RetrogeneDB ID: retro_ocun_820

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:16916887..16917408(-)
• Located in intron of: ENSOCUG00000003110

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000017863
• Aliases: None
• Description: None

Sequence

>retro_ocun_820
AAACCCACCATTCTAGTGAAAAATAAAGAACTGGAAAAGGAAAACGAAAAGTTAAAGCAAGAAAGACTTGAGAGAAGAAA
ACAGCTTGGTATGAAGCAGGAGTGGGAAATGATGTGCAGAGTAAAGCCACACATTGTCAAAGACAAAGAAGCAGAGTGAA
ATCTTCAGAGAACTCCAACGAGGGGAATGGTGCCATTATTTAATGCTGTTCAAAAAGATCAAAAGAATGCTGATGAAAAG
GTTTAAGAAGCTGGAGGCTCTATTAGCAAGTGTGCTAAGTTGATATCAACTGTTTCTAAGAAAGATTTCATCAGTGTTCT
GAGAGGAATGGATGAAGTACAAATGAGAAAAGTTCAAAAGGAAAGATCTCAAAGCCAAACAGACAAGCAAAATGGGAAGA
GGGCCCAGGGTGGATGACCCAACGTGAAGATTTCACGATGGAAGCATCGATGAAAGACTGGGACAAGGAAAGTGATGGGC
CAGATAACAGCAGACCAGAATCTGCAAGTGACTTTGACATG

Alignment

ORF - retro_ocun_820 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.41 %
• Parental protein coverage: 61.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KPTILVKNKELEKEKEKLKQERLERRKQLDKRREWEMMCRVKPDVVKDKEAERNLQRIATRGVVQLFNAV
          KPTILVKNKELEKE.EKLKQERLERRKQL....EWEMMCRVKP..VKDKEAE.NLQR..TRG.V.LFNAV
Retrocopy KPTILVKNKELEKENEKLKQERLERRKQLGMKQEWEMMCRVKPHIVKDKEAE*NLQRTPTRGMVPLFNAV

Parental  QKHQKNVDEKVKEAGGSIRKRAKLISTVSKKDFISVLRGMDG-TANEKSSTEKNSKAKQTKAKSEEGPGW
          QK.QKN.DEKV.EAGGSI.K.AKLISTVSKKDFISVLRGMD....NEKSS..K.SK.....AK.EEGPGW
Retrocopy QKDQKNADEKV*EAGGSISKCAKLISTVSKKDFISVLRGMDE<STNEKSSKGKISKPNR-QAKWEEGPGW

Parental  TILRDDFMMGASMKDWDKESDGPDNSRPESASDSDV
          ...R.DF.M.ASMKDWDKESDGPDNSRPESASD.D.
Retrocopy MTQREDFTMEASMKDWDKESDGPDNSRPESASDFDM

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	6.18 RPM
SRP017611_kidney	0.00 RPM	3.34 RPM
SRP017611_liver	0.08 RPM	1.31 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_820 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_820 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_820 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000174	1 retrocopy	retro_chof_1961,
Callithrix jacchus	ENSCJAG00000012916	2 retrocopies	retro_cjac_3789, retro_cjac_455,
Mus musculus	ENSMUSG00000001305	1 retrocopy	retro_mmus_3531,
Oryctolagus cuniculus	ENSOCUG00000017863	4 retrocopies	retro_ocun_1738, retro_ocun_820 , retro_ocun_962, retro_ocun_992,
Ictidomys tridecemlineatus	ENSSTOG00000001244	1 retrocopy	retro_itri_1554,
Tarsius syrichta	ENSTSYG00000012715	1 retrocopy	retro_tsyr_2006,