RetrogeneDB ID: | retro_sara_636 | ||
Retrocopy location | Organism: | Shrew (Sorex araneus) | |
| Coordinates: | scaffold_246936:8..1764(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | USP48 | ||
| Ensembl ID: | ENSSARG00000008022 | ||
| Aliases: | None | ||
| Description: | ubiquitin specific peptidase 48 [Source:HGNC Symbol;Acc:18533] |
Retrocopy-Parental alignment summary:
>retro_sara_636
GATACTTTGTCTAAACAAAAGAATCCACGTTTGAGTAACATAGTCCAGCAGCAGTTCTGTGGGGAATATGCTTATGTAAC
AGTTTGCAATCGTTGTGGCAATGGGTCTGAACTTTCATCAAAGTTTTATGAGCTCCAGTTAAATATTGAAGGCCACAAGC
TGTTAACAGATTCTATTTCAGATTTTTTGAAAGAAGAAAAATTAGAAGGAGACAATCGATATTTTTGTGAAAACTGTCAA
AGTAAACAAAATGCAACAAGGAAAATTCGGTTACTGAGCCTTCCTTGTACACTGAATCTACAGCTTATGTGCTTTGTCTT
TGACCGAAAAACTGGACACAAGAAAAAGCTGAATACCTACATTAGCTTCTCAGAAATTCTAGATATGAATCCTTATATGG
AACAGAAAGGAGGATCCTGTATGTATGAACTCAGCGCAGTGCTCATACACAGAGGATCGAGTGCTTATTCTGGGCACTAT
GTTGCAAATGTCAAAGATCCTAAGTCTGGTGAATGGTATAAGTTTAATGATGAAAACATAGAAAAACTGGAGGGAAGTAA
ATTAGAATTAGGAATTGAAAATGATATTCCAGTATCTTCTAAGTTTCGTAAACCAAAGTGTGGCAAAGGAATTCACTGCT
CTCGAAATGCATACATGTTGGTTTACAGACTGCAGACACAAGAAAAGCCCATGACGGCTGTTCCATTACCAGATTTTCTT
AAAGATCTTGTAGACCGGGATAATAGCAAGTTTGATAAATGGTGTGCAGAAATGACTGAGAAGCGTAAACAAAATGTTTA
TAAAGAAAAAGCAAAGCATGAAGAGTTTAAGGAGCTATACCCAAGGTTAGTGGTTAGAACGAAGAACGAGCCCTATGAAT
TTGTCTCTCTTGGGTGGCTGAAAACATGGTTGAGTGGATCCAAAATTACCCCACCTATTGATAATACTACTTACCTGTGT
CCTCATGACAAGCTTCATCCTGACAAAATGTTGATCATGAAGCGAATATCCAGCCATGCAGCTGATGTTTTCTACAATAG
ATATGGAGGAGGGCCAAGACTAACTGCGGAATCTTTGTGTAAGGAATGTGTAGTTGAACGTTGTCGTAAAATACATCAGA
AGAACAAACTCAATGTAGATCACAAAATTATTACTAATATGCTAAAAGAAAGTGTACAGGATAACCAGGGATTTTGGGTA
GGAAAATTCTCCTTGAGGAATTGGCGCCAACTAGCTCTTGAACAGATAGGTGAGCAAGATCTAGATCAAAACAATGGAAA
AATGAGCAACTATATCTCGAAGACGCAAGAGTCAAAGGAAGAAGGAGAGAGAGTAACATTTAATGAAGACATTGTTTGTC
TACATGGAGACTTAGTAATAGCTGAGAATGAAAGAAGGCTTGTTTCTCAAGAGATTTGGGGCAAACTGCAATATTATTTC
CCAAAGGCACCTGAGTTTCCAAATGACAAAGAAAGCTGCCCACAGTGTAAGAGTATAGAAAGAGAAGGGGAAAAAAATAA
TGCCTTATACAAGGTCCTTGCAAGTGAGCAAAAGTCGTCTCTTCTGCATTTGTTCCAGGACAAGTGTAGACCTTACCTCA
GTTACTGGCCAGAGAATACAAATGTCCTGTACATTGTGCCACAGATCTTTGTAGAAGAATGGCGCAAATTTATTAGAAAA
CCTACAAGATGCAGTCCCGTGTCATCAATTGTAAATAGTACTGGTCCTGTGTCCTCACGGGGGACTCATGTATACA
ORF - retro_sara_636 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 72.39 % |
| Parental protein coverage: | 57.05 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | DTLSKQKNPDVRNIVQQQFCGEYAYVTVCNQCGRESKLSSKFYELELNIQGHKQLTDCISEFLKEEKLEG |
| DTLSKQKNP...NIVQQQFCGEYAYVTVCN.CG..S.LSSKFYEL.LNI.GHK.LTD.IS.FLKEEKLEG | |
