RetrogeneDB ID: retro_ocun_217

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:59502333..59502744(+)
• Located in intron of: ENSOCUG00000011375

Retrocopy information

• Ensembl ID: ENSOCUG00000027587
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: H3F3A
• Ensembl ID: ENSOCUG00000024644
• Aliases: H3.3A, H3F3A
• Description: H3 histone, family 3A (H3.3A), mRNA [Source:RefSeq mRNA;Acc:NM_001171112]

Sequence

>retro_ocun_217
ATGGCTCGTACAAAGCAGACTGCCCGCAAATCGACTGGTGGTAAAGCACCCAGGAAGCAACTGGCTACAAAAGCCGCTCG
CAAGAGTGCGCCCTCTACTGGAGGGGTGAAGAAACCTCATCGTTACAGGCCCGGTACTGTGGCACTTCGTGAAATCAGAC
GTTATCAGAAGTCCACTGAGCTTCTGATTCGCAAACTCCCCTTCCAGCGTCTGGTGCGAGAAATCGCTCAGGACTTCAAA
ACAGATCTGCACTTCCAGAGCGCAGCTATTGGTGCTTTGCAGGAGGCAAGCGAGGCCTATCTGGCTGGCCTTTTTGAAGA
CACCAACCTGTGTGCTATCCATGCCAAACGTGTAACAATTATGCCAAAAGACATCCAGCTAGCACGCCGCATACGTGGAG
AACGTGCTTAA

Alignment

ORF - retro_ocun_217 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.53 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
          MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
Retrocopy MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR

Parental  LVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
          LVREIAQDFKTDL.FQSAAIGALQEASEAYL.GLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
Retrocopy LVREIAQDFKTDLHFQSAAIGALQEASEAYLAGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

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	1.16 RPM	26.10 RPM
SRP017611_kidney	1.62 RPM	42.67 RPM
SRP017611_liver	0.62 RPM	12.56 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_217 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_217 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_217 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 96 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009765	3 retrocopies	retro_amel_1636, retro_amel_1794, retro_amel_192,
Choloepus hoffmanni	ENSCHOG00000009661	10 retrocopies	retro_chof_1580, retro_chof_1635, retro_chof_1911, retro_chof_2281, retro_chof_2294, retro_chof_2343, retro_chof_2546, retro_chof_454, retro_chof_517, retro_chof_530,
Cavia porcellus	ENSCPOG00000004707	7 retrocopies	retro_cpor_1059, retro_cpor_1390, retro_cpor_1524, retro_cpor_432, retro_cpor_695, retro_cpor_842, retro_cpor_853,
Gorilla gorilla	ENSGGOG00000022928	7 retrocopies	retro_ggor_1964, retro_ggor_2181, retro_ggor_2198, retro_ggor_2357, retro_ggor_2805, retro_ggor_2905, retro_ggor_2987,
Loxodonta africana	ENSLAFG00000021624	4 retrocopies	retro_lafr_172, retro_lafr_410, retro_lafr_546, retro_lafr_832,
Myotis lucifugus	ENSMLUG00000015447	10 retrocopies	retro_mluc_146, retro_mluc_1571, retro_mluc_2286, retro_mluc_2344, retro_mluc_2364, retro_mluc_246, retro_mluc_2468, retro_mluc_2500, retro_mluc_392, retro_mluc_613,
Mus musculus	ENSMUSG00000060743	19 retrocopies	retro_mmus_1053, retro_mmus_1116, retro_mmus_1139, retro_mmus_1151, retro_mmus_1254, retro_mmus_2285, retro_mmus_2614, retro_mmus_2934, retro_mmus_3009, retro_mmus_3213, retro_mmus_3425, retro_mmus_395, retro_mmus_498, retro_mmus_808, retro_mmus_884, retro_mmus_885, retro_mmus_886, retro_mmus_959, retro_mmus_960,
Oryctolagus cuniculus	ENSOCUG00000024644	2 retrocopies	retro_ocun_185, retro_ocun_217 ,
Oreochromis niloticus	ENSONIG00000019975	5 retrocopies	retro_onil_41, retro_onil_46, retro_onil_56, retro_onil_60, retro_onil_63,
Ochotona princeps	ENSOPRG00000015952	2 retrocopies	retro_opri_1180, retro_opri_937,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,
Ictidomys tridecemlineatus	ENSSTOG00000024226	8 retrocopies	retro_itri_315, retro_itri_449, retro_itri_465, retro_itri_505, retro_itri_649, retro_itri_695, retro_itri_764, retro_itri_771,
Tupaia belangeri	ENSTBEG00000006177	13 retrocopies	retro_tbel_110, retro_tbel_1274, retro_tbel_15, retro_tbel_170, retro_tbel_2335, retro_tbel_3341, retro_tbel_3342, retro_tbel_3820, retro_tbel_391, retro_tbel_487, retro_tbel_592, retro_tbel_783, retro_tbel_978,
Vicugna pacos	ENSVPAG00000011531	5 retrocopies	retro_vpac_107, retro_vpac_637, retro_vpac_646, retro_vpac_76, retro_vpac_96,