RetrogeneDB ID: | retro_btau_513 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 13:43280031..43281469(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSBTAG00000035572 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BT.61946 | ||
| Ensembl ID: | ENSBTAG00000003450 | ||
| Aliases: | ATP6V1H, SFD | ||
| Description: | V-type proton ATPase subunit H [Source:RefSeq peptide;Acc:NP_777129] |
Retrocopy-Parental alignment summary:
>retro_btau_513
ATGACCAAGATGGATATTCGGGGCGCTGTGGATGCTGCTGTTCCCAACAACATCATTGCCGCCAAGGCTGCGGAAGTCCG
TGCGAACAAAGTGAACTGGCAGTCCTACCTGCAGGGGCAGATGATTTCTTCTGAAGACTGCGAGTTCATTCAAAGATTTG
AGATGAAAAGAAGTCCTGAGGAGAAGCAGGAGATGCTTCAGACTGAAGGCAGTCAGTGTGCTAAGACATTTATAAATCGG
ATGACTCCTATTTCCAAAGAGCAGACCAGTTCAGTACATACTCACCCTGGTGGATGATACACTGCAGGAAAATCACCAGC
GTGTTAGCATTTTCTTTGACTATGCTAAACGTAGCAAGAACACTGCCTGGTCCTACTTCCTGCCGATGCTGAATCGCCAG
GATCTCTTTACTGTTCGTATGGCAGCAAGAATTATTGCCAAGTTACCAGCTTGGGGAAAAGAACTGATGAAAGGCAGCGA
CTTGAATTACTATTTCAATTGGATAAAGACTCAACTAAGTTCACAGAAACTGTGTGGTAGCGGTATCGCTGCTGAAACAG
AAACAGTCTCTTCAAGCGATAGTTCCCAGTATGTGCAGTGCGTGGCCGGGTGTCTGCAGCTGATGCTCCGAGTCAATGAG
TACCGCTTCGCCTGGGTGGAGGCAGACGGGGTGAACTGCATCATGGGCGTTCTGAGTAACAAGTGTGGCTTTCAGCTCCA
GTATCAGATGATCTTTTCCGTGTGGCTCCTGGCTTTCAGCCCACAGATGTGTGAACACCTGAGGCGCTACAACATCATCC
CTGTCCTGTCCGACATCCTGCAGGAGTCGGTCAAAGAGAAGGTGACGAGGATCATCCTCGCAGCATTCCGTAACTTCTTA
GAAAAGTCAGTTGAACGAGAAACTCGCCAAGAGTATGCCCTGGCGATGATTCAGTGCAAAGTCCTGAAACAGCTGGAGAA
CTTGGAGCAGCAGAAGTACGACGAAGACATCAGTGAGGATATAAAGTTCCTCTTGGAGAAACTCGGTGAAAGTGTCCAGG
ATCTCAGCTCATTTGATGAATACAGTTCAGAACTAAAGTCTGGGAGGTTGGAGTGTAGTCCTGTGCACAAATCTGAGAAA
TTTTGGAGAGAGAATGCTGCGAGGTTAAATGAAAAGAATGATGAGCTCTTGAAAATTTTGACCGAACTTCTGGAGGTGTC
TGACGATCCCCAAGTCTTAGCTGTTGCCGCCCATGACGCTGGGGTGTATGTGCGCCATTACCCACGAGGCAAGCGGGTCA
TGGAACAGCTGGGTGGGAAGCAGCGGGTGATGAACCACGAGGACCAGCAGGTGCGCTACAACGCCCTCCTGGCTGTACAG
AAGCTCATGGTGCACAACTGGGAATATCTTGGTAAACAACTCCAGTCTGAACAGCCGCAGACTGCAGCTGCCCGGAGC
ORF - retro_btau_513 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.45 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MTKMDIRGAVDAAVPTNIIAAKAAEVRANKVNWQSYLQGQMISSEDCEFIQRFEMKRSPEEKQEMLQTEG |
| MTKMDIRGAVDAAVP.NIIAAKAAEVRANKVNWQSYLQGQMISSEDCEFIQRFEMKRSPEEKQEMLQTEG | |
