RetrogeneDB ID: retro_cfam_1774

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 5:82720124..82720717(-)
• Located in intron of: ENSCAFG00000030123

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CCNC
• Ensembl ID: ENSCAFG00000003525
• Aliases: None
• Description: cyclin C [Source:HGNC Symbol;Acc:1581]

Sequence

>retro_cfam_1774
GTGTTAATGGCTCCTACTGTGTGTTTTTGGCATCCAAAGTAGAGGAATTTGGAGTAGTCTCAAATACAAGATTGATTTCT
GCTGCTACTTCTGTATTAAAAACCAGATTTTCATATGCCTTTCCAAAGGAATTTCCTTATAGGATGAACCATATATTAGA
ATGTGAATTCTATCTTTTAGAACTAACGGATTGTTGCTTGATAGTGTATCATCCTTACAGACCTTTGCTCCAGTATGTGC
AGGACGTGGGCCAAGAAGACATGTTGCTTCCCCTTGCATGGAGGATAGTGAATGATACCTACAGAACGGATCTTTGCCTA
CTCTATCCTCCTTTCATGATAGCTTTAGCTTGTCTACATGTAGCTTGTGTTGTTCAGCAGAAAGATGCCAGACAGTGGTT
TGCTGAGCTTTCTGTGGATATGGAGAAGATTTTAGAAATAATCAGGGTTATTTTAAAACTGTATGAGCAGTGGAAGAATT
TTGATGAGCGAAAAGAGATGGCAACTATTCTTAGTAAGATGCCAAAGCCAAAACCTCCTCCAAACAGTGGAGAGCAGGGT
CCAAATGGAAGTCAGAACTCTAGCTACAGCCAA

Alignment

ORF - retro_cfam_1774 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98. %
• Parental protein coverage: 70.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VLMAPT-CVFLASKVEEFGVVSNTRLISAATSVLKTRFSYAFPKEFPYRMNHILECEFYLLELMDCCLIV
          VLMAPT.CVFLASKVEEFGVVSNTRLISAATSVLKTRFSYAFPKEFPYRMNHILECEFYLLEL.DCCLIV
Retrocopy VLMAPT<CVFLASKVEEFGVVSNTRLISAATSVLKTRFSYAFPKEFPYRMNHILECEFYLLELTDCCLIV

Parental  YHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDARQWFAELSV
          YHPYRPLLQYVQD.GQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDARQWFAELSV
Retrocopy YHPYRPLLQYVQDVGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDARQWFAELSV

Parental  DMEKILEIIRVILKLYEQWKNFDERKEMATILSKMPKPKPPPNSEGEQGPNGSQNSSYSQ
          DMEKILEIIRVILKLYEQWKNFDERKEMATILSKMPKPKPPPNS.GEQGPNGSQNSSYSQ
Retrocopy DMEKILEIIRVILKLYEQWKNFDERKEMATILSKMPKPKPPPNS-GEQGPNGSQNSSYSQ

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	0.13 RPM	14.83 RPM
SRP017611_brain	0.16 RPM	9.84 RPM
SRP017611_kidney	0.26 RPM	27.14 RPM
SRP017611_liver	0.00 RPM	8.12 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1774 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1774 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1774 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008954	1 retrocopy	retro_amel_1828,
Canis familiaris	ENSCAFG00000003525	1 retrocopy	retro_cfam_1774 ,
Dasypus novemcinctus	ENSDNOG00000011999	3 retrocopies	retro_dnov_1153, retro_dnov_216, retro_dnov_2243,
Dipodomys ordii	ENSDORG00000008393	2 retrocopies	retro_dord_230, retro_dord_75,
Myotis lucifugus	ENSMLUG00000012815	1 retrocopy	retro_mluc_1582,
Oryctolagus cuniculus	ENSOCUG00000003309	2 retrocopies	retro_ocun_1753, retro_ocun_888,
Ochotona princeps	ENSOPRG00000012972	2 retrocopies	retro_opri_1026, retro_opri_151,
Sus scrofa	ENSSSCG00000004353	1 retrocopy	retro_sscr_760,
Tupaia belangeri	ENSTBEG00000017525	1 retrocopy	retro_tbel_677,