RetrogeneDB ID: retro_cfam_55

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 17:52363463..52363811(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000009503
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CDK2AP2
• Ensembl ID: ENSCAFG00000011370
• Aliases: None
• Description: cyclin-dependent kinase 2 associated protein 2 [Source:HGNC Symbol;Acc:30833]

Sequence

>retro_cfam_55
ATGTCTTACAAACCGAACTTGGCCGCGCACATGCCCGCCGCCTCCCTCAGCGCCGCTGGGAGTGTCCACCCACCCTCCAC
CAGTATGGCCACATCCTCCCAGTACCGCCAGCTGCTGAGTGACTACAGGCCACCATCTCTAGGTTATACTCAGGGAACTG
GGAACAGCCAGGTACCCCAAAGCAAATATGCTGAGCTGCTGGCCATCATTGAAGAGTTGGGGAAAGAGATTAGACCCACC
TATGCAGGGAGCAAGAGCCCCATGGAGAGACTAAAACGAGGCATCATTCACGCCAGAGGACTGGTTCGAGAGTGCTTGGC
TGAGACGGAACGGAAGGCCAGGTCCTAG

Alignment

ORF - retro_cfam_55 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.37 %
• Parental protein coverage: 99.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAGSVPSPSGSVPGAAAPFRPLFNDFGPPSMGYVQAMKPPGAQGSQSTYTDLLSVIEEMGKEIRPTYAGS
          AAGSV..PS.S........R.L..D..PPS.GY.Q.......Q..QS.Y..LL..IEE.GKEIRPTYAGS
Retrocopy AAGSVHPPSTSM-ATSSQYRQLLSDYRPPSLGYTQGTG--NSQVPQSKYAELLAIIEELGKEIRPTYAGS

Parental  KSAMERLKRGIIHARALVRECLAETERNART
          KS.MERLKRGIIHAR.LVRECLAETER.AR.
Retrocopy KSPMERLKRGIIHARGLVRECLAETERKARS

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	1.89 RPM	14.83 RPM
SRP017611_brain	0.56 RPM	7.62 RPM
SRP017611_kidney	0.26 RPM	19.22 RPM
SRP017611_liver	0.22 RPM	4.42 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_55 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_55 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_55 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011370	1 retrocopy	retro_cfam_55 ,
Equus caballus	ENSECAG00000020079	2 retrocopies	retro_ecab_180, retro_ecab_579,
Echinops telfairi	ENSETEG00000006428	3 retrocopies	retro_etel_257, retro_etel_334, retro_etel_437,
Homo sapiens	ENSG00000167797	4 retrocopies	retro_hsap_3699, retro_hsap_4172, retro_hsap_4176, retro_hsap_4268,
Gorilla gorilla	ENSGGOG00000010159	3 retrocopies	retro_ggor_2502, retro_ggor_2799, retro_ggor_2800,
Macaca mulatta	ENSMMUG00000011827	5 retrocopies	retro_mmul_1712, retro_mmul_640, retro_mmul_728, retro_mmul_730, retro_mmul_763,
Nomascus leucogenys	ENSNLEG00000006438	1 retrocopy	retro_nleu_176,
Otolemur garnettii	ENSOGAG00000008275	1 retrocopy	retro_ogar_1584,
Pan troglodytes	ENSPTRG00000003966	9 retrocopies	retro_ptro_2508, retro_ptro_2973, retro_ptro_2976, retro_ptro_3002, retro_ptro_3003, retro_ptro_3004, retro_ptro_3005, retro_ptro_3008, retro_ptro_3009,
Tupaia belangeri	ENSTBEG00000005476	2 retrocopies	retro_tbel_439, retro_tbel_612,