RetrogeneDB ID: | retro_ecab_613 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 23:14514641..14515155(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RFC5 | ||
| Ensembl ID: | ENSECAG00000015326 | ||
| Aliases: | None | ||
| Description: | replication factor C (activator 1) 5, 36.5kDa [Source:HGNC Symbol;Acc:9973] |
Retrocopy-Parental alignment summary:
>retro_ecab_613
ATAGATATCATTCAGAGACCAATTCTGAGCTTTGCCAGTTCAGGACAATGTTTGAGAAAGACTTAAAATTAGAAAGTAAC
GCCATGACTCAAGATACTCAGAATGCCTGAAGAAGAGTGATTGGAAATTTATGAAAAATACCATATTTTGCCTCATCTGT
ACTATCTGTCGAAGATCATCCTTGCATTGCAGTCCTGGTGAATGAGGTTTGAAGTTAGTCCTTCACCCCAGAACTCATTG
TTGCCTATGAAAGACATACCATGGAAGAAGGGAAAGTCGACACAAATGAAGATGGATTGAAAGCACTTGTAATTCCCTCC
GGTGGAGCTATCTGAAGGGCTCTGAAGGTCTTGCAGAGCACCAAATGGTTTCTGGGACAGGTCAGACTGTAAACATGTAT
ATGGAACATCCTTTCAAGTCTAATTTCACCAACATTCTGGGCTGGATATTGAATCAAGACCTCTTCACGGCCTATAGAAA
TATTATGGAGTTGAAAACTTTGAAGAGGGTGGCA
ORF - retro_ecab_613 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 56.52 % |
| Parental protein coverage: | 56.11 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | IDIVRGPILSFAST-RTIFKKGFKLVILDEADAMTQDAQNALRRVIE-KFTENTRFCLICN-YLSKIIPA |
| IDI...PILSFAS..RT.F.K..KL....E..AMTQD.QNA.RRVI..KF..NT.FCLIC..YLSKII.A | |
| Retrocopy | IDIIQRPILSFASS<RTMFEKDLKL----ESNAMTQDTQNA*RRVIG<KFMKNTIFCLICT<YLSKIILA |
| Parental | LQSRCTRFRFGP-LTPELMVPRLQHVVEEEKVAISEDGMKALVTLSSGDMRRALNI-LQSTNMAFGKVTE |
| LQS...RF...P..TPEL.V....H..EE.KV...EDG.KALV..S.G...RAL...L....M..G..T. | |
| Retrocopy | LQSW*MRFEVSP<FTPELIVAYERHTMEEGKVDTNEDGLKALVIPSGGAI*RALKV<LAEHQMVSG--TG |
| Parental | ETVYTCTGHPLKSDIANILDWMLNQDFTTAYRNITELKTLKGLA |
| .TV.....HP.KS...NIL.W.LNQD..TAYRNI.ELKTLK..A | |
| Retrocopy | QTVNMYMEHPFKSNFTNILGWILNQDLFTAYRNIMELKTLKRVA |
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 | 6 .85 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 9 .71 RPM |
| SRP021940_embryo | 0 .00 RPM | 21 .92 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 6 .11 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 7 .36 RPM |
| SRP021940_testis | 0 .00 RPM | 40 .92 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_613 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_613 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_613 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000015326 | 2 retrocopies |
retro_ecab_613 , retro_ecab_946,
|
| Mus musculus | ENSMUSG00000029363 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000010377 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000001134 | 1 retrocopy |