RetrogeneDB ID: retro_ecab_874

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 6:27557544..27557811(+)
• Located in intron of: ENSECAG00000010335

Retrocopy information

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

Parental gene information

• Parental gene symbol: EFCAB2
• Ensembl ID: ENSECAG00000022403
• Aliases: None
• Description: EF-hand calcium binding domain 2 [Source:HGNC Symbol;Acc:28166]

Sequence

>retro_ecab_874
ATGGAGAAGATCAGAAAAATCTTTAGTTCATTAGGATGCTACTCTAGTCAAGGAGAGCTGCAGGATCTGATTGCAGAGGG
AGAGGAAGAAGAACCCACTGGATACGTTTGATTCAAAAAATTTCTTCCAGTGATGACTGAAGCACTGCTAGAAAACGGAC
AGAGACCAATTCCAGAGGATATCCTTCTTCGATTTTTTGAGGTCTTGGAGCCAGCAAAATGTGGGTCTCTTTCTAAGGAA
GAACTGAGCAAGTACATGACTGAAGAA

Alignment

ORF - retro_ecab_874 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.79 %
• Parental protein coverage: 76.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VREIGTIIRSLGCCPSEGELHDLIAEVEEEEPTGYIRYEKFLPVMTQVLLERRYRPIPEDILLRAFEVLD
          ...I..I..SLGC..S.GEL.DLIAE.EEEEPTGY....KFLPVMT..LLE...RPIPEDILLR.FEVL.
Retrocopy MEKIRKIFSSLGCYSSQGELQDLIAEGEEEEPTGYV*FKKFLPVMTEALLENGQRPIPEDILLRFFEVLE

Parental  PAKRGFLSKEELIKYMTEE
          PAK.G.LSKEEL.KYMTEE
Retrocopy PAKCGSLSKEELSKYMTEE

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	0.18 RPM
SRP021940_cerebellum	0.10 RPM	1.35 RPM
SRP021940_embryo	0.08 RPM	0.74 RPM
SRP021940_placental_villous	0.05 RPM	0.05 RPM
SRP021940_synovial_membrane	0.00 RPM	0.05 RPM
SRP021940_testis	0.00 RPM	1.53 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_874 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_874 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_874 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000029154	1 retrocopy	retro_cfam_781,
Callithrix jacchus	ENSCJAG00000016907	1 retrocopy	retro_cjac_3944,
Equus caballus	ENSECAG00000000796	1 retrocopy	retro_ecab_49,
Equus caballus	ENSECAG00000022403	1 retrocopy	retro_ecab_874 ,
Oryctolagus cuniculus	ENSOCUG00000029593	1 retrocopy	retro_ocun_612,
Tarsius syrichta	ENSTSYG00000006254	2 retrocopies	retro_tsyr_1584, retro_tsyr_317,