RetrogeneDB ID: | retro_ecab_421 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 17:42933959..42934678(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FLOT1 | ||
| Ensembl ID: | ENSECAG00000022083 | ||
| Aliases: | None | ||
| Description: | flotillin 1 [Source:HGNC Symbol;Acc:3757] |
Retrocopy-Parental alignment summary:
>retro_ecab_421
CTGAAGGACACTCATGATCATCAGGACTATTTGCACTCCTTGGGGAAGGCTCTAACTTCTCAAGTCCAAAATGATGTTCC
TATTGGGGAGGTGGATGCCAAGAGAGATGCTGGGATCCAGGAGGCCAAAGCCAAAAAGGAAAAGGTGAGTGCTCAGCACC
TGAGTGAGATGGAGATGACCAAGGGGCAGAGGGACTAGGAGCTGAGAAGGCTGTGTATGACATCAAAGTCACCACCAGCA
GCTTGAGCTGGACTGTCAGCTTCAGGTGGCCAAGACTAAGCAGCAGATGGAGGAAAAGTGGGTACAGATGCAGGTGGTGG
AGCAGGCACAGCAGGTGGCAGTGCAGGAGCCAGAGATCGCACACCGAGAGAAGGAGCTGGAGGTCCGAGTTCTGAAGCCA
GTAGAAGTCTAGTGCTACAAGCTGGAGCACCTAGCTGAGGCAGAAACGTCTCAGCTGATTCTGCAGGCAGACAGAAGCCG
AGTCTGTGCAGATGCGGGAGGATGCCAAGGCTTTGCCACAGAGATTGGAGCTCTGGGTCAAGCTTGAGAAGATGGCCAAG
AAGGCAGAAGAGTTCCAGCAGTACCTGGAGGCTGCTTGGCTGGACATTCTGCTAGAGAAGCTGCCCCAGGTGGCAGAGAT
CAGTGGTACCTTGATCTTGGCCAACAAGATCACATTGGGGTCCAGTGGAAGTGGGGCCGTGGGGGTGGCCAAAATGACC
ORF - retro_ecab_421 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.37 % |
| Parental protein coverage: | 57.28 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | LKDIHDDQDYLHSLGKARTAQVQKDARIGEAEAKRDAGIREAKAKQEKVSAQYLSEIEMAKAQRDYELK- |
| LKD.HD.QDYLHSLGKA.T.QVQ.D..IGE..AKRDAGI.EAKAK.EKVSAQ.LSE.EM.K.QRD.EL.. | |
| Retrocopy | LKDTHDHQDYLHSLGKALTSQVQNDVPIGEVDAKRDAGIQEAKAKKEKVSAQHLSEMEMTKGQRD*ELR< |
| Parental | KAAYDIEVNT-RRAQADLAYQLQVAKTKQQIEEQRVQVQVVERAQQVAVQEQEIARREKELEARVRKPAE |
| KA.YDI.V.T......D...Q..VAKTKQQ.EE..VQ.QVVE.AQQVAVQE.EIA.REKELE.RV.KP.E | |
| Retrocopy | KAVYDIKVTT<QQLELDCQLQ--VAKTKQQMEEKWVQMQVVEQAQQVAVQEPEIAHREKELEVRVLKPVE |
| Parental | AERYKLERLAEAEKTQLIMQAEAEAESVRMRGEAEAFAIGARARADA-EQMSKKAEAFQLYQEAAQLDML |
| ...YKLE.LAEAE..QLI.QA..........G....FA....A...A.E.M.KKAE.FQ.Y.EAA.LD.L | |
| Retrocopy | V*CYKLEHLAEAETSQLILQAD-RSRVCADAGGCQGFATEIGALGQA>EKMAKKAEEFQQYLEAAWLDIL |
| Parental | LEKLPQVAEEISGPLTSAKKITLVSSGSGTMGAAKVT |
| LEKLPQVA.EISG.L..A.KITL.SSGSG..G.AK.T | |
| Retrocopy | LEKLPQVA-EISGTLILANKITLGSSGSGAVGVAKMT |
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 | 45 .16 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 117 .83 RPM |
| SRP021940_embryo | 0 .00 RPM | 53 .32 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 131 .01 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 103 .44 RPM |
| SRP021940_testis | 0 .00 RPM | 19 .18 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_421 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_421 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_421 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 | ENSECAG00000022083 | 1 retrocopy |
retro_ecab_421 ,
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