RetrogeneDB ID: | retro_btau_584 | ||
Retrocopylocation | Organism: | Cow (Bos taurus) | |
| Coordinates: | 15:54880351..54880946(+) | ||
| Located in intron of: | ENSBTAG00000000727 | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | GLOD4 | ||
| Ensembl ID: | ENSBTAG00000019160 | ||
| Aliases: | None | ||
| Description: | glyoxalase domain-containing protein 4 [Source:RefSeq peptide;Acc:NP_001095423] |
Retrocopy-Parental alignment summary:
>retro_btau_584
CAGGCCATCAGCAATGCCAGGAAGCTGGAGTGGCCACTCAATGAGGTTGCAGGAGCTATTTTTGAAACCAAAGCCCCTGG
AGGATATAAATTCTGTTTGCAGAACCGCAGTCCACCACAGACAGATCCTATATTAAAAGTAACTCTACCAGAGTCTGATC
TTGAGAAGTCCTTTGGCTACTGGTATAATGTAGTAGGAATGAAAGTTTGTGAAAAAGATGAAAAGAAGCAGAGTAGTTTG
CTGGGCTGTGCTGATAACCAGTGTAAGCTGGAGCTATAGGACATCTTGGAGGCAGTGATCTTGCAGCAGCTTTTGGACAA
ATTGCCTTTTCTTGCCCCTAGAAAGAGTAGTCAGAAGACTTGATAAAATGGGAGAACCGGGGGATTCTGACTCCCATTTG
AGTCTGGACACTCTAGGGAAAGCAACAGTGCAAGTGATCATTCTGCCTAACCCTGATGGACATGAAATTTGCTTTGTGGG
AGATGAAGCATTTTGAAAACTCTAGAAGATGGATCCAGAGAGAAGCAAATTATTGGATGATGCAGTGGCAGAAGATGAAA
GTGATGAATGGTTTGCTTCACAAAATAAAACAAGG
CAGGCCATCAGCAATGCCAGGAAGCTGGAGTGGCCACTCAATGAGGTTGCAGGAGCTATTTTTGAAACCAAAGCCCCTGG
AGGATATAAATTCTGTTTGCAGAACCGCAGTCCACCACAGACAGATCCTATATTAAAAGTAACTCTACCAGAGTCTGATC
TTGAGAAGTCCTTTGGCTACTGGTATAATGTAGTAGGAATGAAAGTTTGTGAAAAAGATGAAAAGAAGCAGAGTAGTTTG
CTGGGCTGTGCTGATAACCAGTGTAAGCTGGAGCTATAGGACATCTTGGAGGCAGTGATCTTGCAGCAGCTTTTGGACAA
ATTGCCTTTTCTTGCCCCTAGAAAGAGTAGTCAGAAGACTTGATAAAATGGGAGAACCGGGGGATTCTGACTCCCATTTG
AGTCTGGACACTCTAGGGAAAGCAACAGTGCAAGTGATCATTCTGCCTAACCCTGATGGACATGAAATTTGCTTTGTGGG
AGATGAAGCATTTTGAAAACTCTAGAAGATGGATCCAGAGAGAAGCAAATTATTGGATGATGCAGTGGCAGAAGATGAAA
GTGATGAATGGTTTGCTTCACAAAATAAAACAAGG
ORF - retro_btau_584 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 67.98 % |
| Parental protein coverage: | 67.45 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | QAVSNARKLKWPLSEMGDGVFETKAPGGYKFYLQDCSPPQSDPVLKVTLAVSDLQKSLNYWSNLLGMKIY |
| QA.SNARKL.WPL.E.....FETKAPGGYKF.LQ..SPPQ.DP.LKVTL..SDL.KS..YW.N..GMK.. | |
| Retrocopy | QAISNARKLEWPLNEVAGAIFETKAPGGYKFCLQNRSPPQTDPILKVTLPESDLEKSFGYWYNVVGMKVC |
| Parental | EEDEKKQRALLGYADNQCKLELRAI-PGKVDHATGFGRIAFSCPQKELSDLEDLMKRENQKILTPL-VSL |
| E.DEKKQ..LLG.ADNQCKLEL..I..G..D.A..FG.IAFSCP.KE.S..EDL.K.EN..ILTP...SL | |
| Retrocopy | EKDEKKQSSLLGCADNQCKLEL*DI<LGGSDLAAAFGQIAFSCP*KE*S--EDLIKWENRGILTPI<LSL |
| Parental | DTPGKATVQVIILADPDGHEICFVGDEAFRELSKVDPEGNKLLDDAISGDKSDEWFAAQKKPK |
| DT.GKATVQVIIL..PDGHEICFVGDEAF..L.K.DPE..KLLDDA...D.SDEWFA.Q.K.. | |
| Retrocopy | DTLGKATVQVIILPNPDGHEICFVGDEAF*KL*KMDPERSKLLDDAVAEDESDEWFASQNKTR |
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 .29 RPM | 68 .71 RPM |
| ERP005899_muscle | 0 .21 RPM | 36 .00 RPM |
| SRP017611_brain | 0 .00 RPM | 47 .60 RPM |
| SRP017611_kidney | 0 .12 RPM | 60 .99 RPM |
| SRP017611_liver | 0 .38 RPM | 43 .72 RPM |
| SRP030211_testis | 0 .09 RPM | 29 .04 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_584 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_584 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_584 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 | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000019160 | 1 retrocopy |
retro_btau_584 ,
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