RetrogeneDB ID: retro_cfam_14

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:23593471..23594596(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000002350
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000013007
• Aliases: None
• Description: None

Sequence

>retro_cfam_14
ATGGCGAACCAGGTTATCAAGTGTAAGGCTGCAGTTGCCTGGGAGGCAGGAAAGCCTCTCTCTATAGAAGAGGTAGAGGT
GGCACCCCCAAAGGCTCATGAAGTTCGAATTAAGATTATTGCCACTGCAGTTTGCCACACCGATGCCTACACCCTGAGTG
GGGCTGATCCTGAAGGAAGTTTTCCAGTGATCCTGGGACATGAAGGTGCTGGAATTGTGGAAAGTGTTGGCGAAGGAGTT
ACTAAGCTGAAAGCAGGTGACACTGTCATCCCACTTTACATCCCACAGTGTGGAGAATGCAAATTTTGTCTAAATCCTAA
AACAAACCTTTGCCAGAAGATAAGAGTTACACAGGGGAAAGGATTAATGCCAGATGGTACTAGCAGATTTACTTGCAAAG
GAAAGACAATTTTACATTATATGGGAACCAGCACATTTTCTGAATATACAGTTGTGGCTGATATCTCTGTTGCTAAAATT
GATCCTTTAGCACCTTTGGATAAAGTCTGCCTTCTCGGTTGTGGCATTTCAACTGGTTATGGTGCTGCTCTGAACACTGC
CAAGGTGGAGCCTGGCTCTACTTGTGCCGTCTTTGGCCTAGGAGGAGTTGGATTGGCGACTATCATGGGCTGTAAAGTGG
CTGGTGCATCCCGGATCATTGGTGTGGACATCAATAAAGATAAATTCTCAAGGGCCAAGGAGTTTGGAGCCTCTGAATGT
ATTAACCCCCAGGACTTTAGTAAACCCATCCAGGAAGTGCTCATTGAAATGACTGACGGGGGAGTGGACTATTCCTTTGA
GTGTATTGGTAACGTGAAAGTCATGAGAGCTGCGCTAGAGGCCTGCCACAAAGGCTGGGGTGTCAGCGTCATAGTTGGAG
TAGCTGCTTCAGGTGAAGAAATCGCCACTCGTCCATTTCAGCTGGTAACAGGGCGTGTATGGAAAGGCACTGCCTTTGGA
GGATGGAAGAGTGTGGAAAGTGTCCCAAAGTTGGTGTCTGAATATATGTCCAGAAAGATAAAAGTTGATGAATTTGTGAC
TCACAGTCTGTCTTTTGACCAAATTAATGAAGCCTTTGACCTGTTGCATGCAGGAAAGAGCATTCGGACTGTTGTAAAGC
TTTAA

Alignment

ORF - retro_cfam_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 98.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QVIKCKAAVAWEAGKPLSIEEVEVAPPKAHEVRIKIIATAVCHTDAYTLSGADPEGSFPVILGHEGAGIV
          QVIKCKAAVAWEAGKPLSIEEVEVAPPKAHEVRIKIIATAVCHTDAYTLSGADPEGSFPVILGHEGAGIV
Retrocopy QVIKCKAAVAWEAGKPLSIEEVEVAPPKAHEVRIKIIATAVCHTDAYTLSGADPEGSFPVILGHEGAGIV

Parental  ESVGEGVTKLKAGDTVIPLYIPQCGECKFCLNPKTNLCQKIRVTQGKGLMPDGTSRFTCKGKTILHYMGT
          ESVGEGVTKLKAGDTVIPLYIPQCGECKFCLNPKTNLCQKIRVTQGKGLMPDGTSRFTCKGKTILHYMGT
Retrocopy ESVGEGVTKLKAGDTVIPLYIPQCGECKFCLNPKTNLCQKIRVTQGKGLMPDGTSRFTCKGKTILHYMGT

Parental  STFSEYTVVADISVAKIDPLAPLDKVCLLGCGISTGYGAALNTAKVEPGSTCAVFGLGGVGLATIMGCKV
          STFSEYTVVADISVAKIDPLAPLDKVCLLGCGISTGYGAALNTAKVEPGSTCAVFGLGGVGLATIMGCKV
Retrocopy STFSEYTVVADISVAKIDPLAPLDKVCLLGCGISTGYGAALNTAKVEPGSTCAVFGLGGVGLATIMGCKV

Parental  AGASRIIGVDINKDKFSRAKEFGASECINPQDFSKPIQEVLIEMTDGGVDYSFECIGNVKVMRAALEACH
          AGASRIIGVDINKDKFSRAKEFGASECINPQDFSKPIQEVLIEMTDGGVDYSFECIGNVKVMRAALEACH
Retrocopy AGASRIIGVDINKDKFSRAKEFGASECINPQDFSKPIQEVLIEMTDGGVDYSFECIGNVKVMRAALEACH

Parental  KGWGVSVIVGVAASGEEIATRPFQLVTGRVWKGTAFGGWKSVESVPKLVSEYMSRKIKVDEFVTHSLSFD
          KGWGVSVIVGVAASGEEIATRPFQLVTGRVWKGTAFGGWKSVESVPKLVSEYMSRKIKVDEFVTHSLSFD
Retrocopy KGWGVSVIVGVAASGEEIATRPFQLVTGRVWKGTAFGGWKSVESVPKLVSEYMSRKIKVDEFVTHSLSFD

Parental  QINEAFDLLHAGKSIRTVVKL
          QINEAFDLLHAGKSIRTVVKL
Retrocopy QINEAFDLLHAGKSIRTVVKL

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	2.98 RPM	21.71 RPM
SRP017611_brain	2.78 RPM	10.80 RPM
SRP017611_kidney	11.09 RPM	52.63 RPM
SRP017611_liver	3.48 RPM	17.04 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_14 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_14 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_14 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013007	1 retrocopy	retro_cfam_14 ,
Callithrix jacchus	ENSCJAG00000007198	2 retrocopies	retro_cjac_1029, retro_cjac_2933,
Homo sapiens	ENSG00000197894	3 retrocopies	retro_hsap_175, retro_hsap_330, retro_hsap_3607,
Gorilla gorilla	ENSGGOG00000028244	2 retrocopies	retro_ggor_2434, retro_ggor_354,
Myotis lucifugus	ENSMLUG00000002722	1 retrocopy	retro_mluc_1702,
Macaca mulatta	ENSMMUG00000003552	1 retrocopy	retro_mmul_299,
Mustela putorius furo	ENSMPUG00000009642	1 retrocopy	retro_mputfur_1625,
Nomascus leucogenys	ENSNLEG00000013946	3 retrocopies	retro_nleu_1772, retro_nleu_2636, retro_nleu_983,
Pongo abelii	ENSPPYG00000014946	3 retrocopies	retro_pabe_176, retro_pabe_359, retro_pabe_453,
Pan troglodytes	ENSPTRG00000016303	3 retrocopies	retro_ptro_166, retro_ptro_2438, retro_ptro_266,
Sus scrofa	ENSSSCG00000009185	1 retrocopy	retro_sscr_659,
Xenopus tropicalis	ENSXETG00000009304	1 retrocopy	retro_xtro_57,