| Retrocopy | DTLSKQKNPRLSNIVQQQFCGEYAYVTVCNRCGNGSELSSKFYELQLNIEGHKLLTDSISDFLKEEKLEG |
| Parental | DNRYFCENCQSKQNATRKIRLLSLPCTLNLQLMRFVFDRQTGHKKKLNTYIGFSEILDMEPYVEHKGGAH |
| DNRYFCENCQSKQNATRKIRLLSLPCTLNLQLM.FVFDR.TGHKKKLNTYI.FSEILDM.PY.E.KGG.. | |
| Retrocopy | DNRYFCENCQSKQNATRKIRLLSLPCTLNLQLMCFVFDRKTGHKKKLNTYISFSEILDMNPYMEQKGGSC |
| Parental | VYELSAVLIHRGVSAYSGHYIAHVKDPQSGEWYKFNDEDIEKMEGKKLQLGIEEDLAEPSKSQTRKPKCG |
| .YELSAVLIHRG.SAYSGHY.A.VKDP.SGEWYKFNDE.IEK.EG.KL.LGIE.D...P..S..RKPKCG | |
| Retrocopy | MYELSAVLIHRGSSAYSGHYVANVKDPKSGEWYKFNDENIEKLEGSKLELGIENDI--PVSSKFRKPKCG |
| Parental | KGSHCSRNAYMLVYRLQSREKISTTVQVPAFLQELVDRDNSKFEEWCIEMAEMRKQSVDKGKAKHEEVKE |
| KG.HCSRNAYMLVYRLQ..EK..T.V..P.FL..LVDRDNSKF..WC.EM.E.RKQ.V.K.KAKHEE.KE | |
| Retrocopy | KGIHCSRNAYMLVYRLQTQEKPMTAVPLPDFLKDLVDRDNSKFDKWCAEMTEKRKQNVYKEKAKHEEFKE |
| Parental | LYQRLPAGA--EPYEFVSLEWLQKWLDESTPTKPIDNHACLCSHDKLHPDKISIMKRISEYAADIFYSRY |
| LY.RL......EPYEFVSL.WL..WL..S..T.PIDN...LC.HDKLHPDK..IMKRIS..AAD.FY.RY | |
| Retrocopy | LYPRLVVRTKNEPYEFVSLGWLKTWLSGSKITPPIDNTTYLCPHDKLHPDKMLIMKRISSHAADVFYNRY |
| Parental | GGGPRLTVKALCKECVVERCRLLRLKNQLNEDYKTVNNLLKTTVKGNDGFWVGKSSLRSWRQLALEQLDE |
| GGGPRLT...LCKECVVERCR....KN.LN.D.K...N.LK..V..N.GFWVGK.SLR.WRQLALEQ..E | |
| Retrocopy | GGGPRLTAESLCKECVVERCRKIHQKNKLNVDHKIITNMLKESVQDNQGFWVGKFSLRNWRQLALEQIGE |
| Parental | QDSEADQNNGKMNGDSLGKDESKEERKEEEEELNFNEDILCPHGELCISENERRLVSQEAWSKLQQYFPK |
| QD...DQNNGKM........ESKEE.........FNEDI.C.HG.L.I.ENERRLVSQE.W.KLQ.YFPK | |
| Retrocopy | QD--LDQNNGKMSNYISKTQESKEEGE----RVTFNEDIVCLHGDLVIAENERRLVSQEIWGKLQYYFPK |
| Parental | APEFPSHRECCSQCKILEREGEENEALHKMIANEQKTSLPNLFQDKNRPCLSNWPEDTDVLYIVSQFFVE |
| APEFP...E.C.QCK..EREGE.N.AL.K..A.EQK.SL..LFQDK.RP.LS.WPE.T.VLYIV.Q.FVE | |
| Retrocopy | APEFPNDKESCPQCKSIEREGEKNNALYKVLASEQKSSLLHLFQDKCRPYLSYWPENTNVLYIVPQIFVE |
| Parental | EWRKFVRKPTRCSPVSAVGNSA-LLCPHGGLMFT |
| EWRKF.RKPTRCSPVS...NS...LCPHGGLM.T | |
| Retrocopy | EWRKFIRKPTRCSPVSSIVNST>VLCPHGGLMYT |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Sorex araneus was not studied using RNA-Seq expression data.
Sorex araneus was not studied using ChIP-Seq data.
Sorex araneus was not studied using EST data.
Sorex araneus was not studied using FANTOM5 data.
retro_sara_636 was not experimentally validated.
Retrocopy orthology:
Sorex araneus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Sorex araneus | ENSSARG00000008022 | 1 retrocopy |
retro_sara_636 ,
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