RetrogeneDB ID: retro_cfam_1267

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 28:15632793..15633196(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000004339
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000019677
• Aliases: None
• Description: Nucleoside diphosphate kinase [Source:UniProtKB/TrEMBL;Acc:F1PEZ2]

Sequence

>retro_cfam_1267
CAGCGGCCCGCGGGCCGGGGTCATGGGCGGCGTCTTGGGGCGCGTCGCGCTGCCGGGGCTGCTGAGTGGCCCGCGGGCCC
CCGGGCCGAGGCTACTCGCGCGCCCCAACTCGGGAGGGTCCTCCTGGACTCGAGAGCGGACCCTGGTTGCAGTGAAGCCG
GATGGGGTGCAGCGGCGGCTTGTGGGGAATGCGATCCAGCGCTTTGAGAGGAGCGTCTTCAAGCTGGTGGGGATGAAGAT
GCTGCAGGCGCCAGAGAGAGTCCTTGTTGAGCACTACCATGACCTGCGGAGGAAGCCCTTCTACCCAGCGCTCATCAGCT
ACAGGACCTCCGGCCCCGTGGTGGCCATGGTCTGGGAAGGCCCCAATGTGGTCTGCTCCTCAAGGACCATGGTCACACCC
ACT

Alignment

ORF - retro_cfam_1267 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.15 %
• Parental protein coverage: 68.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QRPAGRGHGRRLGARRAAG-LMRGPRAPGPCLLARSNSGGSSWTRERTLVAVKPDGVQRRLVGDVIQRFE
          QRPAGRGHGRRLGARRAAG.L..GPRAPGP.LLAR.NSGGSSWTRERTLVAVKPDGVQRRLVG..IQRFE
Retrocopy QRPAGRGHGRRLGARRAAG>LLSGPRAPGPRLLARPNSGGSSWTRERTLVAVKPDGVQRRLVGNAIQRFE

Parental  RRGFKLVGMKMLQAPERVLAEHYHDLQRKPFYPSLISYMTSGPVVAMVWEGPNVVCSSRTMIGHT
          R..FKLVGMKMLQAPERVL.EHYHDL.RKPFYP.LISY.TSGPVVAMVWEGPNVVCSSRTM...T
Retrocopy RSVFKLVGMKMLQAPERVLVEHYHDLRRKPFYPALISYRTSGPVVAMVWEGPNVVCSSRTMVTPT

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	0.59 RPM	14.53 RPM
SRP017611_brain	0.08 RPM	8.73 RPM
SRP017611_kidney	0.40 RPM	60.69 RPM
SRP017611_liver	0.07 RPM	21.32 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1267 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1267 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1267 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007077	3 retrocopies	retro_amel_1271, retro_amel_216, retro_amel_238,
Canis familiaris	ENSCAFG00000019677	4 retrocopies	retro_cfam_1267 , retro_cfam_2209, retro_cfam_447, retro_cfam_71,
Canis familiaris	ENSCAFG00000023628	7 retrocopies	retro_cfam_117, retro_cfam_1645, retro_cfam_37, retro_cfam_676, retro_cfam_69, retro_cfam_832, retro_cfam_96,
Cavia porcellus	ENSCPOG00000006496	1 retrocopy	retro_cpor_1076,
Echinops telfairi	ENSETEG00000014875	1 retrocopy	retro_etel_1833,
Felis catus	ENSFCAG00000008300	3 retrocopies	retro_fcat_1013, retro_fcat_1512, retro_fcat_1672,
Homo sapiens	ENSG00000103202	1 retrocopy	retro_hsap_1740,
Gorilla gorilla	ENSGGOG00000004512	1 retrocopy	retro_ggor_2259,
Macropus eugenii	ENSMEUG00000005455	5 retrocopies	retro_meug_1027, retro_meug_1427, retro_meug_1981, retro_meug_1999, retro_meug_694,
Myotis lucifugus	ENSMLUG00000010061	1 retrocopy	retro_mluc_388,
Macaca mulatta	ENSMMUG00000000612	1 retrocopy	retro_mmul_1221,
Mustela putorius furo	ENSMPUG00000016017	3 retrocopies	retro_mputfur_1024, retro_mputfur_1067, retro_mputfur_846,
Mus musculus	ENSMUSG00000024177	1 retrocopy	retro_mmus_309,
Nomascus leucogenys	ENSNLEG00000008068	1 retrocopy	retro_nleu_2719,
Otolemur garnettii	ENSOGAG00000025808	1 retrocopy	retro_ogar_2689,
Pongo abelii	ENSPPYG00000006908	1 retrocopy	retro_pabe_1442,
Pan troglodytes	ENSPTRG00000007541	1 retrocopy	retro_ptro_1220,
Rattus norvegicus	ENSRNOG00000049152	1 retrocopy	retro_rnor_2679,
Sus scrofa	ENSSSCG00000007986	2 retrocopies	retro_sscr_1113, retro_sscr_852,
Ictidomys tridecemlineatus	ENSSTOG00000004798	1 retrocopy	retro_itri_1629,
Tursiops truncatus	ENSTTRG00000009157	2 retrocopies	retro_ttru_393, retro_ttru_688,
Vicugna pacos	ENSVPAG00000010316	1 retrocopy	retro_vpac_150,