RetrogeneDB ID: retro_ocun_350

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:27006061..27006572(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000005679
• Aliases: None
• Description: None

Sequence

>retro_ocun_350
GTGCTGGATGCCTTTGGCCAGATGTGGCTACTGGTTGTGAGGACTTGGTGCCGCAACGGGCTGCACTTTGGGGGTCTGAC
TGGCCTCAATAAAGCAGAAAGTGCTGCCTCGCATGGTGAGGCCCAGGTGACAATCTGGAGGCACTCCTGCGATGTCCCTC
CACCCCCCACGAAGCCTGATCACCCCTCGGACGCAACGTCAGTAAGGATTGCAAGTATGCAGACCTCACTAAGGATCAGC
TGCCCTCCTGTGCCAGTCTGAAGCACACTATAGCCAGAGCCCTGCCCTTCTGGAATGAAGAGATTATGCCCCAGATCAAG
GAGTGGAAACAGGTACTGATGCAGCCCATGGCAACAGCACCTGGGACACTGCCAATCATCTGGAGGGTTCTCTGAGGAGG
CCGTCATGGAGCTGAACCTGCTGACTGGTATTCCCATTGTGTATGAATTGGACAAAATACTTGAGGCTCATCAAGACCAT
GCGGTTCCTGGGGGAGGAAGAGACTGTACGC

Alignment

ORF - retro_ocun_350 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.14 %
• Parental protein coverage: 82.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VLDAIDQMWLPVVRTWRLNERHYGGLTGLNKAETAAKHGEAQVKIWRRSYDVPPPPMEPDH-PFYSNISK
          VLDA..QMWL.VVRTW..N..H.GGLTGLNKAE.AA.HGEAQV.IWR.S.DVPPPP..PDH.P...N.SK
Retrocopy VLDAFGQMWLLVVRTWCRNGLHFGGLTGLNKAESAASHGEAQVTIWRHSCDVPPPPTKPDH<PLGRNVSK

Parental  DRRYADLTEDQLPSCESLKDTIARALPFWNEEIVPQIKEGKRVLI-AAHGNSLRGIVKHLE-GLSEEAIM
          D..YADLT.DQLPSC.SLK.TIARALPFWNEEI.PQIKE.K.VL..AAHGNS......HLE.G.SEEA.M
Retrocopy DCKYADLTKDQLPSCASLKHTIARALPFWNEEIMPQIKEWKQVLM<AAHGNSTWDTANHLE<GFSEEAVM

Parental  ELNLPTGIPIVYELD-KNLKPIKPMQFLGDEETVR
          ELNL.TGIPIVYELD.K.L..IK.M.FLG.EETVR
Retrocopy ELNLLTGIPIVYELD>KYLRLIKTMRFLGEEETVR

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	183.11 RPM
SRP017611_kidney	0.00 RPM	100.24 RPM
SRP017611_liver	0.00 RPM	25.90 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_350 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_350 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_350 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012697	2 retrocopies	retro_btau_1611, retro_btau_472,
Canis familiaris	ENSCAFG00000009062	1 retrocopy	retro_cfam_1297,
Callithrix jacchus	ENSCJAG00000016575	1 retrocopy	retro_cjac_370,
Cavia porcellus	ENSCPOG00000006844	4 retrocopies	retro_cpor_158, retro_cpor_539, retro_cpor_605, retro_cpor_660,
Echinops telfairi	ENSETEG00000002467	1 retrocopy	retro_etel_1595,
Homo sapiens	ENSG00000171314	12 retrocopies	retro_hsap_1048, retro_hsap_1052, retro_hsap_1142, retro_hsap_2235, retro_hsap_2604, retro_hsap_3083, retro_hsap_3488, retro_hsap_4249, retro_hsap_4686, retro_hsap_4821, retro_hsap_885, retro_hsap_913,
Gorilla gorilla	ENSGGOG00000028602	13 retrocopies	retro_ggor_1220, retro_ggor_1500, retro_ggor_1667, retro_ggor_1824, retro_ggor_2061, retro_ggor_2118, retro_ggor_2353, retro_ggor_2849, retro_ggor_3005, retro_ggor_3034, retro_ggor_716, retro_ggor_738, retro_ggor_827,
Loxodonta africana	ENSLAFG00000015979	1 retrocopy	retro_lafr_886,
Microcebus murinus	ENSMICG00000007657	1 retrocopy	retro_mmur_135,
Macaca mulatta	ENSMMUG00000020027	1 retrocopy	retro_mmul_119,
Monodelphis domestica	ENSMODG00000004242	4 retrocopies	retro_mdom_1342, retro_mdom_1893, retro_mdom_610, retro_mdom_668,
Oryctolagus cuniculus	ENSOCUG00000005679	5 retrocopies	retro_ocun_1016, retro_ocun_1081, retro_ocun_350 , retro_ocun_706, retro_ocun_976,
Pongo abelii	ENSPPYG00000002530	9 retrocopies	retro_pabe_1325, retro_pabe_2309, retro_pabe_2554, retro_pabe_2639, retro_pabe_2881, retro_pabe_3389, retro_pabe_3639, retro_pabe_3749, retro_pabe_671,
Rattus norvegicus	ENSRNOG00000050585	7 retrocopies	retro_rnor_1669, retro_rnor_2241, retro_rnor_2275, retro_rnor_2361, retro_rnor_2568, retro_rnor_691, retro_rnor_703,
Tupaia belangeri	ENSTBEG00000005913	5 retrocopies	retro_tbel_1677, retro_tbel_1708, retro_tbel_2756, retro_tbel_3667, retro_tbel_563,
Drosophila melanogaster	FBgn0014869	1 retrocopy	retro_dmel_57,