RetrogeneDB ID: retro_ecab_817

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 4:66911765..66912004(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRP14
• Ensembl ID: ENSECAG00000000319
• Aliases: None
• Description: signal recognition particle 14kDa (homologous Alu RNA binding protein) [Source:HGNC Symbol;Acc:11299]

Sequence

>retro_ecab_817
ACCCTGAAGAGGTATGATGGTCAAACTATACTCATTCCAAGAAAAGGGTCTGTGGAGGGTTTTAAGCCCTGAGACAACCA
TTGTCTGTTAAGAGCTGCTGTTGGGAAGAAGCAGCTCAGCACTGTGGTGAGCTCCAAAGAATGAGTGAGTTTCAGATGGC
TTATTCGAACCTATCGAGAGCTTACATGGATGGGCTGAACGAGAGGGACAGCAAGAGAAAGAGGGGCAAAGCAGCACAG

Alignment

ORF - retro_ecab_817 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.08 %
• Parental protein coverage: 74.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TLKKYDGRTKPIPRKGSVEGFEPSDNKCLLRATDGKKKISTVVSSKE-VNKFQMAYSNLLRANMDGLKKR
          TLK.YDG.T..IPRKGSVEGF.P.DN.CLLRA..GKK..STVVSSKE....FQMAYSNL.RA.MDGL..R
Retrocopy TLKRYDGQTILIPRKGSVEGFKP*DNHCLLRAAVGKKQLSTVVSSKE<MSEFQMAYSNLSRAYMDGLNER

Parental  DKKSKSKKSKAAQ
          D..SK.K..KAAQ
Retrocopy D--SKRKRGKAAQ

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	30.05 RPM
SRP021940_cerebellum	0.00 RPM	62.27 RPM
SRP021940_embryo	0.00 RPM	34.04 RPM
SRP021940_placental_villous	0.00 RPM	42.82 RPM
SRP021940_synovial_membrane	0.00 RPM	33.85 RPM
SRP021940_testis	0.00 RPM	73.53 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_817 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_817 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_817 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000029889	2 retrocopies	retro_cfam_210, retro_cfam_40,
Callithrix jacchus	ENSCJAG00000020912	3 retrocopies	retro_cjac_1642, retro_cjac_171, retro_cjac_3057,
Equus caballus	ENSECAG00000000319	1 retrocopy	retro_ecab_817 ,
Echinops telfairi	ENSETEG00000011870	1 retrocopy	retro_etel_1094,
Gorilla gorilla	ENSGGOG00000009921	1 retrocopy	retro_ggor_665,
Microcebus murinus	ENSMICG00000007637	1 retrocopy	retro_mmur_487,
Macaca mulatta	ENSMMUG00000016061	4 retrocopies	retro_mmul_1228, retro_mmul_1740, retro_mmul_573, retro_mmul_780,
Monodelphis domestica	ENSMODG00000029204	1 retrocopy	retro_mdom_1806,
Mustela putorius furo	ENSMPUG00000008324	1 retrocopy	retro_mputfur_376,
Otolemur garnettii	ENSOGAG00000029070	2 retrocopies	retro_ogar_2839, retro_ogar_40,
Pongo abelii	ENSPPYG00000006342	3 retrocopies	retro_pabe_1534, retro_pabe_262, retro_pabe_811,
Pteropus vampyrus	ENSPVAG00000002186	2 retrocopies	retro_pvam_152, retro_pvam_323,
Ictidomys tridecemlineatus	ENSSTOG00000015627	9 retrocopies	retro_itri_1334, retro_itri_1501, retro_itri_1633, retro_itri_382, retro_itri_432, retro_itri_707, retro_itri_710, retro_itri_799, retro_itri_824,
Tursiops truncatus	ENSTTRG00000000036	5 retrocopies	retro_ttru_1185, retro_ttru_1288, retro_ttru_594, retro_ttru_74, retro_ttru_782,
Vicugna pacos	ENSVPAG00000010282	1 retrocopy	retro_vpac_20,