RetrogeneDB ID: retro_ecab_519

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:67306221..67306455(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FABP3
• Ensembl ID: ENSECAG00000024852
• Aliases: None
• Description: fatty acid-binding protein, heart [Source:RefSeq peptide;Acc:NP_001157357]

Sequence

>retro_ecab_519
ACATATGGCACCTTCAAGAACACGGAGATCAGCTTCAAGCTGGGGGTGGAGTTTGATGAGACGATGGCGGATGACAGGAA
GGTCAAGTCCCTTGTGATGCTGGATGGAGGCAAACTTGTCCACGTGCAGAAGTGGAATGGGCAAGAGACAACACTGCTGT
GGGAGCTAATTGATGAAAAACTCATCCTGACACTCACCCATGGCAGCGCAATGAGCACTCGCATTTACAGAAAG

Alignment

ORF - retro_ecab_519 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.18 %
• Parental protein coverage: 57.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  THSTFKNTEISFKLGVEFDETTADDRKVKSLVTLDGGKLVHVQKWNGQETTLVRELIDGKLILTLTHGSA
          T..TFKNTEISFKLGVEFDET.ADDRKVKSLV.LDGGKLVHVQKWNGQETTL..ELID.KLILTLTHGSA
Retrocopy TYGTFKNTEISFKLGVEFDETMADDRKVKSLVMLDGGKLVHVQKWNGQETTLLWELIDEKLILTLTHGSA

Parental  VSTRTYEK
          .STR.Y.K
Retrocopy MSTRIYRK

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	9.39 RPM
SRP021940_cerebellum	0.00 RPM	14.54 RPM
SRP021940_embryo	0.03 RPM	54.70 RPM
SRP021940_placental_villous	0.10 RPM	269.04 RPM
SRP021940_synovial_membrane	0.00 RPM	27.01 RPM
SRP021940_testis	0.00 RPM	4.22 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_519 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_519 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_519 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016819	2 retrocopies	retro_btau_1467, retro_btau_295,
Danio rerio	ENSDARG00000023290	1 retrocopy	retro_drer_33,
Dasypus novemcinctus	ENSDNOG00000000511	2 retrocopies	retro_dnov_1510, retro_dnov_2482,
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	ENSG00000121769	1 retrocopy	retro_hsap_1258,
Gorilla gorilla	ENSGGOG00000014432	1 retrocopy	retro_ggor_990,
Macropus eugenii	ENSMEUG00000012501	6 retrocopies	retro_meug_1037, retro_meug_148, retro_meug_1660, retro_meug_273, retro_meug_563, retro_meug_819,
Microcebus murinus	ENSMICG00000009359	4 retrocopies	retro_mmur_1490, retro_mmur_203, retro_mmur_621, retro_mmur_734,
Myotis lucifugus	ENSMLUG00000013609	2 retrocopies	retro_mluc_1144, retro_mluc_1717,
Mus musculus	ENSMUSG00000028773	3 retrocopies	retro_mmus_2804, retro_mmus_3204, retro_mmus_65,
Nomascus leucogenys	ENSNLEG00000001586	1 retrocopy	retro_nleu_2097,
Otolemur garnettii	ENSOGAG00000013757	4 retrocopies	retro_ogar_1148, retro_ogar_1312, retro_ogar_1873, retro_ogar_959,
Pongo abelii	ENSPPYG00000001616	1 retrocopy	retro_pabe_1048,
Pan troglodytes	ENSPTRG00000000457	1 retrocopy	retro_ptro_3047,
Rattus norvegicus	ENSRNOG00000012879	1 retrocopy	retro_rnor_2199,
Ictidomys tridecemlineatus	ENSSTOG00000003842	3 retrocopies	retro_itri_1544, retro_itri_640, retro_itri_641,