RetrogeneDB ID: | retro_ecab_1033 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | Un0004:1253391..1254044(+) | ||
| 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_1033
CAAACAGAAGTTTTGGAGCTAAAGAATACAATAGAGAACTTCAACAGCACACTTGAACAAACAGAAGAGAGAATCAGCGA
GCTAGAAGGCAAATCAATTGAAATTATCCAGTCAGAGGAGAAAAAAGAAAAAGGAATGAAGAAAGCCTACGGGAATTATG
AAACATCATCAAAAGAAATAAGGTACACATAATTGGAGTCCCAGAAGAAGAAGAGAAAGGGATAGAAAGCTTATTTAAAG
AAATAATGGCTGAGAATTTCCCAAACCTAGGAAGAGATTTGGATATCCAAGTTCATGAAACTAATAGGTCGCCTCAAAGT
TTCAATCCAAAATGATCTTCTCCAAGACACATAATACTAAAATTGTCTACAACCAAAGACAAAGAGAAAATTAAAAGCAG
CAAGAGAAAAAAAATTTATTTCCTAAAAGGGAACCCCCATAAGGCTATCAGCAGATTTCTCAGCAGTGAACTTGCAGGTC
AGGAGAAAGTGGGATGATATATTCAGAATGTTAAAAGAAACTGCCCACCAAGAATACTTTAACCAGCAAAGTTGTTCTTC
AGAAATAAAGGAGAGATAAAGAATTTCCCAGATAAACAAAAAGTGAGAGAATTCGTCATCACTAAAGCTGCTTTACAAGA
AATGCTGAAGGGA
ORF - retro_ecab_1033 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 50.22 % |
| Parental protein coverage: | 98.66 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | KSAITEKKSSLNGFNSRFKQVEERINLLDDILEEITRAEQKEEKRIR-QNENSLRELWDNIKCANIHVIG |
| .....E.K.....FNS...Q.EERI..L.....EI....Q.EEK.....NE.SLREL...IK....H.IG | |
| Retrocopy | QTEVLELKNTIENFNSTLEQTEERISELEGKSIEII---QSEEKKEK<RNEESLREL*NIIKRNKVHIIG |
| Parental | VPEERQRG-RKLFEEIIAEIFPNLRKETDTQVQEAQRVPNKTSPKRPTSRHIIIKMSKIKDKERILKAAR |
| VPEE...G...LF.EI.AE.FPNL....D.QV.E..R.P....PK....RHII.K.S..KDKE.I.K... | |
| Retrocopy | VPEEEEKGIESLFKEIMAENFPNLGRDLDIQVHETNRSPQSFNPK*SSPRHIILKLSTTKDKEKI-KSSK |
| Parental | -ERQQVTYKGKPIRLSVDFSAKTLQVRREWHDIFKV-KEKNLQPRILYPARLSFTMEGEIKSFQDKQKLK |
| .E......KG.PIRLS.DFSA..LQVRR.W.DIF......N..PRIL.PA.L.F...GEIK.F.DKQK.. | |
| Retrocopy | >EKKFIS*KGTPIRLSADFSAVNLQVRRKWDDIFRM<VKRNCPPRIL*PAKLFFRNKGEIKNFPDKQKVR |
| Parental | EFITKKPILQEMLKG |
| EF...K..LQEMLKG | |
| Retrocopy | EFVITKAALQEMLKG |
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 .00 RPM | 0 .00 RPM |
| SRP021940_synovial_membrane | 0 .00 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_1033 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_1033 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_1033 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,
|