RetrogeneDB ID: retro_ecab_474

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 19:32228584..32228881(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000005108
• Aliases: None
• Description: None

Sequence

>retro_ecab_474
AACACCACAGTGCCCAATGCCACCCAGGCCAATAGTGACTCCATGGTGGGCTATGTGTTGGGGCCTCTCCTCCTCATCAC
CCTGGTCGGTGTGGTGGTGGCTGTGGTAATGTATGTACAGAAGAAAAAGTGGGTGGGCCACCTTCACCATCACTTGCTCC
CCATGTGCAGCTACCACCCCACTGAAGAGCTACACGTGGCTGAGCAGGAGCTGCTCTTTGACATGGGAGACCCCAAGGTG
GCACGTGGCTGGCAGAGGGGCTACCAGCACAAACAGATGCCCTTGCTGGATGTCAGA

Alignment

ORF - retro_ecab_474 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 97.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NTTVPNAPQANSDSMVGYVLGPFFLITLVGVVVAVVMYVQKKKRVDRLRHHLLPMYSYDPAEELHEAEQE
          NTTVPNA.QANSDSMVGYVLGP..LITLVGVVVAVVMYVQKKK.V..L.HHLLPM.SY.P.EELH.AEQE
Retrocopy NTTVPNATQANSDSMVGYVLGPLLLITLVGVVVAVVMYVQKKKWVGHLHHHLLPMCSYHPTEELHVAEQE

Parental  LLSDVGDPKVVHGWQSGYQHKRMPLLDVK
          LL.D.GDPKV..GWQ.GYQHK.MPLLDV.
Retrocopy LLFDMGDPKVARGWQRGYQHKQMPLLDVR

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	1.30 RPM
SRP021940_cerebellum	0.00 RPM	10.65 RPM
SRP021940_embryo	0.00 RPM	2.25 RPM
SRP021940_placental_villous	0.00 RPM	5.10 RPM
SRP021940_synovial_membrane	0.00 RPM	3.68 RPM
SRP021940_testis	0.00 RPM	3.26 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_474 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_474 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_474 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_261

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001058	1 retrocopy	retro_amel_1014,
Bos taurus	ENSBTAG00000034519	1 retrocopy	retro_btau_261,
Equus caballus	ENSECAG00000005108	3 retrocopies	retro_ecab_236, retro_ecab_474 , retro_ecab_700,
Myotis lucifugus	ENSMLUG00000011876	1 retrocopy	retro_mluc_137,
Mus musculus	ENSMUSG00000062753	1 retrocopy	retro_mmus_1543,
Oryctolagus cuniculus	ENSOCUG00000013398	1 retrocopy	retro_ocun_625,
Pelodiscus sinensis	ENSPSIG00000004692	1 retrocopy	retro_psin_32,