RetrogeneDB ID: | retro_ecab_615 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 23:18005246..18005913(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSECAG00000019846 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ecab_615
GAAATGAAGAATACAATACTGGAAATGAAAAATTCACTAGAGGGACTCAATAGCAGAGTAGATGATACAGAAGAATGGAT
TAGTGAGCTGGATGAAAGAGTAGAGGAAATCACCCAAGCTGAACAGATAAAAGAAAAAAGAATTAGACATAATGAGAACA
ATCTAAGGGAACTCTGAGACAATATCAAGTGCACTAACATTCATATAATAGGTGTCCCAGGAGAAGAGAGGGGAAGAGAA
TCTATTTGAAGAAATAATAGCTGAAAACTTTCCTAATCTAAGGAAGGAAACAGACATTCAAGTACAGGAAGCACAGAGAG
CACCAAACAAGATGAACACCAAGAGGCCCACACGAAGACACATTATAATTAAAATACCCAAAATTAAAGATAAAGAGAGA
ATCCTAAAAGCAGCAAGAGAAAGGCAACAAGTGACAGACAAAGGAAAGCCCATAAGGCTATCAGTGGACTTCTCAGCCGA
AACCCTACAGGCTAGAAGAGAGTGGCATGACATATTTAACGTGCTGAAGGGAAAAAACCAACAGCCGAGAATACTCTATC
CAACATGGTTATTCAGAATGGAAGGAGACATAAAGAACTTCCTAGACAAGCAAAAATTAAAGGAGTTTATCACCAAGAAA
CCAGTTCTACAAGAAATGCTGAAAGGG
ORF - retro_ecab_615 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.56 % |
| Parental protein coverage: | 99.55 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | EVKSAITEKKSSLNGFNSRFKQVEERINLLDDILEEITRAEQKEEKRIRQNENSLRELWDNIKCANIHVI |
| E.K..I.E.K.SL.G.NSR....EE.I..LD...EEIT.AEQ..EKRIR.NEN.LREL.DNIKC.NIH.I | |
| Retrocopy | EMKNTILEMKNSLEGLNSRVDDTEEWISELDERVEEITQAEQIKEKRIRHNENNLREL*DNIKCTNIHII |
| Parental | GVPEERQRGRK-LFEEIIAEIFPNLRKETDTQVQEAQRVPNKTSPKRPTSRHIIIKMSKIKDKERILKAA |
| GVP.E..RGR..LFEEIIAE.FPNLRKETD.QVQEAQR.PNK...KRPT.RHIIIK..KIKDKERILKAA | |
| Retrocopy | GVPGE-ERGRE>LFEEIIAENFPNLRKETDIQVQEAQRAPNKMNTKRPTRRHIIIKIPKIKDKERILKAA |
| Parental | RERQQVTYKGKPIRLSVDFSAKTLQVRREWHDIFKV-KEKNLQPRILYPARLSFTMEGEIKSFQDKQKLK |
| RERQQVT.KGKPIRLSVDFSA.TLQ.RREWHDIF.V.K.KN.QPRILYP..L.F.MEG.IK.F.DKQKLK | |
| Retrocopy | RERQQVTDKGKPIRLSVDFSAETLQARREWHDIFNVLKGKNQQPRILYPTWL-FRMEGDIKNFLDKQKLK |
| Parental | EFITKKPILQEMLKG |
| EFITKKP.LQEMLKG | |
| Retrocopy | EFITKKPVLQEMLKG |
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 .05 RPM | 0 .00 RPM |
| SRP021940_synovial_membrane | 0 .08 RPM | 0 .00 RPM |
| SRP021940_testis | 0 .00 RPM | 0 .00 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_615 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_615 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_615 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 8 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000019846 | 8 retrocopies |
retro_ecab_1033, retro_ecab_391, retro_ecab_528, retro_ecab_531, retro_ecab_540, retro_ecab_574, retro_ecab_615 , retro_ecab_918,
|