RetrogeneDB ID: | retro_ecab_687 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 28:23866205..23866561(+) | ||
| Located in intron of: | ENSECAG00000011449 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MRPL40 | ||
| Ensembl ID: | ENSECAG00000009876 | ||
| Aliases: | None | ||
| Description: | mitochondrial ribosomal protein L40 [Source:HGNC Symbol;Acc:14491] |
Retrocopy-Parental alignment summary:
>retro_ecab_687
TCACAAATTAGAGACACCCACCAGCGAGCTTCATTGTTGACCTTCTGGAACTCATTCCCATGACAGCAGACCCTTTCTGC
GAAAGAAGGTAAATCCTAAAAAGACCAAGCAGGAAATGACCTTTTAACAAAGAGGATCCGACTACCGGGAAAACTAGCCA
AGAGATAATTCCCATCGAAGATTTTATTACTCCTGTGAGGTTCTTGAATAAAGCAAGACAGCGGCCTCAGGTGGAGTTCC
TTTTTGAAGAGGGTAAGAGGAGAGCTCTGCTTCTGAAAAAGTGGTTGCTGTACAAGCAGCGAAAGCATGAGATGGAGAGG
GACGCCATCAGGTCCGTGCTTGAGGCTCAGCAGGAA
ORF - retro_ecab_687 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 69.6 % |
| Parental protein coverage: | 64.36 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | TQIRDTRRRASLLSFW-DLVPMRAE-PLRKKKKVDPK-KDQAVKDRLKKRIR-RLEKASQELIPIEDFIT |
| .QIRDT..RASLL.FW..L.PM.A..P...KK.V.PK.KDQA..D.L.KRIR....K.SQE.IPIEDFIT | |
| Retrocopy | SQIRDTHQRASLLTFW<ELIPMTAD<PFLRKK-VNPK<KDQAGNDLLTKRIR<TTGKTSQEIIPIEDFIT |
| Parental | PVKFLDQARQRPHTELPFEEGERRALLLKKWSLYKQREHEMERDTIRSMLEAQQE |
| PV.FL..ARQRP..E..FEEG.RRALLLKKW.LYKQR.HEMERD.IRS.LEAQQE | |
| Retrocopy | PVRFLNKARQRPQVEFLFEEGKRRALLLKKWLLYKQRKHEMERDAIRSVLEAQQE |
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 | 7 .32 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 24 .36 RPM |
| SRP021940_embryo | 0 .00 RPM | 20 .41 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 13 .57 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 13 .89 RPM |
| SRP021940_testis | 0 .00 RPM | 26 .60 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_687 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_687 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_687 has 1 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Canis familiaris | retro_cfam_662 |
Parental genes homology:
Parental genes homology involve 13 parental genes, and 13 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Anolis carolinensis | ENSACAG00000001053 | 1 retrocopy | |
| Ailuropoda melanoleuca | ENSAMEG00000011421 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000001584 | 1 retrocopy | |
| Equus caballus | ENSECAG00000009876 | 1 retrocopy |
retro_ecab_687 ,
|
| Homo sapiens | ENSG00000185608 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000012336 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000002456 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000016081 | 1 retrocopy | |
| Mustela putorius furo | ENSMPUG00000003865 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000005372 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000011578 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000049686 | 1 retrocopy | |
| Tarsius syrichta | ENSTSYG00000014747 | 1 retrocopy |