RetrogeneDB ID:

retro_ecab_242

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:10:53576500..53577434(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ZP4
Ensembl ID:ENSECAG00000010697
Aliases:None
Description:zona pellucida glycoprotein 4 [Source:HGNC Symbol;Acc:15770]


Retrocopy-Parental alignment summary:






>retro_ecab_242
GTGATGGCAACACACACCTTTGCCCCTTTCCAGTTTCCATTTACTTCCTGTGGTACCACAAGACAGATCACTGGAGACTA
GGCAGTGTATGAAAATGAGCTAGTTGCGGCTAGGGAGGTGAGAACTTGGGGCCATGGTTTTATCACCTTCAACAGTATCC
TCAGGGTTAGAGTCAGCTGCAGCTTCTCTGGTAAATAGCAACGCATCCCTGGTTTAATATCGTGGTTCTTACTCTCTCAA
TCACTCCTTTTCTGAGACCCAGCCCGGACCCCTCACTCCGGGAACCTCAGGATTGCCAGGAGATAAAAAACCTATGGCTC
CTACTACACTGTTGGTGACTACCCAGTGGTGAAGTTATTCAGGACCCCTTTCATGTGGATTTCTCCATTCATCACAGAAC
AGACCCCTACCGAGGGCTGCTTCTATGTCAGTGTTGGGCCATGCCCAGCACAACCCCCTGCATCAGTCACGGTGGCCTAC
GCTGGTTAAGGGGATGCTCCTAGACTGGAGATAATTATCAGACCCAACTGATCCCTGTTCAGAAAGCCTTGGATCTGCCA
TTTCCTTCTCCCTACCAGTGCTTTAACTTTTTCACCTTCAGCTTTGAGGACTCCATGGCAAAGTGGGCACTCAGGAGACT
GGTGTATCTGCACTGCTGTCCATCAGTCTGCCAGCCTACTGGGACATCATCCTATATGATAACCTTTCCTGTTGCCAGGT
GAAGAAGAAGCTCTGACATCCATTGTCAGAACAGTCCTGTAAGCATTTCTAGAAGAGTCCCATGATTCTAATCCAAGTCA
CTAAGGACTCTTTAGAAAAACTCTAGAATTACTCAAGCTCTCCTGTAGACTCCCAAGCTCTGTGAGTGGCAGGCCTTTCT
GGGACCTTAATAGTTGGAGACTTGTTAGTATCTTACTTGGCTATCAGGAAACAG

ORF - retro_ecab_242 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.24 %
Parental protein coverage: 56.91 %
Number of stop codons detected: 6
Number of frameshifts detected 7


Retrocopy - Parental Gene Alignment:

ParentalVMATHAFALFRFPFSSCGTTRRVTGDQAVYENELVATRDVRTWSHGSITRDSIFRFQVSCSYS-VSSNAF
VMATH.FA.F.FPF.SCGTTR..TGD.AVYENELVA.R.VRTW.HG.IT..SI.R..VSCS.S.V.SNA.
RetrocopyVMATHTFAPFQFPFTSCGTTRQITGD*AVYENELVAAREVRTWGHGFITFNSILRVRVSCSFS>VNSNAS
ParentalPV-NVQVFTLP-PPLPETQPGPLTLE-LRIAKD-KHYISYYNVSDYPVVKL-LQDPIYVEVSILHRTDPY
.V.N..V.TL...P.....P.P...E.LRIA...K.Y.SYY.V.DYPVVKL..QDP..V..SI.HRTDPY
RetrocopyLV>NIVVLTLSITPFLRPSPDPSLRE>LRIARR*KTYGSYYTVGDYPVVKL<IQDPFHVDFSIHHRTDPY
ParentalLGLMLHQCWATPST-NPLHQPQWPLLVKG-CPYTGDSYQTQLIPVQKALDLPFPSHYQRFSIFTFSFVDS
.GL.L.QCWA.PST.NPLHQ..WP.LVKG.C..TGD.YQTQLIPVQKALDLPFPS.YQ.F..FTFSF.DS
RetrocopyRGLLLCQCWAMPST<NPLHQSRWPTLVKG>CS*TGDNYQTQLIPVQKALDLPFPSPYQCFNFFTFSFEDS
ParentalVAKRAFKGLVYLHCSASVCQPAGTPPCMITCPVTRRRRSSDIRFQNSTASISS-KGPMILLQATKDSSEK
.AK.A...LVYLHC..SVCQP.GT...MIT.PV.R.RRSSDI..QNS..SIS..K.PMIL.Q.TKDS.EK
RetrocopyMAKWALRRLVYLHCCPSVCQPTGTSSYMITFPVAR*RRSSDIHCQNSPVSISR<KSPMILIQVTKDSLEK
ParentalLHKYSTSPVDSQSLWVAGLSGTFIVGASLVSYLAIRKQ
L..YS.SPVDSQ.L.VAGLSGT.IVG..LVSYLAIRKQ
RetrocopyL*NYSSSPVDSQAL*VAGLSGTLIVGDLLVSYLAIRKQ

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

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 .00 RPM
SRP021940_placental_villous 0 .00 RPM 0 .00 RPM
SRP021940_synovial_membrane 0 .00 RPM 0 .00 RPM
SRP021940_testis 0 .00 RPM 1 .21 RPM

ChIP-Seq - click to see more details

Equus caballus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ecab_242 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_242 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_242 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Equus caballus ENSECAG00000010697 1 retrocopy
retro_ecab_242 ,


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