| Retrocopy | MTKMDIRGAVDAAVPNNIIAAKAAEVRANKVNWQSYLQGQMISSEDCEFIQRFEMKRSPEEKQEMLQTEG |
| Parental | SQCAKTFINLMTHISKEQT-VQYILTLVDDTLQENHQRVSIFFDYAKRSKNTAWSYFLPMLNRQDLFTVH |
| SQCAKTFIN.MT.ISKEQT.VQYILTLVDDTLQENHQRVSIFFDYAKRSKNTAWSYFLPMLNRQDLFTV. | |
| Retrocopy | SQCAKTFINRMTPISKEQT>VQYILTLVDDTLQENHQRVSIFFDYAKRSKNTAWSYFLPMLNRQDLFTVR |
| Parental | MAARIIAKLAAWGKELMEGSDLNYYFNWIKTQLSSQKLRGSGVTAETGTVSSSDSSQYVQCVAGCLQLML |
| MAARIIAKL.AWGKELM.GSDLNYYFNWIKTQLSSQKL.GSG..AET.TVSSSDSSQYVQCVAGCLQLML | |
| Retrocopy | MAARIIAKLPAWGKELMKGSDLNYYFNWIKTQLSSQKLCGSGIAAETETVSSSDSSQYVQCVAGCLQLML |
| Parental | RVNEYRFAWVEADGVNCIMGVLSNKCGFQLQYQMIFSVWLLAFSPQMCEHLRRYNIIPVLSDILQESVKE |
| RVNEYRFAWVEADGVNCIMGVLSNKCGFQLQYQMIFSVWLLAFSPQMCEHLRRYNIIPVLSDILQESVKE | |
| Retrocopy | RVNEYRFAWVEADGVNCIMGVLSNKCGFQLQYQMIFSVWLLAFSPQMCEHLRRYNIIPVLSDILQESVKE |
| Parental | KVTRIILAAFRNFLEKSVERETRQEYALAMIQCKVLKQLENLEQQKYDDEDISEDIKFLLEKLGESVQDL |
| KVTRIILAAFRNFLEKSVERETRQEYALAMIQCKVLKQLENLEQQKYD.EDISEDIKFLLEKLGESVQDL | |
| Retrocopy | KVTRIILAAFRNFLEKSVERETRQEYALAMIQCKVLKQLENLEQQKYD-EDISEDIKFLLEKLGESVQDL |
| Parental | SSFDEYSSELKSGRLEWSPVHKSEKFWRENAARLNEKNYELLKILTKLLEVSDDPQVLAVAAHDVGEYVR |
| SSFDEYSSELKSGRLE.SPVHKSEKFWRENAARLNEKN.ELLKILT.LLEVSDDPQVLAVAAHD.G.YVR | |
| Retrocopy | SSFDEYSSELKSGRLECSPVHKSEKFWRENAARLNEKNDELLKILTELLEVSDDPQVLAVAAHDAGVYVR |
| Parental | HYPRGKRVIEQLGGKQLVMNHMHHEDQQVRYNALLAVQKLMVHNWEYLGKQLQSEQPQTAAARS |
| HYPRGKRV.EQLGGKQ.VMNH...EDQQVRYNALLAVQKLMVHNWEYLGKQLQSEQPQTAAARS | |
| Retrocopy | HYPRGKRVMEQLGGKQRVMNH---EDQQVRYNALLAVQKLMVHNWEYLGKQLQSEQPQTAAARS |
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 .14 RPM | 11 .54 RPM |
| ERP005899_muscle | 0 .37 RPM | 23 .07 RPM |
| SRP017611_brain | 0 .82 RPM | 108 .90 RPM |
| SRP017611_kidney | 0 .89 RPM | 73 .62 RPM |
| SRP017611_liver | 0 .08 RPM | 10 .42 RPM |
| SRP030211_testis | 2 .21 RPM | 59 .63 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_513 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_513 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_513 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 | ENSBTAG00000003450 | 1 retrocopy |
retro_btau_513 ,
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