RetrogeneDB ID: retro_cfam_1847

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 7:25941842..25942194(+)
• Located in intron of: ENSCAFG00000014590

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX7A2L
• Ensembl ID: ENSCAFG00000032040
• Aliases: None
• Description: cytochrome c oxidase subunit VIIa polypeptide 2 like [Source:HGNC Symbol;Acc:2289]

Sequence

>retro_cfam_1847
CTGTATCACCGGTTTAGCGGCTTCACGCAGAAGTTGATTGGAACGTGGGCTTCGAAGCCTATAATAGCCCGCAGGGATTA
AGGCCTGTGGTTTCCCCAGAAGCACCACCTACCACATTTGCCACACCAACCAAACTGGAGTTCTGATTTTACTGTATATG
ATTATGCTGGGAAAAACAAAGTTCCCTCTGGAACTTTGCAGAAGTTTTTCCAGAAGTCTGATGGTGTGCCCATCCACCTG
AAACGAGGCCTACCTGACCAAATGCTTTACCGGACCACCATGGCACTGACATTGTGGGGGGACCATCTGCTGTCTGATCG
CTCTCTACCTGGCTTTGCAGCGCAGAAACAAA

Alignment

ORF - retro_cfam_1847 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MYYKFSGFTQKLTGTWAS-DAY-SPQGLRPVVSTEAPPIIFATPTKL-SSDFTAYDYAGKNKVPE--LQK
          .Y..FSGFTQKL.GTWAS..AY.SPQGLRPVVS.EAPP..FATPTKL.SSDFT.YDYAGKNKVP...LQK
Retrocopy LYHRFSGFTQKLIGTWAS<EAYNSPQGLRPVVSPEAPPTTFATPTKL>SSDFTVYDYAGKNKVPSGTLQK

Parental  FFQKSDGVPIHLKRGLPDQMLYRTTMALTL-GGTIYCLIALYMASQPRNK
          FFQKSDGVPIHLKRGLPDQMLYRTTMALTL.GGTI.CLIALY.A.Q.RNK
Retrocopy FFQKSDGVPIHLKRGLPDQMLYRTTMALTL>GGTICCLIALYLALQRRNK

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	34.06 RPM
SRP017611_brain	0.00 RPM	42.32 RPM
SRP017611_kidney	0.00 RPM	69.34 RPM
SRP017611_liver	0.00 RPM	28.79 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1847 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1847 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1847 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032040	1 retrocopy	retro_cfam_1847 ,
Macaca mulatta	ENSMMUG00000016278	1 retrocopy	retro_mmul_110,
Mustela putorius furo	ENSMPUG00000008875	1 retrocopy	retro_mputfur_97,
Mus musculus	ENSMUSG00000024248	2 retrocopies	retro_mmus_32, retro_mmus_926,
Oryctolagus cuniculus	ENSOCUG00000027189	3 retrocopies	retro_ocun_1617, retro_ocun_1781, retro_ocun_28,
Otolemur garnettii	ENSOGAG00000016029	1 retrocopy	retro_ogar_114,
Sarcophilus harrisii	ENSSHAG00000012014	1 retrocopy	retro_shar_479,
Ictidomys tridecemlineatus	ENSSTOG00000012922	1 retrocopy	retro_itri_21,
Tupaia belangeri	ENSTBEG00000014124	3 retrocopies	retro_tbel_2384, retro_tbel_4472, retro_tbel_4545,