RetrogeneDB ID: retro_cfam_721

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 16:8131630..8131810(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED10
• Ensembl ID: ENSCAFG00000010346
• Aliases: None
• Description: mediator complex subunit 10 [Source:HGNC Symbol;Acc:28760]

Sequence

>retro_cfam_721
TGCAGACAGCAGCTTCATAATATTACTCCACCTTCAGAAGTTTTTCAATATATAGATCAAGACTGAAACTCCCAACCTGA
TATGGAAACATGCTTAGAGATGTCTCTAGCTAAAAATGAATAAGCTAAAGGCAAAATGGACACAATAAGGACATTTAAAA
CCCTTCTGTTTCAAGAACTG

Alignment

ORF - retro_cfam_721 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.33 %
• Parental protein coverage: 57.69 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CRQQLHDITVPLEVFEYIDQGRNPQLYTKECLERALAKNEQVKGKIDTMKKFKSLLIQEL
          CRQQLH.IT.P.EVF.YIDQ..N.Q.....CLE..LAKNE..KGK.DT...FK.LL.QEL
Retrocopy CRQQLHNITPPSEVFQYIDQD*NSQPDMETCLEMSLAKNE*AKGKMDTIRTFKTLLFQEL

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	4.96 RPM
SRP017611_brain	0.00 RPM	5.56 RPM
SRP017611_kidney	0.00 RPM	6.34 RPM
SRP017611_liver	0.00 RPM	1.02 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_721 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_721 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_721 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_796

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006767	1 retrocopy	retro_amel_1034,
Canis familiaris	ENSCAFG00000010346	1 retrocopy	retro_cfam_721 ,
Dasypus novemcinctus	ENSDNOG00000004579	1 retrocopy	retro_dnov_1286,
Equus caballus	ENSECAG00000023738	1 retrocopy	retro_ecab_796,
Echinops telfairi	ENSETEG00000000027	1 retrocopy	retro_etel_1758,
Monodelphis domestica	ENSMODG00000002025	1 retrocopy	retro_mdom_399,
Otolemur garnettii	ENSOGAG00000005988	1 retrocopy	retro_ogar_1830,
Ochotona princeps	ENSOPRG00000015506	1 retrocopy	retro_opri_834,
Tupaia belangeri	ENSTBEG00000014579	2 retrocopies	retro_tbel_1647, retro_tbel_4561,
Tarsius syrichta	ENSTSYG00000002763	1 retrocopy	retro_tsyr_792,