RetrogeneDB ID: retro_cfam_1682

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:11134941..11135498(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000012382
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NIP7
• Ensembl ID: ENSCAFG00000029835
• Aliases: None
• Description: NIP7, nucleolar pre-rRNA processing protein [Source:HGNC Symbol;Acc:24328]

Sequence

>retro_cfam_1682
CTGCAACCCAGCGGGAACGTGCGGCCATTGACTGGAGGAGAGAGCCGCGTAACGTTTGAGAAGATGGCGAAATACGTCGG
CGAGAATCTTCAGCGGCTGTCGACAGGCCGGACGGCACCTCCTGTTTCAGGCTGCACAACGACCGGGTGTACTACGTGAG
CGAGAAGATGCTGAAGTTGGCCGCCAACATCTCTGGGGACAAGCCGGTGTCGCTGGGGACCTGCTTCAGGAAATTCACCA
AGAGTCACAGATTCCGGTTACACATCACAGCTCTGGATTACCCCGCACCCTGTGCCAAGTATGGAGTGTGGATAAAGCCT
GGAGCAGAGCAGTCTTTCCTGTATGGGAACCATGTGTTGAAATCGGGACTGGGTCGAATCACTGAAAATACTTGCCAGTA
CCAGGGAGTGGTGGTGTACTCCATGGCAGACGTCCCTTTGGGTTTTGGGGTGGCAGCAAAGTCTACACAAGGCTGCGGGA
AAGTAGACCCCGTGGTGATTGTGGTATTTCATCAAGCAGACATTGGGGAATGTGTGCGGCATGAAGAGACATTGACC

Alignment

ORF - retro_cfam_1682 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.24 %
• Parental protein coverage: 97.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LRPGGNMRPLTEEETRVMFEKMAKYIGENLQLL-VDRPDGTYCFRLHNDRVYYVSEKILKLAANISGDKL
          L.P.GN.RPLT..E.RV.FEKMAKY.GENLQ.L.VDRPDGT.CFRLHNDRVYYVSEK.LKLAANISGDK.
Retrocopy LQPSGNVRPLTGGESRVTFEKMAKYVGENLQRL<VDRPDGTSCFRLHNDRVYYVSEKMLKLAANISGDKP

Parental  VSLGTCFGKFTKSHRFRLHITALDYLAPYAKYKVWIKPGAEQSFLYGNHVLKSGLGRITENTCQYQGVVV
          VSLGTCF.KFTKSHRFRLHITALDY.AP.AKY.VWIKPGAEQSFLYGNHVLKSGLGRITENTCQYQGVVV
Retrocopy VSLGTCFRKFTKSHRFRLHITALDYPAPCAKYGVWIKPGAEQSFLYGNHVLKSGLGRITENTCQYQGVVV

Parental  YSMADVPLGFGVAAKSTQDCRKVDPMAIVVFHQADIGEYVRHEETLT
          YSMADVPLGFGVAAKSTQ.C.KVDP..IVVFHQADIGE.VRHEETLT
Retrocopy YSMADVPLGFGVAAKSTQGCGKVDPVVIVVFHQADIGECVRHEETLT

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	13.61 RPM
SRP017611_brain	0.00 RPM	7.78 RPM
SRP017611_kidney	0.00 RPM	15.39 RPM
SRP017611_liver	0.00 RPM	6.89 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1682 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1682 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1682 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007542	1 retrocopy	retro_amel_938,
Bos taurus	ENSBTAG00000001666	1 retrocopy	retro_btau_353,
Canis familiaris	ENSCAFG00000029835	2 retrocopies	retro_cfam_1346, retro_cfam_1682 ,
Callithrix jacchus	ENSCJAG00000015364	2 retrocopies	retro_cjac_2466, retro_cjac_4212,
Dasypus novemcinctus	ENSDNOG00000006821	2 retrocopies	retro_dnov_2114, retro_dnov_74,
Homo sapiens	ENSG00000132603	2 retrocopies	retro_hsap_2707, retro_hsap_3648,
Gorilla gorilla	ENSGGOG00000022785	2 retrocopies	retro_ggor_1886, retro_ggor_2464,
Microcebus murinus	ENSMICG00000009664	1 retrocopy	retro_mmur_5,
Myotis lucifugus	ENSMLUG00000011835	3 retrocopies	retro_mluc_1119, retro_mluc_2171, retro_mluc_2508,
Macaca mulatta	ENSMMUG00000016635	2 retrocopies	retro_mmul_1801, retro_mmul_192,
Monodelphis domestica	ENSMODG00000002782	2 retrocopies	retro_mdom_1011, retro_mdom_1709,
Mus musculus	ENSMUSG00000031917	2 retrocopies	retro_mmus_1858, retro_mmus_2281,
Nomascus leucogenys	ENSNLEG00000005492	2 retrocopies	retro_nleu_1579, retro_nleu_510,
Oryctolagus cuniculus	ENSOCUG00000017652	5 retrocopies	retro_ocun_1013, retro_ocun_1262, retro_ocun_1292, retro_ocun_491, retro_ocun_721,
Otolemur garnettii	ENSOGAG00000008066	2 retrocopies	retro_ogar_1619, retro_ogar_2453,
Pongo abelii	ENSPPYG00000007503	2 retrocopies	retro_pabe_2258, retro_pabe_2995,
Pan troglodytes	ENSPTRG00000008279	2 retrocopies	retro_ptro_1828, retro_ptro_2473,
Rattus norvegicus	ENSRNOG00000020391	8 retrocopies	retro_rnor_1279, retro_rnor_1566, retro_rnor_1567, retro_rnor_1674, retro_rnor_1676, retro_rnor_485, retro_rnor_655, retro_rnor_865,
Sorex araneus	ENSSARG00000000303	1 retrocopy	retro_sara_665,
Ictidomys tridecemlineatus	ENSSTOG00000012871	1 retrocopy	retro_itri_1368,
Tursiops truncatus	ENSTTRG00000010012	2 retrocopies	retro_ttru_1783, retro_ttru_676,