RetrogeneDB ID: retro_cfam_1117

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 23:9330452..9330857(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000004916
• Aliases: None
• Description: Histone H3 [Source:UniProtKB/TrEMBL;Acc:E2R6K5]

Sequence

>retro_cfam_1117
ATGGCTCTTACAAGGCCGCCCGCCCACCTGTACACCGGCGTTAAAGCCGGGAGGAGGCAAACGACTACAAATGCCGCTAG
CAAAAGTGCGGCCTCCACTGGAAGGGTGAAGAAACTTCGTGGTTAGAGACGTGGTACTGTGGCACTCCGTGAAATTAGAC
CTTATCAGAAACCAGCTGAACTTCACAGACTTCCTTTCCAATGTCGGGTGCAAAAAACTTGCTCAGGACTTCAACAAAAT
AGATCTGTACTTCAGAGTGCACCTATAGGTGCTTTGCAGGAGACAAGGGAGCCCTATCTAGTGGACCTTTATGCAGACAC
CAACCTGTGTGCTGTCCCGGCCAAATTTGTCACAATTATGCCAAAAGACTTTGGGCTAGCATGCTGCATAAGTGGAGAAT
GTGCT

Alignment

ORF - retro_cfam_1117 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.15 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
          MA.T...A...TG.KA.R.Q..T.AA.KSA.STG.VKK....R.GTVALREIR.YQK..EL....LPFQ.
Retrocopy MALTRPPAHLYTGVKAGRRQTTTNAASKSAASTGRVKKLRG*RRGTVALREIRPYQKPAEL--HRLPFQC

Parental  LV-REIAQDF-KTDLRF-QSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
          .V....AQDF.K.DL.F.QSA.IGALQE..E.YLV.L..DTNLCA..AK.VTIMPKD..LA..I.GE.A
Retrocopy RV>KKLAQDFNKIDLYF<QSAPIGALQETREPYLVDLYADTNLCAVPAKFVTIMPKDFGLACCISGECA

