RetrogeneDB ID: retro_cfam_690

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 15:51225972..51226551(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000008287
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CDK4
• Ensembl ID: ENSCAFG00000000280
• Aliases: None
• Description: cyclin-dependent kinase 4 [Source:HGNC Symbol;Acc:1773]

Sequence

>retro_cfam_690
ATGGCTACTCCTCGGTACGAGCCAGTGGCTGAGATTGGGGTTGGTGCCTATGGAACGGTATACAAGGCCCATGATCCGCA
CAGCGGCCACTTCGTGGCCCTCAAGAGCGTTAGAGTCCCTAAAGGAGGAGGTGCCGGAGGGGGCCTTCCCATCAGCACAG
TTCCTGAAGTGGCATTGCTGAGGAGGCTGGAGGCTTTTGAGCATCCCAACGTTGTCCGGCTGATGGACGTCTGCGCCACT
GCCCGAACCGACCGGGAGACCAAAGTGACCCTGGTGTTTGAGCACGTGGACCAAGACCTGAGAACGTACCTGGACAAGGC
ACCCCCACCGGGCTTGCCAGTGGAGACCATCAAGGATCTGATGCGCCAGTTTCTAAGAGGCCTAGATTTCCTTCATGCCA
ACTGCATCCTTCACCGAGACCTGAAGCCCGAGAACATTCTGGTGACCAGTGGTGGGACAGTCAAGCTGGCTGACTTTGGC
CTGGCCAGAATCTACAGCTACCAGATGGCACTTACGCCTGTGGTTGTTACACTCTGGTATCCTGCTCCAGAAGTTCTTCT
GCAGTCTACGTATGCAACA

Alignment

ORF - retro_cfam_690 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.41 %
• Parental protein coverage: 63.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATPRYEPVAEIGVGAYGTVYKARDPHSGHFVALKSVRVPNGGGAGGGLPISTVREVALLRRLEAFEHPN
          MATPRYEPVAEIGVGAYGTVYKA.DPHSGHFVALKSVRVP.GGGAGGGLPISTV.EVALLRRLEAFEHPN
Retrocopy MATPRYEPVAEIGVGAYGTVYKAHDPHSGHFVALKSVRVPKGGGAGGGLPISTVPEVALLRRLEAFEHPN

Parental  VVRLMDVCATARTDRETKVTLVFEHVDQDLRTYLDKAPPPGLPVETIKDLMRQFLRGLDFLHANCIVHRD
          VVRLMDVCATARTDRETKVTLVFEHVDQDLRTYLDKAPPPGLPVETIKDLMRQFLRGLDFLHANCI.HRD
Retrocopy VVRLMDVCATARTDRETKVTLVFEHVDQDLRTYLDKAPPPGLPVETIKDLMRQFLRGLDFLHANCILHRD

Parental  LKPENILVTSGGTVKLADFGLARIYSYQMALTPVVVTLWYRAPEVLLQSTYAT
          LKPENILVTSGGTVKLADFGLARIYSYQMALTPVVVTLWY.APEVLLQSTYAT
Retrocopy LKPENILVTSGGTVKLADFGLARIYSYQMALTPVVVTLWYPAPEVLLQSTYAT

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	0.08 RPM	45.23 RPM
SRP017611_brain	0.00 RPM	14.37 RPM
SRP017611_kidney	0.26 RPM	61.88 RPM
SRP017611_liver	0.00 RPM	14.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_690 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_690 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_690 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007160	1 retrocopy	retro_btau_738,
Canis familiaris	ENSCAFG00000000280	1 retrocopy	retro_cfam_690 ,
Callithrix jacchus	ENSCJAG00000006697	3 retrocopies	retro_cjac_2163, retro_cjac_2891, retro_cjac_2951,
Felis catus	ENSFCAG00000029663	1 retrocopy	retro_fcat_516,
Gorilla gorilla	ENSGGOG00000001404	1 retrocopy	retro_ggor_275,
Macropus eugenii	ENSMEUG00000014609	1 retrocopy	retro_meug_23,
Microcebus murinus	ENSMICG00000003789	1 retrocopy	retro_mmur_893,
Myotis lucifugus	ENSMLUG00000023651	2 retrocopies	retro_mluc_1137, retro_mluc_354,
Macaca mulatta	ENSMMUG00000023694	1 retrocopy	retro_mmul_401,
Mus musculus	ENSMUSG00000006728	5 retrocopies	retro_mmus_1219, retro_mmus_1298, retro_mmus_2878, retro_mmus_3109, retro_mmus_636,
Nomascus leucogenys	ENSNLEG00000017205	1 retrocopy	retro_nleu_1847,
Pan troglodytes	ENSPTRG00000005147	1 retrocopy	retro_ptro_180,
Tarsius syrichta	ENSTSYG00000011937	3 retrocopies	retro_tsyr_1383, retro_tsyr_1701, retro_tsyr_544,