RetrogeneDB ID: retro_cfam_658

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 15:27431514..27431873(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNIH
• Ensembl ID: ENSCAFG00000031178
• Aliases: None
• Description: cornichon homolog (Drosophila) [Source:HGNC Symbol;Acc:19431]

Sequence

>retro_cfam_658
GCCATGCCTTTTACATTCAGGGACTTCTTCTTTGCCAGTCGGCATATTATAGGATTTGATAAGTTGAAGACTGATTACAA
GAACACCTTGAATGTTCTTCCAGTGTAATACCTTGAATCTCTTATATTTCCAGAAAACTTTATCTAGGTTTTCTTCTGTG
TCGTGCTTCTTTGTGCACCTTGTGCAAGGTGGCTTATCCTGGGTCTCAATATGCCCCCTTTGGCATATTGTATTTGGAGG
TGTATGAATTGACCAGTCATGAGTAGACCAGGTATCATGACACCATGACCATCATGAATGTAGATATTCTGGTGTATTGT
CAGAAAGAAGGATGGTGCAATTTGCTTTTTTATCTTCTA

Alignment

ORF - retro_cfam_658 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.5 %
• Parental protein coverage: 80.56 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ALLLTAALIFFAIWHIIAFDELKTDYKNPIDQCNT--LNPLVLPEYLIHAFFCVMFLCA--AEWLTLGLN
          A...T....FFA..HII.FD.LKTDYKN.........L..L..PE..I..FFCV..LCA..A.WL.LGLN
Retrocopy AMPFTFRDFFFASRHIIGFDKLKTDYKNTLNVLPV*YLESLIFPENFI*VFFCVVLLCAPCARWLILGLN

Parental  MPLLAYHIWRYMSRPVMSGPGL-YDPTTIMNADILAYCQKEGWCKLAFYLL
          MP.LAY.IWR.M..PVMS.PG...D..TIMN.DIL.YCQKEGWC.L.FYLL
Retrocopy MPPLAYCIWRCMN*PVMSRPGI<HDTMTIMNVDILVYCQKEGWCNLLFYLL

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	0.00 RPM	20.29 RPM
SRP017611_brain	0.00 RPM	14.85 RPM
SRP017611_kidney	0.00 RPM	37.31 RPM
SRP017611_liver	0.00 RPM	7.03 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_658 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_658 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_658 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_685

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031178	2 retrocopies	retro_cfam_658 , retro_cfam_697,
Callithrix jacchus	ENSCJAG00000007306	1 retrocopy	retro_cjac_103,
Equus caballus	ENSECAG00000026814	1 retrocopy	retro_ecab_685,
Loxodonta africana	ENSLAFG00000014841	1 retrocopy	retro_lafr_963,
Nomascus leucogenys	ENSNLEG00000012704	1 retrocopy	retro_nleu_1896,
Otolemur garnettii	ENSOGAG00000024582	1 retrocopy	retro_ogar_2271,
Ochotona princeps	ENSOPRG00000005287	4 retrocopies	retro_opri_198, retro_opri_269, retro_opri_366, retro_opri_894,
Tupaia belangeri	ENSTBEG00000010265	3 retrocopies	retro_tbel_2080, retro_tbel_3728, retro_tbel_572,
Tarsius syrichta	ENSTSYG00000011295	1 retrocopy	retro_tsyr_1540,
Tursiops truncatus	ENSTTRG00000008259	1 retrocopy	retro_ttru_261,