RetrogeneDB ID: | retro_ecab_386 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 16:55884774..55885374(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BABAM1 | ||
| Ensembl ID: | ENSECAG00000017099 | ||
| Aliases: | None | ||
| Description: | BRISC and BRCA1 A complex member 1 [Source:HGNC Symbol;Acc:25008] |
Retrocopy-Parental alignment summary:
>retro_ecab_386
TCCAACACTGAGGGGGCTGAGGACCAGGCACTGGAGGCCCAGGCCAGGCTGGGCAGCCACAGTAAGGCAGAGGATGAGGC
AGCCAGTGCTGATGAGGACTCCGAGCCCTCCAGGAGCTGGCTCCAATCCCTGGCAGGAGTCCCTGCTTGTCCCTGAGGTC
CAGGTGCAGATGCCAACGGCCAACTGTCCAGAAGGTGATCATCTGCCTGGACCTGTTGAAGGAAATGTTGCTGCTAAAGC
TGGAGTCGTTCAACAGCACCAAGATCAACGTGCTCAACGTCTCCCAGGAGATGAGGATAAAATACAAGAACAAAAGCCAC
GAATTCAGGCTGGTGGTGCTGAACGAGGACACAGCCTGGCTGTCTGGCCTGACCTCCAGCCCCCACAAGCACGGCAGCTG
CCTCTAGACCTGGAGATAGCCTTTTGTTCCATCTTCAATCTAGAAGGTCTCTTCAGCCTCATCCAGAAGAAGACTGAGCT
GCCAGTCACTAAGCACTTGTAGACGATCCCCTGCCAAGTGTGGTCCACACCATCCTTGTCTACAGCTGTTTGCTGTGCCA
GCCCCAGGTCTCCCTGCAGCGAGTGAAGAAATGTTCCAGG
ORF - retro_ecab_386 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 54.25 % |
| Parental protein coverage: | 66.45 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | SNPEGAEDRALGAQASVGSRSEGEGEAASADDG-TPNPPGAG-PKPWQVPPPAPEIQVRTPRVNCPEKVI |
| SN.EGAED.AL.AQA..GS.S..E.E.A...D..TP.PPGAG.P.P...P........R..R.....KVI | |
| Retrocopy | SNTEGAEDQALEAQARLGSHSKAEDE-AASADE>TPSPPGAG>PIPGRSPCLSLRSRCRCQRPTV-QKVI |
| Parental | LCLDLSEEMALPKLESFNGSKTNALNVSQKMIEMFVRTKHKIDKSHEFALVVVNDDIAWLSGLTSDPREL |
| .CLDL..EM.L.KLESFN..K....NV.....EM....K....KSHEF.LVV.N.D.AWLSGLTS.P... | |
| Retrocopy | ICLDLLKEMLLLKLESFNSTK---INVLNVSQEMRIKYKN---KSHEFRLVVLNEDTAWLSGLTSSPHKH |
| Parental | CSCL-YDLETASCSAFNLEGLVSLIQQKTELPVTENVQTI-PPPYVIRTILVYSRPPCQPQHGVTRVPNA |
| .SCL..DLE.A.CS.FNLEGL.SLIQ.KTELPVT....TI.P.P.V..TILVYS...CQPQ....RV... | |
| Retrocopy | GSCL<LDLEIAFCSIFNLEGLFSLIQKKTELPVTKHL*TI<PLPSVVHTILVYSCLLCQPQVSLQRVKKC |
| Parental | GK |
| .. | |
| Retrocopy | SR |
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 | 46 .57 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 89 .53 RPM |
| SRP021940_embryo | 0 .05 RPM | 103 .70 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 54 .08 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 69 .51 RPM |
| SRP021940_testis | 0 .00 RPM | 100 .84 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_386 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_386 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_386 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000017099 | 1 retrocopy |
retro_ecab_386 ,
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