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:
| Parental | VMATHAFALFRFPFSSCGTTRRVTGDQAVYENELVATRDVRTWSHGSITRDSIFRFQVSCSYS-VSSNAF |
| VMATH.FA.F.FPF.SCGTTR..TGD.AVYENELVA.R.VRTW.HG.IT..SI.R..VSCS.S.V.SNA. | |
| Retrocopy | VMATHTFAPFQFPFTSCGTTRQITGD*AVYENELVAAREVRTWGHGFITFNSILRVRVSCSFS>VNSNAS |
| Parental | PV-NVQVFTLP-PPLPETQPGPLTLE-LRIAKD-KHYISYYNVSDYPVVKL-LQDPIYVEVSILHRTDPY |
| .V.N..V.TL...P.....P.P...E.LRIA...K.Y.SYY.V.DYPVVKL..QDP..V..SI.HRTDPY | |
| Retrocopy | LV>NIVVLTLSITPFLRPSPDPSLRE>LRIARR*KTYGSYYTVGDYPVVKL<IQDPFHVDFSIHHRTDPY |
| Parental | LGLMLHQCWATPST-NPLHQPQWPLLVKG-CPYTGDSYQTQLIPVQKALDLPFPSHYQRFSIFTFSFVDS |
| .GL.L.QCWA.PST.NPLHQ..WP.LVKG.C..TGD.YQTQLIPVQKALDLPFPS.YQ.F..FTFSF.DS | |
| Retrocopy | RGLLLCQCWAMPST<NPLHQSRWPTLVKG>CS*TGDNYQTQLIPVQKALDLPFPSPYQCFNFFTFSFEDS |
| Parental | VAKRAFKGLVYLHCSASVCQPAGTPPCMITCPVTRRRRSSDIRFQNSTASISS-KGPMILLQATKDSSEK |
| .AK.A...LVYLHC..SVCQP.GT...MIT.PV.R.RRSSDI..QNS..SIS..K.PMIL.Q.TKDS.EK | |
| Retrocopy | MAKWALRRLVYLHCCPSVCQPTGTSSYMITFPVAR*RRSSDIHCQNSPVSISR<KSPMILIQVTKDSLEK |
| Parental | LHKYSTSPVDSQSLWVAGLSGTFIVGASLVSYLAIRKQ |
| L..YS.SPVDSQ.L.VAGLSGT.IVG..LVSYLAIRKQ | |
| Retrocopy | L*NYSSSPVDSQAL*VAGLSGTLIVGDLLVSYLAIRKQ |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(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 |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_242 retrocopy.
Equus caballus was not studied using FANTOM5 data.
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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