RetrogeneDB ID: | retro_btau_665 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 17:46486456..46487639(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SCFD1 | ||
| Ensembl ID: | ENSBTAG00000017565 | ||
| Aliases: | None | ||
| Description: | sec1 family domain-containing protein 1 [Source:RefSeq peptide;Acc:NP_001178294] |
Retrocopy-Parental alignment summary:
>retro_btau_665
AACTTTATTTCTGCCCTTTCAAGGAGTAAACTGGAATATATTGCAAATGTAGAAGTAGCAGCCATGCAGTTACTCAAGTA
TCCAGCTTTTGATCAGTATCTCAGTTTTATTACTTTGGAAAATGATATGCCTGTATGATACAATCAAAAATGAGGAAATG
TTTCATATTGTGCCATTAACAGTTCAGAAATCACAAATGCGGAAATGAAAACTGTTACGAACCGGAATGTTGACAGCCTC
TTCTGCTTTTCTGTTATGCTGGGTACTCTTCCTATAATCAGATAATTAGCAGGAACAGCAATGGAAATGAGAGCAGTGAA
AATAGATAAGAAGTTTCCGGAACATCTAAGAGATGCCAAAAAATGGTTTTACTACAGGTGATGCACTGGGAGCTGGCAGC
CTCAGCTTTCAAAGCCTTCTTCACTCCTGTTGACAGAAACATGGATCTGGCAACTCCTTTACATCATATTTGGACATATC
AATCCTACGCGTGTGATGTAGTGGATTTCCATGTACACAGAGTTAACCTGGAGGAATCTTCAGGAGTGAAAAAGTCCCTG
GCTGGTGCTAGTGTGACCTAGAGAAAAAACCAGGAAGTCGTATGATTTAACTCCAGTTGATACATTTTGGCAGAAACGTA
AAGGAAGTCCCTTCCCAGAGGTTTGGGAATCAGTTCAGCAAGAACTAGAATCTTAGAGCAGAGCACCAGAAGATGAGGTC
AAACGCCTGAGAAGTATGGGACCAGAAGGGAAAGATGAAGGGGCCACGAGGATGCTTCCTGACAACACTGCTCAGGTATC
CTCAGCTTTTGGTTCTTTGCCAGAAGACCTTGGAGAGGGGACAAAGACTTACTGATCTCCATAAAATGTTGCCACTGCTG
TCTTAGGACATGTAAAGGCATGAAAACTGGATGTATGTTTTGAATATAAAGAAAAAATAATGAGCAAAGCTTTCCTGGGC
AAATCTCTTCTAGAAGAAATATCAGACTCTGACGCAGGTAATCCAGGAGATAAATGAGGCATTTCTTATCTATCATGTAA
GTGCACAGCAAACAGCTTCTGAGGCTGATTTGGAGCCACACCAAAAAGCTGGAACTGACGCAGGATGCAACCTTAATTCC
TTACAATATATCAAACAGAGGAAGGCTTTTGCTAGGATGGCTTCAGCTCCTGCCATCTCAGGC
ORF - retro_btau_665 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 66.17 % |
| Parental protein coverage: | 61.47 % |
| Number of stop codons detected: | 6 |
| Number of frameshifts detected: | 8 |
Retrocopy - Parental Gene Alignment:
| Parental | NFISAISRSKLEDIANAALAASAVTQVAKVFDQYLNFITLEDDMFVLCNQNKELVSYRAINRPDITDTEM |
| NFISA.SRSKLE.IAN...AA.........FDQYL.FITLE.DM.V..NQ....VSY.AIN...IT..EM | |
| Retrocopy | NFISALSRSKLEYIANVEVAAMQLLKYP-AFDQYLSFITLENDMPV*YNQK*GNVSYCAINSSEITNAEM |
| Parental | ETVMDTIVDSLFCFFVTLGAVPIIRCSRGTAAEMVAVKLDKKLRENLRDA-RNSLFTGDTLGAGQFSFQ- |
| .TV....VDSLFCF.V.LG..PIIR...GTA.EM.AVK.DKK..E.LRDA..N...TGD.LGAG..SFQ. | |
| Retrocopy | KTVTNRNVDSLFCFSVMLGTLPIIR*LAGTAMEMRAVKIDKKFPEHLRDA>KNGFTTGDALGAGSLSFQ< |
| Parental | RPLLVL-IDRNIDLATPLHHTWTYQALVHDVLDFHLNRVNLEESSGMENSPAGARPK-RKN-KKSYDLTP |
| .P...L..DRN.DLATPLHH.WTYQ....DV.DFH..RVNLEESSG...S.AGA....RKN..KSYDLTP | |
| Retrocopy | KPSSLL<VDRNMDLATPLHHIWTYQSYACDVVDFHVHRVNLEESSGVKKSLAGASVT*RKN>RKSYDLTP |
| Parental | VDKFWQKHKGSPFPEVAESVQQELES-YRAQEDEVKRLKSIMGLEGEDEGAISMLSDNTAKLTSAVSSLP |
| VD.FWQK.KGSPFPEV.ESVQQELES..RA.EDEVKRL.S.MG.EG.DEGA..ML.DNTA...SA..SLP | |
| Retrocopy | VDTFWQKRKGSPFPEVWESVQQELES*SRAPEDEVKRLRS-MGPEGKDEGATRMLPDNTAQVSSAFGSLP |
| Parental | E-LLEK-KRLIDLHT-NVATAVLEHIKARKLDVYFEYEEKIMSKTTLDKSLLDIISDPDAGTPEDK-MRL |
| E..LE...RL.DLH..NVATAVL.H.KA.KLDV.FEY.EKIMSK..L.KSLL..ISD.DAG.P.DK.MR. | |
| Retrocopy | E>TLERGQRLTDLHK<NVATAVLGHVKA*KLDVCFEYKEKIMSKAFLGKSLLEEISDSDAGNPGDK<MRH |
| Parental | F-LIYYISAQQAPSEADLEQYKKALTDAGCNLNPLQYIKQWKAFAKMASAPTSYG |
| F.LIY..SAQQ..SEADLE...KA.TDAGCNLN.LQYIKQ.KAFA.MASAP...G | |
| Retrocopy | F<LIYHVSAQQTASEADLEPHQKAGTDAGCNLNSLQYIKQRKAFARMASAPAISG |
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 | 33 .81 RPM |
| ERP005899_muscle | 0 .00 RPM | 38 .48 RPM |
| SRP017611_brain | 0 .00 RPM | 30 .10 RPM |
| SRP017611_kidney | 0 .00 RPM | 41 .31 RPM |
| SRP017611_liver | 0 .00 RPM | 33 .07 RPM |
| SRP030211_testis | 0 .05 RPM | 33 .11 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_665 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_665 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_665 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 | ENSBTAG00000017565 | 1 retrocopy |
retro_btau_665 ,
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