RetrogeneDB ID: | retro_btau_987 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 22:12647620..12648419(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ST6GALNAC6 | ||
| Ensembl ID: | ENSBTAG00000044129 | ||
| Aliases: | ST6GALNAC6, siat7f, st6GalNAc-VI | ||
| Description: | Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 6 [Source:UniProtKB/Swiss-Prot;Acc:Q08E15] |
Retrocopy-Parental alignment summary:
>retro_btau_987
CCCCAGGGGAGGTGTGACCCCACACCCCTACCCCCTGGGCCATCTGCAGGATGCCGGCCTCTGCCCCACAGCAGTCACCA
GAGAGAGATGAGTAACAACAAACAGCAGCGGTCAGCAGCGTTCCTGATCCTCTTTGCTCTCATCACCACCCTCATCCTCT
GTAGCCCCAACAGTGCGAGTGAGGCCTCTCATTACAGCTCCCTGCGGGGCCAGATCCGCCAGCTGGTCAACCTCAAGAAG
TAGGGCATCACTGACGGCTACATCCCCATTCTCACCCACAAGACACTGCCCTCCTGGTGCTACCAATGTGATTGTCACCA
GCTCCAGCCACCTGCTAGGAACCAAACTGGGCCCTGAGGTCAAGCAGGCAGAGTGCACAATCTGCATGAACGACACCCCC
ACCACAGGCTACTCAGACCACCTTGTGGGTAACAAGACCACCTTCTGCGTAGGGGCCCATTCCAGTGTATTCCGTGTGCT
GTGGAGACTCTAGGAGTTCATCAACCAGACCTCCGAAACCGTGTTCATCTTCTGGGGTGTTCCAAACAAGACGCAGAAGC
CCCAGGACAGCCTGGTGCACGTCGTCCAGTGGGCAGGCCTGGTGTTCCCCAACATGAACGCTTACGCCATCTCTCTTGGC
TGCATGAGCCAGTCTGATGACCTCTTCCAGAGTGAGACGGGCAAGGACAGGGAAGAGTCCTACTCGTGGCTGAGCACAGG
CTGGTTCACCATGGCGACTGCAGTGGAGTAGTGTGACCACGTGCCCATCTATGGCATGGTGCCCCCGGACTACTGCAGC
ORF - retro_btau_987 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.9 % |
| Parental protein coverage: | 79.82 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | PLSQCDHTPLP-GPPAGHWPLPLSRRRREMKSNKEQRSAVFVILFALITILILYSSSSANEVFHYGSLRG |
| P...CD.TPLP.GP.AG..PLP.S...REM..NK.QRSA.F.ILFALIT.LIL.S..SA.E..HY.SLRG | |
| Retrocopy | PQGRCDPTPLPPGPSAGCRPLPHSSHQREMSNNKQQRSAAFLILFALITTLILCSPNSASEASHYSSLRG |
| Parental | RTRRPVNLRKWSITDGYIPILGNKTLPSRCGQC-VIVTSSSHLLGTKLGPEIERAECTIRMNDAPTTGYS |
| ..R..VNL.K..ITDGYIPIL..KTLPS.C.QC.....S.SHLLGTKLGPE...AECTI.MND.PTTGYS | |
| Retrocopy | QIRQLVNLKK*GITDGYIPILTHKTLPSWCYQC>IVTSS-SHLLGTKLGPEVKQAECTICMNDTPTTGYS |
| Parental | AD-VGNKTTFRVVAHSSVFHVLRRPQEFVNRTPETVFIFWGPPNKMQKPQGSLVRVIQRAGLVFPNMEAY |
| ...VGNKTTF.V.AHSSVF.VL.R..EF.N.T.ETVFIFWG.PNK.QKPQ.SLV.V.Q.AGLVFPNM.AY | |
| Retrocopy | DHLVGNKTTFCVGAHSSVFRVLWRL*EFINQTSETVFIFWGVPNKTQKPQDSLVHVVQWAGLVFPNMNAY |
| Parental | AISLSRMRQFDDLFRSETGKDREKSHSWLSTGWFTMVIAVELCDHVHVYGMVPPDYCS |
| AISL..M.Q.DDLF.SETGKDRE.S.SWLSTGWFTM..AVE.CDHV..YGMVPPDYCS | |
| Retrocopy | AISLGCMSQSDDLFQSETGKDREESYSWLSTGWFTMATAVE*CDHVPIYGMVPPDYCS |
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 | 6 .85 RPM |
| ERP005899_muscle | 0 .00 RPM | 11 .67 RPM |
| SRP017611_brain | 0 .00 RPM | 43 .30 RPM |
| SRP017611_kidney | 0 .00 RPM | 8 .12 RPM |
| SRP017611_liver | 0 .00 RPM | 20 .76 RPM |
| SRP030211_testis | 0 .00 RPM | 3 .33 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_987 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_987 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_987 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000010357 | 1 retrocopy | |
| Bos taurus | ENSBTAG00000044129 | 1 retrocopy |
retro_btau_987 ,
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