RetrogeneDB ID: | retro_ecab_1124 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | X:84088808..84089924(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FBXL3 | ||
| Ensembl ID: | ENSECAG00000011128 | ||
| Aliases: | None | ||
| Description: | F-box and leucine-rich repeat protein 3 [Source:HGNC Symbol;Acc:13599] |
Retrocopy-Parental alignment summary:
>retro_ecab_1124
GATCAGGCCCGCGCATCTTCTGTATGTAGGAGATGGAATGAAGTTTTTCATATCCCTGACCATTGGAGAAAGTTTGAATT
TGAACTGAACCAATCAGCGACTTTGTCTTTTCAAGCCACTCCTCGTGATCTCATTCAGCAGATCTTTAAAAGGCATGTTG
CCTGTCTCCAGTATGTCAGCTTTAAGGTTGATAGCAGTACTGAATCAGCAGAGGCTGCCTGTGATATACTTTCTCAGCTG
GGAAATGGTTCTCCACACCTTGGGCTTGATTTCTAGGGCCAATCCAAGTTTTATGAACGTGTCAAAGTCTCATTTTGTGT
CAGCACTTACACTTGCTTGTGTCAACTCAAAATCATTATCATCAATCAAACTTGAAGACCCACCAGTGGATGACCCTTCA
CTGAAGGTTCTGGTGGCCAATAATAGTGATACTCTAACACTCCTAAAAATGAGCAGCTGTCCTTATGTTTCATCTGATGG
AATCCTTTGTGTAGCCGATCATTGTCAAGGCCTTAGAGAACTGGCATTGAATTATTACATTCCAAGTGATGAACTTCTGG
CCCTTTCAAGTGAGACTCATGTTAACCTTGAACATCTTCGAATTGATGTTGTGAGTGAAAATCCTGGACAAATTAAATTT
CATTCCATTAAAAAACAAAGTTGAGATGCACTTATTAAACACTCCCCTGGAGTTAATGTTGTCATATGCTTCTTTTTAAA
CGAAGAGGAATTTGAGACATTCTTCACAGAAGAATCCCCTGTCACTCATCTTTATTTCTGTCGGTCAGTAAGCAAAGCGG
TCCTAGGACGGATAGGTCCTAACTGCCCACGCCTAGTTGAGTTAGTGGTGTGTGCAAACGTTCTTCAGACTCTTGGTAAT
GAGCTGATCTGTATTGCTCAACACTGTAAAAACTGAACAGCCTTGGGCCTCAGTGCATGTGAAGTTCGCTGCAGTGCCGT
GGTTGAGTTTGTAAGGCTGGGTGGGAGGAGGCTCGCGCAGCTCTCTGTGATGGAGGAGGTTCTGACCCCGATGGGGATTA
CAGCCTGGATAAAATTCACGCTGAAGCCTCCAAATACCTGGGAAGAACGTGGTTCCCGGATGTCATGCCTGGCTGG
ORF - retro_ecab_1124 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.74 % |
| Parental protein coverage: | 87.38 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | DRAHASQVCRSWNQVFHMPDLWRCFEFELNQPATSYLKATHPELIKQIIKRHSNHLQYVSFKVDSSKESA |
| D.A.AS.VCR.WN.VFH.PD.WR.FEFELNQ.AT....AT...LI.QI.KRH...LQYVSFKVDSS.ESA | |
| Retrocopy | DQARASSVCRRWNEVFHIPDHWRKFEFELNQSATLSFQATPRDLIQQIFKRHVACLQYVSFKVDSSTESA |
| Parental | EAACDILSQLVNCSLKTLGL-ISTARPSFMDLPKSHFISALTVVFVNSKSLSSLKIDDTPVDDPSLKVLV |
| EAACDILSQL.N.S...LGL.IS.A.PSFM...KSHF.SALT...VNSKSLSS.K..D.PVDDPSLKVLV | |
| Retrocopy | EAACDILSQLGNGS-PHLGL>ISRANPSFMNVSKSHFVSALTLACVNSKSLSSIKLEDPPVDDPSLKVLV |
| Parental | ANNSDTLKLLKMSSCPHVSPAGILCVADQCHGLRELALNYHLLSDELLLALSSEKHVRLEHLRIDVVSEN |
| ANNSDTL.LLKMSSCP.VS..GILCVAD.C.GLRELALNY...SDE.LLALSSE.HV.LEHLRIDVVSEN | |
| Retrocopy | ANNSDTLTLLKMSSCPYVSSDGILCVADHCQGLRELALNYYIPSDE-LLALSSETHVNLEHLRIDVVSEN |
| Parental | PGQTHFHTIQKSSWDAFIRHSPKVNLVMYFFLYEEEFDPFFRYEIPATHLYFGRSVSKDVLGRVGMTCPR |
| PGQ..FH.I.K.S.DA.I.HSP.VN.V..FFL.EEEF..FF..E.P.THLYF.RSVSK.VLGR.G..CPR | |
| Retrocopy | PGQIKFHSIKKQS*DALIKHSPGVNVVICFFLNEEEFETFFTEESPVTHLYFCRSVSKAVLGRIGPNCPR |
| Parental | LVELVVCANGLRPLDEELIRIAERCKNLSAIGLGECEVSCSAFVEFVKMCGGRLSQLSIMEEVLI-PDQK |
| LVELVVCAN.L..L..ELI.IA..CKN..A.GL..CEV.CSA.VEFV...G.RL.QLS.MEEVL..PD.. | |
| Retrocopy | LVELVVCANVLQTLGNELICIAQHCKN*TALGLSACEVRCSAVVEFVRLGGRRLAQLSVMEEVLT<PDGD |
| Parental | YSLEQIHWEVSKHLGRVWFPDMMPTW |
| YSL..IH.E.SK.LGR.WFPD.MP.W | |
| Retrocopy | YSLDKIHAEASKYLGRTWFPDVMPGW |
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 | 29 .22 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 21 .45 RPM |
| SRP021940_embryo | 0 .00 RPM | 13 .48 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 16 .45 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 14 .71 RPM |
| SRP021940_testis | 0 .00 RPM | 24 .87 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_1124 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_1124 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_1124 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000011128 | 3 retrocopies |
retro_ecab_1048, retro_ecab_1049, retro_ecab_1124 ,
|
| Otolemur garnettii | ENSOGAG00000000250 | 1 retrocopy |