies	retro_chof_109, retro_chof_1108, retro_chof_1136, retro_chof_1255, retro_chof_1614, retro_chof_1689, retro_chof_1770, retro_chof_1971, retro_chof_2126, retro_chof_2493, retro_chof_2576, retro_chof_2587, retro_chof_453, retro_chof_511, retro_chof_856, retro_chof_979, retro_chof_998,
Callithrix jacchus	ENSCJAG00000001215	3 retrocopies	retro_cjac_1072, retro_cjac_3154, retro_cjac_3289,
Felis catus	ENSFCAG00000008955	4 retrocopies	retro_fcat_1311, retro_fcat_1339, retro_fcat_58, retro_fcat_965,
Mus musculus	ENSMUSG00000039985	4 retrocopies	retro_mmus_1234, retro_mmus_1471, retro_mmus_1557, retro_mmus_3331,
Oryctolagus cuniculus	ENSOCUG00000008618	1 retrocopy	retro_ocun_1176 ,
Rattus norvegicus	ENSRNOG00000046048	1 retrocopy	retro_rnor_2858,
Rattus norvegicus	ENSRNOG00000049943	2 retrocopies	retro_rnor_1121, retro_rnor_2917,
Sarcophilus harrisii	ENSSHAG00000006261	1 retrocopy	retro_shar_670,
Ictidomys tridecemlineatus	ENSSTOG00000007097	1 retrocopy	retro_itri_16,
Tursiops truncatus	ENSTTRG00000008465	3 retrocopies	retro_ttru_1162, retro_ttru_1498, retro_ttru_984,