RetrogeneDB ID: retro_ecab_595

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 22:29479100..29479426(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNPH1
• Ensembl ID: ENSECAG00000006660
• Aliases: None
• Description: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 [Source:HGNC Symbol;Acc:21218]

Sequence

>retro_ecab_595
GGGGAAGATGCGGCTCGGGGCCACAAGCTCATGGATGAGCAGGACCTGGCCTGGCTGCAGCAAGGCAGATGTGGTCATGG
CAGAAAGGACCCAGCCATCCTCAGTTGTAAGCTACAGCCTGGCTCGGCTGTGACTCTCAATAAGCGAACCCTGCGCCCGT
TTCGCCCGCGATCTGGGCGAGAGCTTCCAGCCATGATCGGGGAGCAGCAGAGGGCTCACAGCTCCAGGTGTGGGACTCCA
AAGAGGGATGGCTGCAGGCCATGCTGAGTTGACACTTTGAGGCCGATCCTCCTGAGCAGGTGGCTGCTTCCCCTGACCCC
ACCGCC

Alignment

ORF - retro_ecab_595 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.07 %
• Parental protein coverage: 96.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GEEAAGGDKLIHERDLAWLQQ-ADVVVAEVTQPSLGVGYELGR-AVALNKRILCLFRPQSGRVLSAMI-R
          GE.AA.G.KL..E.DLAWLQQ.ADVV.AE.TQPS..V.Y.L.R.AV.LNKR.L..FRP.SGR.L.AMI.R
Retrocopy GEDAARGHKLMDEQDLAWLQQ>ADVVMAERTQPSSVVSYSLAR<AVTLNKRTLRPFRPRSGRELPAMI<R

Parental  GAADGLRFQVWDYEEGEVEAMLDRYFEADPSEEVAASPEPTA
          GAA.G...QVWD..EG...AML...FEADP.E.VAASP.PTA
Retrocopy GAAEGSQLQVWDSKEGWLQAMLS*HFEADPPEQVAASPDPTA

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	2.24 RPM
SRP021940_cerebellum	0.00 RPM	3.17 RPM
SRP021940_embryo	0.00 RPM	7.65 RPM
SRP021940_placental_villous	0.00 RPM	4.62 RPM
SRP021940_synovial_membrane	0.00 RPM	4.09 RPM
SRP021940_testis	0.00 RPM	3.52 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_595 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_595 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_595 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_1148

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012390	1 retrocopy	retro_amel_1012,
Bos taurus	ENSBTAG00000019913	1 retrocopy	retro_btau_518,
Canis familiaris	ENSCAFG00000001837	1 retrocopy	retro_cfam_1148,
Callithrix jacchus	ENSCJAG00000005337	1 retrocopy	retro_cjac_3948,
Equus caballus	ENSECAG00000006660	1 retrocopy	retro_ecab_595 ,
Felis catus	ENSFCAG00000009722	1 retrocopy	retro_fcat_365,
Homo sapiens	ENSG00000112667	1 retrocopy	retro_hsap_2562,
Nomascus leucogenys	ENSNLEG00000000516	1 retrocopy	retro_nleu_1515,
Pongo abelii	ENSPPYG00000016635	1 retrocopy	retro_pabe_1888,
Pan troglodytes	ENSPTRG00000029662	1 retrocopy	retro_ptro_1493,
Pteropus vampyrus	ENSPVAG00000008743	1 retrocopy	retro_pvam_1400,
Rattus norvegicus	ENSRNOG00000018397	1 retrocopy	retro_rnor_580,
Tursiops truncatus	ENSTTRG00000007022	1 retrocopy	retro_ttru_1520,