RetrogeneDB ID: retro_cfam_556

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 13:50192769..50193024(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000010890
• Aliases: None
• Description: None

Sequence

>retro_cfam_556
CTCTTTGACCGAATTTTGGTTGAAACTGTAACCAAAAGAGGTATTATGCTTTCATAAAAATCTCAAGAATAAGTGTTGCA
AGCAACAGTAGTAGTTGTTGGATCAGGTTCTAAAGGAAAAGGTGCAGAGATTCAACCAATTAGTGTGAAAGTTGGAGATA
AAGTTCTCGCAGAATATGAAGGCACCAAAGTAGTTCTAGAAGACAAGTATTATTCCTTATTTAGACATGGTGACATTCTC
AGAATGTATGTGGAC

Alignment

ORF - retro_cfam_556 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.42 %
• Parental protein coverage: 84.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVERSAAETVTKGGIMLPEKSQGKVLQATVVAVGSGSKGKGGEIQPVSVKVGDKVLLPEYGGTKVVLDDK
          L..R...ETVTK.GIML..KSQ..VLQATVV.VGSGSKGKG.EIQP.SVKVGDKV.L.EY.GTKVVL.DK
Retrocopy LFDRILVETVTKRGIMLS*KSQE*VLQATVVVVGSGSKGKGAEIQPISVKVGDKV-LAEYEGTKVVLEDK

Parental  DYFLFRDGDILGKYVD
          .Y.LFR.GDIL..YVD
Retrocopy YYSLFRHGDILRMYVD

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
SRP012049_cerebellum	0.04 RPM	42.71 RPM
SRP017611_brain	0.00 RPM	30.25 RPM
SRP017611_kidney	0.00 RPM	161.92 RPM
SRP017611_liver	0.00 RPM	41.99 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_556 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_556 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_556 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 141 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013769	18 retrocopies	retro_amel_1027, retro_amel_1083, retro_amel_1084, retro_amel_1100, retro_amel_133, retro_amel_1504, retro_amel_1513, retro_amel_1623, retro_amel_1699, retro_amel_1819, retro_amel_199, retro_amel_23, retro_amel_269, retro_amel_310, retro_amel_329, retro_amel_491, retro_amel_506, retro_amel_922,
Bos taurus	ENSBTAG00000012589	4 retrocopies	retro_btau_1118, retro_btau_624, retro_btau_760, retro_btau_801,
Canis familiaris	ENSCAFG00000010890	4 retrocopies	retro_cfam_1768, retro_cfam_1883, retro_cfam_208, retro_cfam_556 ,
Choloepus hoffmanni	ENSCHOG00000007417	17 retrocopies	retro_chof_1048, retro_chof_1160, retro_chof_143, retro_chof_1476, retro_chof_1561, retro_chof_1755, retro_chof_1880, retro_chof_2052, retro_chof_2053, retro_chof_226, retro_chof_303, retro_chof_414, retro_chof_420, retro_chof_86, retro_chof_907, retro_chof_91, retro_chof_940,
Dasypus novemcinctus	ENSDNOG00000013246	27 retrocopies	retro_dnov_1088, retro_dnov_1117, retro_dnov_1214, retro_dnov_1375, retro_dnov_1391, retro_dnov_1405, retro_dnov_1412, retro_dnov_1428, retro_dnov_1445, retro_dnov_1546, retro_dnov_1647, retro_dnov_1652, retro_dnov_1686, retro_dnov_1821, retro_dnov_2176, retro_dnov_2291, retro_dnov_2413, retro_dnov_2569, retro_dnov_2625, retro_dnov_2652, retro_dnov_418, retro_dnov_481, retro_dnov_483, retro_dnov_490, retro_dnov_524, retro_dnov_554, retro_dnov_966,
Equus caballus	ENSECAG00000026874	1 retrocopy	retro_ecab_716,
Erinaceus europaeus	ENSEEUG00000005040	6 retrocopies	retro_eeur_132, retro_eeur_278, retro_eeur_474, retro_eeur_611, retro_eeur_657, retro_eeur_698,
Felis catus	ENSFCAG00000014455	9 retrocopies	retro_fcat_114, retro_fcat_1174, retro_fcat_1406, retro_fcat_1686, retro_fcat_1723, retro_fcat_457, retro_fcat_681, retro_fcat_794, retro_fcat_97,
Loxodonta africana	ENSLAFG00000000057	1 retrocopy	retro_lafr_69,
Myotis lucifugus	ENSMLUG00000000878	4 retrocopies	retro_mluc_1724, retro_mluc_1972, retro_mluc_1979, retro_mluc_2086,
Mus musculus	ENSMUSG00000073676	11 retrocopies	retro_mmus_1005, retro_mmus_1719, retro_mmus_1750, retro_mmus_1934, retro_mmus_2483, retro_mmus_2485, retro_mmus_301, retro_mmus_3077, retro_mmus_386, retro_mmus_872, retro_mmus_877,
Oryctolagus cuniculus	ENSOCUG00000010360	1 retrocopy	retro_ocun_127,
Otolemur garnettii	ENSOGAG00000034434	24 retrocopies	retro_ogar_1018, retro_ogar_1441, retro_ogar_1512, retro_ogar_1690, retro_ogar_1744, retro_ogar_1899, retro_ogar_191, retro_ogar_1921, retro_ogar_200, retro_ogar_2030, retro_ogar_2129, retro_ogar_2310, retro_ogar_235, retro_ogar_2439, retro_ogar_2636, retro_ogar_2928, retro_ogar_3088, retro_ogar_3350, retro_ogar_3419, retro_ogar_389, retro_ogar_777, retro_ogar_824, retro_ogar_829, retro_ogar_834,
Rattus norvegicus	ENSRNOG00000014868	6 retrocopies	retro_rnor_1094, retro_rnor_1320, retro_rnor_1334, retro_rnor_2245, retro_rnor_2296, retro_rnor_984,
Vicugna pacos	ENSVPAG00000005805	8 retrocopies	retro_vpac_173, retro_vpac_209, retro_vpac_292, retro_vpac_299, retro_vpac_329, retro_vpac_410, retro_vpac_443, retro_vpac_46,