RetrogeneDB ID: | retro_sscr_903 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 7:58955487..58956600(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | WRNIP1 | ||
| Ensembl ID: | ENSSSCG00000001010 | ||
| Aliases: | None | ||
| Description: | Werner helicase interacting protein 1 [Source:HGNC Symbol;Acc:20876] |
Retrocopy-Parental alignment summary:
>retro_sscr_903
ATTTCGTGGGGCAGGGCAGGTGGCGCCCTGCTGAGCTCACTGCTGGAGGCCATGGAGGTGCCCTCGCTCATCCTGTGGGG
GCTCTTGGGCTGGGGCAAGACCTTGCTGGCCCACATTCTCACTAACAACAGCAAGAAACAGCGCAAGATTTGTGACCTTC
TCCGAAACCAGCTCCAAGACAACTGACTGGATGATGTCATCAAACAAGCTCAGAATGAGAAGAGCTTTTTCAAGAGGCAA
ACCATCCTTTATATTGACGAGATTTATCGATTCAATAAATCTCATCAGGACAGGTTCCTTCCTCACCTGGAGTATGAAAA
CCTGAACCTGATCTGGGCCACCACGCGGAACCCCTCTTTCCAGATCAATGCCGCTCTGCTGAGCCACTGTCAGGTGATCT
TCTTGAGAAGTTTCCAGTGGAGGCTGTGGTGACTGTCCTCACCCGGGTGACCAACTCCTTTGGGATCAAGGACCTGGACT
CTAGCTGCTCCGACGACCCTCTGAGCCACAGCAGCAACAGCAGTTCTGAGCCCCCCTTATTCACAGAGGACAAAGTGGTG
GACACACTGGCCCACCTCAGCGACAGGGACATCTGGGCTGGACTCAACAGACTGCTGATGGCAGTGGTGGCCAGGATCAG
CGCCAGGAAGGTTGTCGGGAAGAAGAGCAGGCAGACCTACCCTCCCAGCAGAGTCCTGGTCACCGAGAGTGACATGAAGA
AAGGCCTCCAGCACTCTCCCACCCTTTGTGACCACGCAGGAGAGGGCATTACCACTTCTGCGAGCTTCACACTGGCATGC
GGGGCTCTGAGCAGAGCGTGTCACTGCACAGGCTGGGCCATATGCTAGAGGGTAGAAAGGACCCACTCTATGCAGCCAGG
CAGCTCATGAAGTTTGCCAGAGAGGACCTGGGTCTGGCAGACCTGCCTGTATTAACCCAAGCCGTGGCCGCCCACCAGGG
CAGTCACTTTATTGGCAGGCTGAACGCCAGGTGCTCCTGGCCCAGTGCAGGGTCTACTTGGCCCGAGCCCCCAAGTCCAT
CGAGGTGTACAGCGCCTACCACAACGTTAAGGCCTGCCTGCGGAGCAACCAGGACCCCTGCGCCCCACTCCCC
ORF - retro_sscr_903 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 68.24 % |
| Parental protein coverage: | 73.44 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | VGQGRAVGPETLLRSLLEANEVPSLILWGPPGCGKTTLAHIIANNSKK-HSIRFVTLSATSAKTTD-VRD |
| ...GRA.G...LL.SLLEA.EVPSLILWG..G.GKT.LAHI...N..K..S.RFVT.S.TS.KTTD...D | |
| Retrocopy | ISWGRAGG--ALLSSLLEAMEVPSLILWGLLGWGKTLLAHILT-NNSK>NSARFVTFSETSSKTTD<LDD |
| Parental | VIKQAQNEKSFFKRKTILFIDEIHRFNKSQQDTFLPHVECGTITLIGATTENPSFQVNAALLSRCRVI-V |
| VIKQAQNEKSFFKR.TIL.IDEI.RFNKS.QD.FLPH.E.....LI.ATT.NPSFQ.NAALLS.C.VI.. | |
| Retrocopy | VIKQAQNEKSFFKRQTILYIDEIYRFNKSHQDRFLPHLEYENLNLIWATTRNPSFQINAALLSHCQVI<L |
| Parental | LEKLPVEAVVTILMRAINSLGIHVLDSSRPADPLSHSSNSSSEPSVFIEDKAVDTLAHLSDGDARAGLNG |
| LEK.PVEAVVT.L.R..NS.GI..LDSS...DPLSHSSNSSSEP..F.EDK.VDTLAHLSD.D..AGLN. | |
| Retrocopy | LEKFPVEAVVTVLTRVTNSFGIKDLDSSCSDDPLSHSSNSSSEPPLFTEDKVVDTLAHLSDRDIWAGLNR |
| Parental | LQLAVLARLSARKVFGKKTGQTYPPGRVLVTEGDVKEGLQRSHILYDRAGE-EHYNCISALHKAMRGSDQ |
| L..AV.AR.SARKV.GKK..QTYPP.RVLVTE.D.K.GLQ.S..L.D.AGE..HY.....LH..MRGS.Q | |
| Retrocopy | LLMAVVARISARKVVGKKSRQTYPPSRVLVTESDMKKGLQHSPTLCDHAGE<GHYH-FCELHTGMRGSEQ |
| Parental | NAALYWLGRMLEGGEDPLYVARRLVRFASEDVGLADPSALTQAVAAYQGCHFIG-MPECEVLLAQCVVYL |
| ...L..LG.MLEG..DPLY.AR.L..FA.ED.GLAD...LTQAVAA.QG.HFIG...E..VLLAQC.VYL | |
| Retrocopy | SVSLHRLGHMLEGRKDPLYAARQLMKFAREDLGLADLPVLTQAVAAHQGSHFIG<QAERQVLLAQCRVYL |
| Parental | ARAPKSIEVYSAYSNVKACLRSHQGPLPPVP |
| ARAPKSIEVYSAY.NVKACLRS.Q.P..P.P | |
| Retrocopy | ARAPKSIEVYSAYHNVKACLRSNQDPCAPLP |
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 |
|---|---|---|
| SRP014902_placenta | 0 .00 RPM | 117 .33 RPM |
| SRP014902_testis | 0 .00 RPM | 152 .20 RPM |
| SRP018288_heart | 0 .00 RPM | 29 .89 RPM |
| SRP018288_kidney | 0 .00 RPM | 49 .94 RPM |
| SRP018288_liver | 0 .00 RPM | 31 .98 RPM |
| SRP018288_lung | 0 .00 RPM | 69 .34 RPM |
| SRP018856_adipose | 0 .00 RPM | 66 .49 RPM |
| SRP035408_brain | 0 .00 RPM | 85 .72 RPM |
| SRP035408_liver | 0 .00 RPM | 24 .63 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_903 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_903 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_903 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 | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000002843 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000001010 | 1 retrocopy |
retro_sscr_903 ,
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