RetrogeneDB ID: retro_ecab_796

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 4:93875676..93875903(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED10
• Ensembl ID: ENSECAG00000023738
• Aliases: None
• Description: mediator complex subunit 10 [Source:HGNC Symbol;Acc:28760]

Sequence

>retro_ecab_796
CAGAAGCTCAATTGTACTGCTACTGGTTTACAGGATACCAATAAATACAAACAGCAGCTTCGTAATATTACTCTACCTTT
GGAAGTTTTTAGTATACAGATCGAGGTTGAAATTCCAAACCCTGTATGGTAGAGTGCTTAGGGAGGTCTCTAGCCAGAAG
TGAACAAGTTAAAGGCAAAATTGACACAATAAAGAAATTTAAAAGCCTTTTCCTTCAACAACTGACT

Alignment

ORF - retro_ecab_796 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.44 %
• Parental protein coverage: 71.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RELNFIVTGLQDIDKCRQQLHDITVPLEVFE-YIDQGRNPQLYTKECLERALAKNEQVKGKIDTMKKFKS
          ..LN...TGLQD..K..QQL..IT.PLEVF..Y.D.G.N......ECL.R.LA..EQVKGKIDT.KKFKS
Retrocopy QKLNCTATGLQDTNKYKQQLRNITLPLEVFS<YTDRG*NSKPCMVECLGRSLARSEQVKGKIDTIKKFKS

Parental  LLIQELS
          L..Q.L.
Retrocopy LFLQQLT

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
SRP021940_articular_cartilage	0.00 RPM	3.19 RPM
SRP021940_cerebellum	0.00 RPM	9.61 RPM
SRP021940_embryo	0.00 RPM	8.72 RPM
SRP021940_placental_villous	0.00 RPM	6.59 RPM
SRP021940_synovial_membrane	0.00 RPM	7.80 RPM
SRP021940_testis	0.00 RPM	13.17 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_796 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_796 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_796 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_721

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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,