RetrogeneDB ID: | retro_btau_1808 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | X:32859933..32860684(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSBTAG00000046143 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_btau_1808
GTCTGGGGCACCCTGGAGGAGGTGGCTGCTACTGCAACAACCAGTTTCCCCCAGAGCCCTCTAGGTGTCTGCTCCTCTCC
CACTGCCATGGCTGCCAATCTTGGGAGCCAGTCTGAAGACCATGGCCTCAGCAGACAAGATGAAGTGCCAGACACCTCAC
GTGACCAGGAAGATGCAAAGTCCTTGCTCCAAGATGCACTATGGGTGAAGAAGAAAGAGCTGGTGTGATTCCTGCTCAGC
AAGTATCTTGCCAAGGAGCCGATCACAAAGGCAGAAGTGCTGAATAGTGTCCTCAAAGATTACCAGGACTACTTCCTGGT
GGTCCTCGGTCAAGCCTCAGAGTACCTGCAGCTGATCTTTGGTTTGGAGATGAAGGAGGTGGATCAGAGTGAGCAGACCT
ATATCCTGGTCCCCACCTTGGGCCTCACCCTCAATGAGATGCTGAGGGATGGGCAGGGGTTGCCCAAGGCCGGCCTCCTG
GTGGTGATCCTGTGCCTGATCACTGTGGAAGACAACCGTGCCCCTGAGGAGGAGGTCTGGGAAGCATTCAGCAGGATGGG
GGTGTCCTGGGAGGGAGCACTACATGTATGGGGATCCCAGGGAGCTGCTGACCCAAGTGTGGGTGCGGGAGGGGTACCTG
GAATACCGGTAGGTGCCTGACAACGGCCCTGCTCGATACAAGTTCCTGTGGGCTTCCTGGGCCTATGCAGAGACCAGCAA
GTTTAAAGTCCTGGAGTATCTGGACAGAGTC
ORF - retro_btau_1808 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.9 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | VRGTLEEVAAAATPSLPQSPLGVWPSPNAMAATLGSQYEENGLSRQDEVLSTSCDQED--EFFKYALRVK |
| V.GTLEEVAA.AT.S.PQSPLGV..SP.AMAA.LGSQ.E..GLSRQDEV..TS.DQED.......AL.VK | |
| Retrocopy | VWGTLEEVAATATTSFPQSPLGVCSSPTAMAANLGSQSEDHGLSRQDEVPDTSRDQEDAKSLLQDALWVK |
| Parental | KNELVQFLLSRCLAKEPITKAEVLNSVLKDYQDHFLVVFGQASEYLQLVFSLEVKEVDPSEHTYILVPSL |
| K.ELV.FLLS..LAKEPITKAEVLNSVLKDYQD.FLVV.GQASEYLQL.F.LE.KEVD.SE.TYILVP.L | |
| Retrocopy | KKELV*FLLSKYLAKEPITKAEVLNSVLKDYQDYFLVVLGQASEYLQLIFGLEMKEVDQSEQTYILVPTL |
| Parental | GLTLSEMLSDGQRLPKAGLLVVILCLIAVEDGHAPEEEIWGALSRMGVCL-GEHFIYGEPRELLTQVWVQ |
| GLTL.EML.DGQ.LPKAGLLVVILCLI.VED..APEEE.W.A.SRMGV....EH..YG.PRELLTQVWV. | |
| Retrocopy | GLTLNEMLRDGQGLPKAGLLVVILCLITVEDNRAPEEEVWEAFSRMGVSW>REHYMYGDPRELLTQVWVR |
| Parental | EGYLVYRQVPDDDPACYEFLWGPQGYVETSKFKDLEYLDRV |
| EGYL.YR.VPD..PA.Y.FLW....Y.ETSKFK.LEYLDRV | |
| Retrocopy | EGYLEYR*VPDNGPARYKFLWASWAYAETSKFKVLEYLDRV |
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 .00 RPM |
| ERP005899_muscle | 0 .00 RPM | 0 .00 RPM |
| SRP017611_brain | 0 .00 RPM | 0 .00 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .00 RPM |
| SRP030211_testis | 0 .00 RPM | 0 .00 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1808 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1808 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1808 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000046143 | 2 retrocopies |
retro_btau_1808 , retro_btau_198,
|
| Canis familiaris | ENSCAFG00000019160 | 1 retrocopy |