RetrogeneDB ID: retro_ecab_128

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:57249023..57249836(+)
• Located in intron of: ENSECAG00000000471

Retrocopy information

• Ensembl ID: ENSECAG00000008345
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CYP2R1
• Ensembl ID: ENSECAG00000007597
• Aliases: None
• Description: cytochrome P450, family 2, subfamily R, polypeptide 1 [Source:HGNC Symbol;Acc:20580]

Sequence

>retro_ecab_128
TCAGCCTTTCCATGGATTGGCATCTTACCTTTTGGAAAACATCAACAGCTGCTTAGAAATGCAGCTGTGGCCTACGATTT
TTCTCCCCAGGCTTATTGAAAAAGTTCCTGGTGACAAAAAGCCTCAGTTGCCTCAGCATTTTGTTGGTGCTTATTTAGAT
GAGATGGATCAAGGTAAAAATGACCCATCGTCTGCTTTCTCCAAAGAAAAGCTAATTTTCTCTGTGGATGAACTCATCAT
TGCTGGAACCAAAACTATAACCAATGTGCTATGGTGGGCAGTTCTTTTCATGGCCCTTTATCCTAACATTCAAGGACGGG
TTCAGAAGGAGCTTGATTTAATTATGGGACCCAGTGGGAAGCCATCTTGGGATGACACATGCAAAATGCCTTATACTGAG
GCAGTTTTGTGTGAAGTTTTAAGATTCTGTAATATAGCGCCATTAGCGATTTTCCATGGAGCCTCTGTAGATGTAGTTGT
ATGTGGTGATTCCATTCCTAAAGGCAAAGCAGTTATTACAAATCTTTATTCTGTACACTTCAATGAAGAGTACTGGAGAG
ACCCAGAAGTATTCTATCCTGAGCAATTTCTGGACAGCAGTGGACTTTTTGCCGAGAAGGAAGCTTTGCTTCCTTTTTGC
TTAGGAAGAAGAGATGGTCCTGGAGAACAGCTGGCTCAGTGGAAATGTTCCTGTTTTTTACAGCATTGCTTCAGCTGTTT
CACTTGCATTCTCCAGATGAACTGGTTCCAAATCTGAAGCCCAGGTTAGGCATGACATGCCAACCGCAGCCTTACCTCAT
CTGTGCAGAAAGA

Alignment

ORF - retro_ecab_128 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.85 %
• Parental protein coverage: 62.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NAFPWIGILPFGKLQQLFRNADVVYEF-LSRLIEKVSVNRKPQLPQHFVDAYLDEMDQGQNDPSSTFSKE
          .AFPWIGILPFGK.QQL.RNA.V.Y.F.L.RLIEKV....KPQLPQHFV.AYLDEMDQG.NDPSS.FSKE
Retrocopy SAFPWIGILPFGKHQQLLRNAAVAYDF>LPRLIEKVPGDKKPQLPQHFVGAYLDEMDQGKNDPSSAFSKE

Parental  NLIFSVGELIIAGTETTTNVLRWAILFMALYPNIQGQVQKEIDLIMGPSGKPSWDDKCKMPYTEAVLHEV
          .LIFSV.ELIIAGT.T.TNVL.WA.LFMALYPNIQG.VQKE.DLIMGPSGKPSWDD.CKMPYTEAVL.EV
Retrocopy KLIFSVDELIIAGTKTITNVLWWAVLFMALYPNIQGRVQKELDLIMGPSGKPSWDDTCKMPYTEAVLCEV

Parental  LRFCNIVPLGIFHATSEDTVVRGYSIPKGTTVITNLYSVHFDEKYWRDPEIFYPERFLDSSGYFAKKEAF
          LRFCNI.PL.IFH..S.D.VV.G.SIPKG..VITNLYSVHF.E.YWRDPE.FYPE.FLDSSG.FA.KEA.
Retrocopy LRFCNIAPLAIFHGASVDVVVCGDSIPKGKAVITNLYSVHFNEEYWRDPEVFYPEQFLDSSGLFAEKEAL

Parental  IPFSLGRRHCLGEQLAR-MEMFLFFTALLQRFHLHFPHELVPNLKPRLGMTLQPQAYLICAER
          .PF.LGRR...GEQLA...EMFLFFTALLQ.FHLH.P.ELVPNLKPRLGMT.QPQ.YLICAER
Retrocopy LPFCLGRRDGPGEQLAQ<VEMFLFFTALLQLFHLHSPDELVPNLKPRLGMTCQPQPYLICAER

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	0.35 RPM
SRP021940_cerebellum	0.00 RPM	0.00 RPM
SRP021940_embryo	0.00 RPM	0.66 RPM
SRP021940_placental_villous	0.00 RPM	0.67 RPM
SRP021940_synovial_membrane	0.00 RPM	0.33 RPM
SRP021940_testis	0.00 RPM	10.61 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_128 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_128 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_128 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000015305	1 retrocopy	retro_cpor_595,
Equus caballus	ENSECAG00000007597	1 retrocopy	retro_ecab_128 ,
Ochotona princeps	ENSOPRG00000006268	1 retrocopy	retro_opri_1208,