RetrogeneDB ID: | retro_ecab_75 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 10:21525986..21527669(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSECAG00000006349 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSECAG00000023688 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ecab_75
TATGAACATAATTTATGTGCAAAGGCTTTCAGCATGGTGACAAATCTTAAGAGATGTCGCAGAATTCACATAGAAGGGAA
ACCTTATGAATGTAGTGAATGTCCAAAATCCTTCAGGTATAGGTCAAAACTCATAATACACCAGAGAACTCACACAGGGG
AAAAGCCATACAGATGTGATGAATGTCAGAAAGCTTTCAGTACCAAATGTCATCTCACTCTGCACCAGAGAACTCATACA
GGAGAGAAACCGTATGGATGTACGGAGTGTCAGAAATCTTTCAGAACAAAGTATCATCTCATTCTACACCATAGGACTCA
TACAGGAGAGAAACCCTATGAATGCAAAGAATGTGGGAAAGCTTACAGGGAGAAGACGAAGCTCAGATTACATTACAGAA
CACACACAGGAGAGAAACCTTTTGAGTGTAGTGATTGTGGGAAAGGTTTTATGCAGAAGTCAAACCTGATTATCCATCAA
AGAATTCATACGGGAGATAAACCCTATGGATGTGGAGACTGTGAAAAGGCCTTCTGTAGTAAATCTCAGCTTGTTGTTCA
CCAGCGAATTCATACAGGAGAAAAATCTTATGAATGCAGGGAATGTGGGAAAGCCTTCAATAAAAACTCGCACCTCATGA
CACATCAGAGAATTCATATAGGAGAGAAACCTTATGAATGTAGTGAATGTGGAAAAGCTTTTGTACACACATCACAGCTC
ATTGTACATCAGAGAAATCATACTGGAAGAAAACCGTATGAATGCAAGGAATGTGGGAAAGCTTTTAACAAAAAGTCACA
CTTTGTAACACATGAGAGAATTCATACTGGAGAGAAGCCATATGAATGCAGTGAATGTGGAAAAGCTTTCATAGACAACT
CACAGCTTATTGTTCATCGAAGAACTCATACAGGAGAGAAACCTTATGAATGCAAGGAATGTAGGAAAGCCTTTAATAAA
AGGTCATCTCTCATAACACATCAGAGAATTCATACAGGAGAGAAGCCTTATGAATGCAGTGAATGTGGAAAGTCTTTTAT
AGACAAGTCACATCTCATTGTCCATCAGAGAACTCATACAGGAGAGAAACCCTATGAATGCAGTGAATGTGGAAAAGCTT
TCATACGAAAGGCAATGCTCATTGTACATCAGAGGACACATACAGGAGAGAAACCCTTTGCGTGTCTTGAATGCCAGAAA
GCTTTTAGCAGTATGGCAATGCTCAGTAGACATCAGTTGATTCATACAGGAGAGAAACCCCATGGATGCAATGAATGTGG
AAAAACTTTCCGGCAAAAAAGCCATCTTATTATCCATCAACGATGCCATACTGGAGAGAAACCCTATGGATGCATTCCAT
GTGGTCAAATCTTCAACCAGAAGTCACAGCTCATTAGACATCAGAGACGTCACACAGGAGAGAAACCGTATCAGTGCACT
CAATGTGGGAAAGCCTTTTTTGAGAAATCATACCTCAATGTCCATCAGAGAAGTCATGCAGGACAGAAACCTTATGAATG
CAGTCAGTGTGGGAAAACTTTCTCTGTCAAGTTCTTTCTTACTTCACATGAGGAAATTCATAGAGCAAAGAAGTCTCAGG
AACACAGCGAGTGCTGGAAAGACTTTAGTGAGATGCCACATCTCACTGAATACAAAAGAATTCACACAAGAGAGACCCTT
TGA
ORF - retro_ecab_75 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 59.82 % |
| Parental protein coverage: | 65.8 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | CGKTFSKKSQLIVHQRTHTGEKPYGCGQCGKAFSQKSLLTIHQRTHSGEKPYGCGECQKAFSRKSLLVLH |
| C.K.FS....L....R.H...KPY.C..C.K.F...S.L.IHQRTH.GEKPY.C.ECQKAFS.K..L.LH | |
| Retrocopy | CAKAFSMVTNLKRCRRIHIEGKPYECSECPKSFRYRSKLIIHQRTHTGEKPYRCDECQKAFSTKCHLTLH |
| Parental | QRTHTGEKPYSCRECGKAFSRKSQLKRHQRTHTVEKPYGCSDCGKAFSQKLKLISHQRMHTGEKPYKCGD |
