RetrogeneDB ID: retro_ecab_710

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 3:13822579..13823045(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM192A
• Ensembl ID: ENSECAG00000009324
• Aliases: None
• Description: family with sequence similarity 192, member A [Source:HGNC Symbol;Acc:29856]

Sequence

>retro_ecab_710
AGGAATCAGAAACTAACAGAAAAGCAACAAAGAGAAGAACTGAAAGAAATGAAGGAATACAAAAGCAATCTCAATGAGGT
TGGGATTTCTCCAGAAAACAAGAAAGAAGTGGAGAAGTAACTGGCTGTGAAACCTAGAGGAACCAAGAACAAGTTCTCCC
AGGCACAGCTGTTGCCAGGAGCTCTGAAGCATGAGAGCTCAGAGAGTGGCCACAGTGTGAAAAGACTGAAATTGGACCCT
GACTCAGATGATAACAATCAAGAGGCTCTGTCCTGCGTGTCTCTTGGAAGTACATCCCTGAGTGGTCCCTCCATCTACTG
CCCCTCCACTGCAGTCTGTAATGGCATCCTCCCAGGCTTGGGCATCTAGTCTGGGATAGTGACTCTGAGTCCAGCTCATA
CAGCAAAGCACTCTCAGTGCCATGGCCTAGATTGTCTCCTCCATCTCCCAAACCAACATCTTCCTT

Alignment

ORF - retro_ecab_710 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.44 %
• Parental protein coverage: 61.81 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RQQELIEKQRREEELKELKEYRISFNHVGISSENKKEVEKKVAVKPMETRNKFSQAKLLAGAVKHKSSES
          R.Q.L.EKQ.REE.LKE.KEY....N.VGIS.ENKKEVEK..AVKP..T.NKFSQA.LL.GA.KH.SSES
Retrocopy RNQKLTEKQQREE-LKEMKEYKSNLNEVGISPENKKEVEK*LAVKPRGTKNKFSQAQLLPGALKHESSES

Parental  GNSVKRLKSDPDPDDKNQEALPCVSLGSASLSAPSIHCPSAAVCIGILPGLGAYSG-SSDSESSSDS-EG
          G.SVKRLK.DPD.DD.NQEAL.CVSLGS.SLS.PSI.CPS.AVC.GILPGLG..SG..SDSESSS.S...
Retrocopy GHSVKRLKLDPDSDDNNQEALSCVSLGSTSLSGPSIYCPSTAVCNGILPGLGI*SG<DSDSESSSYS<QS

Parental  TINATGKIVSSIFRTNTFL
          T..A...IVSSI..TN.FL
Retrocopy TLSAMA*IVSSISQTNIFL

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	14.58 RPM
SRP021940_cerebellum	0.00 RPM	40.25 RPM
SRP021940_embryo	0.00 RPM	29.00 RPM
SRP021940_placental_villous	0.00 RPM	18.38 RPM
SRP021940_synovial_membrane	0.00 RPM	19.44 RPM
SRP021940_testis	0.00 RPM	81.21 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_710 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_710 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_710 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002242	1 retrocopy	retro_btau_1133,
Cavia porcellus	ENSCPOG00000001392	1 retrocopy	retro_cpor_122,
Equus caballus	ENSECAG00000009324	1 retrocopy	retro_ecab_710 ,
Echinops telfairi	ENSETEG00000014379	1 retrocopy	retro_etel_930,
Homo sapiens	ENSG00000172775	1 retrocopy	retro_hsap_2994,
Gorilla gorilla	ENSGGOG00000003938	1 retrocopy	retro_ggor_2074,
Macaca mulatta	ENSMMUG00000013492	1 retrocopy	retro_mmul_189,
Mus musculus	ENSMUSG00000031774	1 retrocopy	retro_mmus_428,
Nomascus leucogenys	ENSNLEG00000002716	1 retrocopy	retro_nleu_745,
Ochotona princeps	ENSOPRG00000006909	2 retrocopies	retro_opri_175, retro_opri_579,
Pongo abelii	ENSPPYG00000007382	1 retrocopy	retro_pabe_2480,
Pan troglodytes	ENSPTRG00000008148	1 retrocopy	retro_ptro_2025,
Tarsius syrichta	ENSTSYG00000013300	1 retrocopy	retro_tsyr_884,
Tursiops truncatus	ENSTTRG00000012791	1 retrocopy	retro_ttru_1884,
Vicugna pacos	ENSVPAG00000005973	1 retrocopy	retro_vpac_321,