RetrogeneDB ID: | retro_btau_1024 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 23:27900054..27900587(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SAP30L | ||
| Ensembl ID: | ENSBTAG00000004000 | ||
| Aliases: | None | ||
| Description: | histone deacetylase complex subunit SAP30L [Source:RefSeq peptide;Acc:NP_001178301] |
Retrocopy-Parental alignment summary:
>retro_btau_1024
ATGAACGGCTTTAGCACCGAGAAGAACTGCCGTGAAGGGCCCCCCGCCGCCGCCGCGGGCTACGGCCTGAGCTGCCTCAT
CAGCTAGGACTGCGAGCGCTGGGTCCCGCCCGAGGTCAACGCCTCCTTCAAGTAGAGTCCAGAAGAGCATCTCACAGAAG
AAACTCAAGCCGGACATCGACGAGAGCCTTAGCACCTGTATATTTGTGATTTCCACGAGAATTTCATCCAGAGTGTACAA
AATAAAAGGCAGAGAAAGACAACTGACGATGGCGGAGATTCTCCTGAGCACGACACAGACATTCCTGAGGTTGATCTGTT
CCAGCTGCAGGTGAATACTCTCCGAGTTATAAACGACACTACAAATTGCAGACCAGATCAGGCTTCACTAAGGCCCAGTT
AGCAGACACTGTCAGCCAACACTTCAGGAACACACCTGTGAATGAAAAGGAGACCCTCACTTACTTCATCTACATGGTGA
AGAGTAACAAGAGTAGACTGGACCAGAAGTCAGAGGGTGGCAAGCAGCTTGAG
ORF - retro_btau_1024 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.38 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MNGFSTEEDSREGPPAAPAAAPGYGQSCCLIEDGERCV-RPAGNASFSKRVQKSISQKKLKLDIDKSVR- |
| MNGFSTE...REGP...PAAA.GYG.SC....D.ER.V.RP......S.RVQKSISQKKLK.DID.S... | |
| Retrocopy | MNGFSTEKNCREGP---PAAAAGYGLSCLIS*DCERWV>RPRSTPP-SSRVQKSISQKKLKPDIDESLS< |
| Parental | HLYICDFHKNFIQSVRNKRKRKTSDDGGDSPEHDTDIPEVDLFQLQVNTLR-RYKRHYKLQTRPGFNKAQ |
| HLYICDFH.NFIQSV.NKR.RKT.DDGGDSPEHDTDIPEVDLFQLQVNTLR..YKRHYKLQTR.GF.KAQ | |
| Retrocopy | HLYICDFHENFIQSVQNKRQRKTTDDGGDSPEHDTDIPEVDLFQLQVNTLR<SYKRHYKLQTRSGFTKAQ |
| Parental | LAETVSRHFRNIPVNEKETLAYFIYMVKSNKSRLDQKSESGKQLE |
| LA.TVS.HFRN.PVNEKETL.YFIYMVKSNKSRLDQKSE.GKQLE | |
| Retrocopy | LADTVSQHFRNTPVNEKETLTYFIYMVKSNKSRLDQKSEGGKQLE |
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 |
|---|---|---|
| ERP005899_liver | 0 .00 RPM | 5 .05 RPM |
| ERP005899_muscle | 0 .00 RPM | 7 .71 RPM |
| SRP017611_brain | 0 .00 RPM | 6 .26 RPM |
| SRP017611_kidney | 0 .00 RPM | 10 .02 RPM |
| SRP017611_liver | 0 .00 RPM | 5 .51 RPM |
| SRP030211_testis | 0 .74 RPM | 20 .60 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1024 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1024 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1024 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 6 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ailuropoda melanoleuca | ENSAMEG00000016695 | 1 retrocopy | |
| Bos taurus | ENSBTAG00000004000 | 1 retrocopy |
retro_btau_1024 ,
|
| Canis familiaris | ENSCAFG00000017642 | 1 retrocopy | |
| Felis catus | ENSFCAG00000014985 | 1 retrocopy | |
| Mustela putorius furo | ENSMPUG00000013575 | 1 retrocopy | |
| Ochotona princeps | ENSOPRG00000014552 | 2 retrocopies |