RetrogeneDB ID: retro_ecab_761

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 31:17406837..17407159(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FABP12
• Ensembl ID: ENSECAG00000023552
• Aliases: None
• Description: fatty acid binding protein 12 [Source:HGNC Symbol;Acc:34524]

Sequence

>retro_ecab_761
GGAATAGGAAGAGCTGGCAGGAAACCAGGCTGTCTCGCAAACCCACTGAACCCAACAGCACAAATGGAGATGTGATTGCT
GTAAAAACCAAAAGCATCTTTAAAATTAATGAGATCTCCTTTAAGTGGAGAGGAGAATTTGAGGAAACCATAGCAGGTGG
CCACAAAATCAAGAGCACGGTAACTTTAGGTAATGACTCCTTGATTCAGGTTCAGGACCAGGTTGGCAAGGAGCCCCCGG
TAAAGGGAAAGTCAGTGGATGGAAAATGGGGCAGGGAAGTGCTGTGAACAATGTGACCTGCACCGGGACATATGAGAGTA
TA

Alignment

ORF - retro_ecab_761 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.64 %
• Parental protein coverage: 81.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GIGRVSRKLGCLA-KPTVTINTKEDVITIKTKSIFKNNEISFKLGEEFEETTPAGRKIKSLVTLDNDSLV
          GIGR..RK.GCLA.KPT....T..DVI..KTKSIFK.NEISFK...EFEET...G.KIKS.VTL.NDSL.
Retrocopy GIGRAGRKPGCLA<KPTEPNSTNGDVIAVKTKSIFKINEISFKWRGEFEETIAGGHKIKSTVTLGNDSLI

Parental  QVKDWEGKETTITRRLVDG-KMVVESAVNNVTCTQTYERV
          QV.D..GKE.......VDG.KM...SAVNNVTCT.TYE..
Retrocopy QVQDQVGKEPPVKGKSVDG<KMGQGSAVNNVTCTGTYESI

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	0.00 RPM
SRP021940_cerebellum	0.00 RPM	0.00 RPM
SRP021940_embryo	0.00 RPM	0.03 RPM
SRP021940_placental_villous	0.00 RPM	0.10 RPM
SRP021940_synovial_membrane	0.00 RPM	0.00 RPM
SRP021940_testis	0.00 RPM	5.63 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_761 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_761 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_761 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3679
Pan troglodytes	retro_ptro_2493
Gorilla gorilla	retro_ggor_2488
Pongo abelii	retro_pabe_3016
Macaca mulatta	retro_mmul_1787
Callithrix jacchus	retro_cjac_2486

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014554	1 retrocopy	retro_amel_945,
Callithrix jacchus	ENSCJAG00000000433	1 retrocopy	retro_cjac_2486,
Equus caballus	ENSECAG00000008270	2 retrocopies	retro_ecab_894, retro_ecab_938,
Equus caballus	ENSECAG00000015978	1 retrocopy	retro_ecab_416,
Equus caballus	ENSECAG00000023552	1 retrocopy	retro_ecab_761 ,
Equus caballus	ENSECAG00000024852	1 retrocopy	retro_ecab_519,
Homo sapiens	ENSG00000197416	1 retrocopy	retro_hsap_3679,
Gorilla gorilla	ENSGGOG00000016835	1 retrocopy	retro_ggor_2488,
Latimeria chalumnae	ENSLACG00000008511	3 retrocopies	retro_lcha_37, retro_lcha_45, retro_lcha_57,
Microcebus murinus	ENSMICG00000005319	1 retrocopy	retro_mmur_1131,
Macaca mulatta	ENSMMUG00000019337	1 retrocopy	retro_mmul_1787,
Nomascus leucogenys	ENSNLEG00000002515	1 retrocopy	retro_nleu_528,
Oryzias latipes	ENSORLG00000008282	1 retrocopy	retro_olat_7,
Pongo abelii	ENSPPYG00000018703	1 retrocopy	retro_pabe_3016,
Pan troglodytes	ENSPTRG00000022654	1 retrocopy	retro_ptro_2493,