RetrogeneDB ID: | retro_btau_1067 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 25:2766126..2766969(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SNX17 | ||
| Ensembl ID: | ENSBTAG00000019515 | ||
| Aliases: | None | ||
| Description: | Sorting nexin-17 [Source:UniProtKB/Swiss-Prot;Acc:Q5EA77] |
Retrocopy-Parental alignment summary:
>retro_btau_1067
ATGTACTCTTCCATTCTTGAAACCGAGTCACACAGCGAGGAGAGCGGCGGCTCAGCCAATGTGGTTTATAACATTCACGT
GAATGGAGTCCTGCAGTGTTGCGTGCGCAACAGGCAGCTCCTGGGGTTGCACGAGCAGCTTCGGAAGGAATATGGGGCCA
ATGTGCTTCCTGCATTTCCCCCAAAAAAGCTTTTGGCTTTGACACCGGCAGAGTGAAACAGGAGACAGCAGTTAGAGAAG
TACATGCAAGCTGTTCGGGAAGACCCATTGCTTGGGAGCAGTGAGACCTTCAATAGTTTCCTTCGTCGGGCACAGCAGGA
GGTCCTCACAGAAGAGGTCTCTTTGGAAATGCCACTCAGCAACGGGCAGAAAGTTCTGGTCAACGTGCTAACTTCAGATC
AGACTGAATATGTCCTGGAGGGTGTGGCTGCAATGCTGGATATTCCAGATGACTTGATCAGCTACTTCAGTCTCTTTCTA
GTTCGAGAAAAATAGGATGGAGCCTTTTTGTTTGTACGGAAGTTGCAAGAGTTTGAGTTGCCTTATGTGTCTGTTACCAG
TCTTCAGAGTCAAGACTGTAAGATTCTGCTAAGGAAGAGTTATTTGGACTCTACCTACGACGACAATGTCATGGAGAACC
GGGTTGGCCTGAACCTGCTTTATGCTCAGATGGTAGCAGACATTAAGCGTGTGTGGATCCTGGTGGCCAAGGAACAGTAG
CAGCTCAAATCACTGCAGGAGGAGGTCTCCAAGAAGGAGTTCCTGCGGCTGGCCCAGACACTGCGGCACTATGGCTACTT
GCGCTTTGATGCCTGTTTGGCTGTCTTCTCAGAGAAGGACTGT
ORF - retro_btau_1067 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.87 % |
| Parental protein coverage: | 60.85 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MHFSIPETESRSGDSGGSAYVAYNIHVNGVLHCRVRYSQLLGLHEQLRKEYGANVLPAFPPKKLFSLTPA |
| M..SI.ETES.S..SGGSA.V.YNIHVNGVL.C.VR..QLLGLHEQLRKEYGANVLPAFPPKKL..LTPA | |
| Retrocopy | MYSSILETESHSEESGGSANVVYNIHVNGVLQCCVRNRQLLGLHEQLRKEYGANVLPAFPPKKLLALTPA |
| Parental | EVEQRREQLEKYMQAVRQDPLLGSSETFNSFLRRAQQETQQVPTEEVSLEVLLSNGQKVLVNVLTSDQTE |
| E...RR.QLEKYMQAVR.DPLLGSSETFNSFLRRAQQE...V.TEEVSLE..LSNGQKVLVNVLTSDQTE | |
| Retrocopy | E*N-RRQQLEKYMQAVREDPLLGSSETFNSFLRRAQQE---VLTEEVSLEMPLSNGQKVLVNVLTSDQTE |
| Parental | DVLEAVAAKLDLPDDLIGYFSLFLVREKEDGAFSFVRKLQEFELPYVSVTSLRSQEYKIVLRKSYWDSAY |
| .VLE.VAA.LD.PDDLI.YFSLFLVREK.DGAF.FVRKLQEFELPYVSVTSL.SQ..KI.LRKSY.DS.Y | |
| Retrocopy | YVLEGVAAMLDIPDDLISYFSLFLVREK*DGAFLFVRKLQEFELPYVSVTSLQSQDCKILLRKSYLDSTY |
| Parental | DDDVMENRVGLNLLYAQTVADIERGWILVTKEQHRQLKSLQEKVSKKEFLRLAQTLRHYGYLRFDACVAD |
| DD.VMENRVGLNLLYAQ.VADI.R.WILV.KEQ..QLKSLQE.VSKKEFLRLAQTLRHYGYLRFDAC.A. | |
| Retrocopy | DDNVMENRVGLNLLYAQMVADIKRVWILVAKEQ-*QLKSLQEEVSKKEFLRLAQTLRHYGYLRFDACLAV |
| Parental | FPEKDC |
| F.EKDC | |
| Retrocopy | FSEKDC |
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 | 25 .74 RPM |
| ERP005899_muscle | 0 .00 RPM | 62 .40 RPM |
| SRP017611_brain | 0 .00 RPM | 50 .11 RPM |
| SRP017611_kidney | 0 .06 RPM | 69 .64 RPM |
| SRP017611_liver | 0 .00 RPM | 36 .62 RPM |
| SRP030211_testis | 0 .05 RPM | 43 .95 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1067 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1067 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1067 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 | ENSBTAG00000019515 | 1 retrocopy |
retro_btau_1067 ,
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