| QRTHTGEKPY.C.EC.K.F..K..L..H.RTHT.EKPY.C..CGKA...K.KL..H.R.HTGEKP..C.D | |
| Retrocopy | QRTHTGEKPYGCTECQKSFRTKYHLILHHRTHTGEKPYECKECGKAYREKTKLRLHYRTHTGEKPFECSD |
| Parental | CGKAFFWKSQLITHQRTHTGKKPYACSECEKAFSRNSLLIRHQRIHTGEKPYECRECGEAFIRKPQLLIR |
| CGK.F..KS.LI.HQR.HTG.KPY.C..CEKAF...S.L..HQRIHTGEK.YECRECG.AF..K...L.. | |
| Retrocopy | CGKGFMQKSNLIIHQRIHTGDKPYGCGDCEKAFCSKSQLVVHQRIHTGEKSYECRECGKAF-NKNSHLMT |
| Parental | HQKTHLGEKPYGCVECGKTFFGKSQLLTHQRTHTGEKPYECSECGKAFTQRSSLMSHQRTHTGEKPYECS |
| HQ..H.GEKPY.C.ECGK.F...SQL..HQR.HTG.KPYEC.ECGKAF...S....H.R.HTGEKPYECS | |
| Retrocopy | HQRIHIGEKPYECSECGKAFVHTSQLIVHQRNHTGRKPYECKECGKAFNKKSHFVTHERIHTGEKPYECS |
| Parental | ECGKAFSEKSSLIHHQRTHTGEKPFECGECRKAFAWKPQLLRHQRIHTGEKPYECSECGKAFVQKVQLIK |
| ECGKAF...S.LI.H.RTHTGEKP.EC.ECRKAF.....L..HQRIHTGEKPYECSECGK.F..K..LI. | |
| Retrocopy | ECGKAFIDNSQLIVHRRTHTGEKPYECKECRKAFNKRSSLITHQRIHTGEKPYECSECGKSFIDKSHLIV |
| Parental | HQRNHTGEKTYGCSDCAKAFFEKAQLIIHQRIHTGERPYECGECGKSFTRKSHLMRHQRIHTGDKYYGCT |
| HQR.HTGEK.Y.CS.C.KAF..KA.LI.HQR.HTGE.P..C.EC.K.F.....L.RHQ.IHTG.K..GC. | |
| Retrocopy | HQRTHTGEKPYECSECGKAFIRKAMLIVHQRTHTGEKPFACLECQKAFSSMAMLSRHQLIHTGEKPHGCN |
| Parental | ECGTAFSRKKSRFVVHQRTRTGEKPFKCSERGKGFSQKSHLVTHHTVHTGEKLYGC-ECGKAFSRKSHLI |
| ECG..F.R.KS....HQR..TGEKP..C...G..F.QKS.L..H...HTGEK.Y.C..CGKAF..KS.L. | |
| Retrocopy | ECGKTF-RQKSHLIIHQRCHTGEKPYGCIPCGQIFNQKSQLIRHQRRHTGEKPYQCTQCGKAFFEKSYLN |
| Parental | THKRTHTGEKPYECSDCNKVFSQTSQLIIHQRSHTGEKPYGCGECGRAFSGKSQLITHKRTHIDE |
| .H.R.H.G.KPYECS.C.K.FS....L..H...H...K.....EC...FS....L...KR.H..E | |
| Retrocopy | VHQRSHAGQKPYECSQCGKTFSVKFFLTSHEEIHRAKKSQEHSECWKDFSEMPHLTEYKRIHTRE |
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 | 1 .24 RPM | 3 .19 RPM |
| SRP021940_cerebellum | 0 .47 RPM | 7 .84 RPM |
| SRP021940_embryo | 3 .73 RPM | 16 .03 RPM |
| SRP021940_placental_villous | 0 .24 RPM | 2 .21 RPM |
| SRP021940_synovial_membrane | 0 .44 RPM | 4 .39 RPM |
| SRP021940_testis | 0 .51 RPM | 1 .60 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_75 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_75 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_75 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 | |
|---|---|---|---|
| Equus caballus | ENSECAG00000010608 | 1 retrocopy | |
| Equus caballus | ENSECAG00000021667 | 1 retrocopy | |
| Equus caballus | ENSECAG00000023688 | 1 retrocopy |
retro_ecab_75 ,
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