RetrogeneDB ID: | retro_btau_865 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 2:42174112..42174834(-) | ||
| Located in intron of: | ENSBTAG00000005562 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BT.105251 | ||
| Ensembl ID: | ENSBTAG00000026676 | ||
| Aliases: | None | ||
| Description: | syndecan-3 precursor [Source:RefSeq peptide;Acc:NP_001193460] |
Retrocopy-Parental alignment summary:
>retro_btau_865
ATAAGGACCACTGGCGTAAGTAGGCTTCTGCCTCTTCCACTGACCACAGTGGCCACAGCCTACGGGCCACCACCCCAGCG
GTGCCCTCACCTCCCACCATAGTGGCTGTCTTGGACACAGAGGCCCCCAGCTCCCAGGCTGGTCAGCACAGCTACCTCCA
GGCTAAGGGCCCTTCCTAGACCAGCTACCACCCAGAAGCCTGACATCTCTGAGAAGAGCACCCTGCCCCTGGGGACCACT
GCCCATGGACCCATGGAGGTGGCTCAGACCCCAACTCCAGAGTCCTTCCCGACCACCATCCGGGATAAGCCAGAAATGCC
AGCGAGCGGGGGACCCAGTGGGGACTTTGAGCTGTCAGAAGAAGAGACCACACAGCCAGACACAGCCAATGAGGTGGTGG
CTGTGGGTGGGCCACAGCCAAGCTATCACCTCTACCTGGGATGCTGCCCAAGGGTGCCCACCCAGGCCCTGGCCTCCTGG
ACAGTGTTGTTGACTCAGGCAGCTCAGGGGCTCAGCTTTCCCAGAAGAGCATCCTGGAGTGGAAGAAGGTGCCTGTAGCT
GTGATCATGGGTGGGGTTTTAAGTGCCCTCTTTGCTGCCTTCCTGGTCACACTGTTCATCTGTGGCATGAAGAAGAAGAA
CAAGGGCACCTACACGTTGGAGGAGCCCAATCAGGCAAGCGTCACATACCAGAAGCCTAACAAGCAAGAGGAGTTCTATG
CC
ORF - retro_btau_865 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.79 % |
| Parental protein coverage: | 54.3 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | VRTTGVRRLLPLPL-TTAA-TARATTPAVPSPPTTVAVLDTEAPT-PRLVSTATSRPRALPRPATTQKPD |
| .RTTGV.RLLPLPL.T.A....RATTPAVPSPPT.VAVLDTEAP..PRLVSTATSR.RALPRPATTQKPD | |
| Retrocopy | IRTTGVSRLLPLPLTTVAT<SLRATTPAVPSPPTIVAVLDTEAPS>PRLVSTATSRLRALPRPATTQKPD |
| Parental | IPEKSTLPLGTTAPGPTEVAQTPTPESFLTTIRDEPEMPVSGGPSGDFELSEEETTQPDTANEVVAVGG- |
| I.EKSTLPLGTTA.GP.EVAQTPTPESF.TTIRD.PEMP.SGGPSGDFELSEEETTQPDTANEVVAVGG. | |
| Retrocopy | ISEKSTLPLGTTAHGPMEVAQTPTPESFPTTIRDKPEMPASGGPSGDFELSEEETTQPDTANEVVAVGG< |
| Parental | AEAKPSPPPGTLPKGAHPGPGLLDNAIDSGSSAAQLPQKSILERKEVLVAVIVGGVVGALFAAFLVTLLI |
| A.AK.SP.PG.LPKGAHPGPGLLD...DSGSS.AQL.QKSILE.K.V.VAVI.GGV..ALFAAFLVTL.I | |
| Retrocopy | ATAKLSPLPGMLPKGAHPGPGLLDSVVDSGSSGAQLSQKSILEWKKVPVAVIMGGVLSALFAAFLVTLFI |
| Parental | YRMKKKDEGSYTLEEPKQASVTYQKPDKQEEFYA |
| ..MKKK..G.YTLEEP.QASVTYQKP.KQEEFYA | |
| Retrocopy | CGMKKKNKGTYTLEEPNQASVTYQKPNKQEEFYA |
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 | 0 .72 RPM |
| ERP005899_muscle | 0 .00 RPM | 9 .19 RPM |
| SRP017611_brain | 0 .00 RPM | 79 .89 RPM |
| SRP017611_kidney | 0 .00 RPM | 23 .18 RPM |
| SRP017611_liver | 0 .00 RPM | 18 .73 RPM |
| SRP030211_testis | 0 .00 RPM | 5 .03 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_865 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_865 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_865 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 | ENSBTAG00000026676 | 1 retrocopy |
retro_btau_865 ,
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