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	0.00 RPM	286.22 RPM
SRP017611_brain	0.00 RPM	57.96 RPM
SRP017611_kidney	0.00 RPM	89.48 RPM
SRP017611_liver	0.00 RPM	20.23 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1117 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1117 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1117 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 30 parental genes, and 183 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014588	7 retrocopies	retro_amel_1023, retro_amel_1026, retro_amel_144, retro_amel_570, retro_amel_687, retro_amel_711, retro_amel_903,
Bos taurus	ENSBTAG00000024561	3 retrocopies	retro_btau_156, retro_btau_204, retro_btau_47,
Canis familiaris	ENSCAFG00000004916	2 retrocopies	retro_cfam_1117 , retro_cfam_622,
Canis familiaris	ENSCAFG00000016119	4 retrocopies	retro_cfam_168, retro_cfam_1845, retro_cfam_650, retro_cfam_673,
Dipodomys ordii	ENSDORG00000008132	9 retrocopies	retro_dord_238, retro_dord_283, retro_dord_43, retro_dord_589, retro_dord_678, retro_dord_685, retro_dord_719, retro_dord_765, retro_dord_774,
Erinaceus europaeus	ENSEEUG00000013796	1 retrocopy	retro_eeur_2,
Felis catus	ENSFCAG00000003617	4 retrocopies	retro_fcat_1085, retro_fcat_1953, retro_fcat_592, retro_fcat_830,
Felis catus	ENSFCAG00000030424	5 retrocopies	retro_fcat_1251, retro_fcat_1532, retro_fcat_1533, retro_fcat_2011, retro_fcat_674,
Homo sapiens	ENSG00000163041	5 retrocopies	retro_hsap_2825, retro_hsap_2889, retro_hsap_3102, retro_hsap_3214, retro_hsap_4800,
Gorilla gorilla	ENSGGOG00000022526	11 retrocopies	retro_ggor_1179, retro_ggor_1809, retro_ggor_1837, retro_ggor_1919, retro_ggor_2003, retro_ggor_2837, retro_ggor_2956, retro_ggor_3082, retro_ggor_393, retro_ggor_736, retro_ggor_944,
Gadus morhua	ENSGMOG00000014306	1 retrocopy	retro_gmor_9,
Macropus eugenii	ENSMEUG00000004090	5 retrocopies	retro_meug_1041, retro_meug_1065, retro_meug_1819, retro_meug_281, retro_meug_573,
Microcebus murinus	ENSMICG00000010469	6 retrocopies	retro_mmur_1185, retro_mmur_1243, retro_mmur_1249, retro_mmur_1543, retro_mmur_827, retro_mmur_83,
Macaca mulatta	ENSMMUG00000031483	9 retrocopies	retro_mmul_108, retro_mmul_147, retro_mmul_201, retro_mmul_213, retro_mmul_215, retro_mmul_286, retro_mmul_337, retro_mmul_346, retro_mmul_7,
Monodelphis domestica	ENSMODG00000005983	3 retrocopies	retro_mdom_1037, retro_mdom_1132, retro_mdom_175,
Mustela putorius furo	ENSMPUG00000013811	3 retrocopies	retro_mputfur_1159, retro_mputfur_787, retro_mputfur_881,
Mus musculus	ENSMUSG00000016559	18 retrocopies	retro_mmus_1058, retro_mmus_1188, retro_mmus_1269, retro_mmus_1535, retro_mmus_1635, retro_mmus_2021, retro_mmus_2083, retro_mmus_2377, retro_mmus_2771, retro_mmus_2867, retro_mmus_2972, retro_mmus_3002, retro_mmus_3144, retro_mmus_3477, retro_mmus_3667, retro_mmus_896, retro_mmus_961, retro_mmus_962,
Nomascus leucogenys	ENSNLEG00000001577	2 retrocopies	retro_nleu_25, retro_nleu_35,
Otolemur garnettii	ENSOGAG00000024312	11 retrocopies	retro_ogar_1086, retro_ogar_1790, retro_ogar_1863, retro_ogar_2364, retro_ogar_2463, retro_ogar_2581, retro_ogar_2746, retro_ogar_3415, retro_ogar_478, retro_ogar_842, retro_ogar_955,
Otolemur garnettii	ENSOGAG00000025933	14 retrocopies	retro_ogar_1285, retro_ogar_1364, retro_ogar_1449, retro_ogar_1575, retro_ogar_1576, retro_ogar_2200, retro_ogar_2316, retro_ogar_2449, retro_ogar_2634, retro_ogar_3235, retro_ogar_42, retro_ogar_733, retro_ogar_937, retro_ogar_952,
Oreochromis niloticus	ENSONIG00000015805	7 retrocopies	retro_onil_45, retro_onil_47, retro_onil_51, retro_onil_54, retro_onil_61, retro_onil_65, retro_onil_69,
Procavia capensis	ENSPCAG00000004484	2 retrocopies	retro_pcap_171, retro_pcap_95,
Pongo abelii	ENSPPYG00000000168	14 retrocopies	retro_pabe_1285, retro_pabe_2151, retro_pabe_2204, retro_pabe_2252, retro_pabe_2391, retro_pabe_2679, retro_pabe_2722, retro_pabe_2805, retro_pabe_2938, retro_pabe_3078, retro_pabe_323, retro_pabe_3420, retro_pabe_3637, retro_pabe_3697,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,
Pan troglodytes	ENSPTRG00000002045	20 retrocopies	retro_ptro_1045, retro_ptro_1704, retro_ptro_1770, retro_ptro_1867, retro_ptro_1954, retro_ptro_2098, retro_ptro_2183, retro_ptro_2228, retro_ptro_2229, retro_ptro_2230, retro_ptro_2232, retro_ptro_2233, retro_ptro_2363, retro_ptro_279, retro_ptro_2834, retro_ptro_2936, retro_ptro_2978, retro_ptro_300, retro_ptro_3111, retro_ptro_3164,
Pteropus vampyrus	ENSPVAG00000008459	2 retrocopies	retro_pvam_218, retro_pvam_52,
Rattus norvegicus	ENSRNOG00000003220	4 retrocopies	retro_rnor_121, retro_rnor_191, retro_rnor_336, retro_rnor_44,
Sarcophilus harrisii	ENSSHAG00000005807	1 retrocopy	retro_shar_565,
Sus scrofa	ENSSSCG00000023971	2 retrocopies	retro_sscr_31, retro_sscr_712,
Tursiops truncatus	ENSTTRG00000015889	7 retrocopies	retro_ttru_1094, retro_ttru_1306, retro_ttru_18, retro_ttru_451, retro_ttru_738, retro_ttru_814, retro_ttru_92,