RetrogeneDB ID:

retro_mmus_1022

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:13:64509487..64511096(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000094597
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Snw1
Ensembl ID:ENSMUSG00000021039
Aliases:Snw1, 2310008B08Rik, AW048543, NCoA-62, SKIP, Skiip
Description:SNW domain containing 1 [Source:MGI Symbol;Acc:MGI:1913604]


Retrocopy-Parental alignment summary:






>retro_mmus_1022
ATGTCCCTCACCAGCTTTTTACCTGCACTCACTCAGCTATCTCAGGACCAACTTGAAGCTGAAGAAAGGGCAAGGTCTCA
GAGATCACAGTGGACCTCTCTGGTCTCCTTTCGAAGAGAGCCTCCCTCATATGGATTCAGGAAAGGCTGGATTCCGCGGG
TGCTGGAGGATTTTGGAGATGGAGGTTCTTTCCCCGAAATCCACGTGGCCCAGTATCCTCTGGATATGGGTAATCAGAAA
AAAAATATCCAATGCTCTGGCCATTCAGCTGGATCATGAAGGGAAAATTAAATATGATATAATTGCTCGACAGGGACATT
CCAAAGGCAAGGTCATTTATAGCAAATACACTGACCTAATTCCAAAGGAGGTTATGAATCCAGATGACCCAGACCTACAA
AGGCCTGATAAAGAGACGGTTAAAGAAATAACAGAAAGGACAAGAATAGCCTTGGAGAAGATAATATCAAGGAAGGTTGA
TGCGGCCAGACCTGTTCATGCAGCTGAGAAGTATACTCCTGATAAGTATATCCACTACACGCCATCTCAACAAGGAGGAA
CATTCAATTATGGACCTAAGCAGAGGGTTATTCGGATCATAGAAATGCAGAAAGACCTAATGGAGCCTCCGAGATTCAGG
ATTAATAAGAAAATTCCCCGTGGACCACCGTCTCCTACTGTACCTGTAATGCACTCGCCTCCTCGGAAGAACACTGTCAA
AGAACAGCACGAGTGGGAGATCCCTCCGTGTATATCTAGGTGGAAGAACTCGAAGGGTTATACGATTCCACTGGATAAAC
GGCTGGCTGCTGATGGAAGAGGACTTCAGACTGTCCACATAAATGAAAAATTTGTCAAGCTAGCTGAAGTGCTGTACATC
GGTGAGCGGAAGGCTCGAGAAGCCGTGGAAACGCGAGCCCAAGTAGAGAGAAAGGTGGCTCAAAAAGAAAAGGAGAAACA
CGAAGAGAAACTTAGAGAAATGGCCCAGAAAGCCAGAGAAAGGAGAGCTGGGATCAAAACCCACACGGAAAAAGAGGATG
GTGAGGCCCGTGAAAGAGATGAAATCCGTCATGACCGGCGAAAAGAGAGGCAGCACGACCGGAAACTTTCCAGGGCAGCT
CCTGATAAGAGGTCAAGGCTACAGAGAAATGAAAATCGAGATATCAGTGAAGTCATTGCTCTTGGTGTGCCCAATCCTCG
AACTTCCAATGAAGTTCAATATGACCAAAGGCTCTTCAATCAATCCAAGGGTATGGGCAGTGGATTTGCAGGCGGAGAAG
ATGAAATTTACAATGTTTATGATCAGGCCTGGAAAGGTGGCAAAGATATGGCACAGAGTATCTACAGGCCCAGTAAGAGT
CTGGACAAGGACATGTATGGTGATGACCTCGAAACCAGGATAAAGACCAACAGATTTGTTCCTGATAAGGCATTTTCTGG
TTCAGACCTTAGACAGAGAGGCCGAGAAGGACCAGTGCAGTTTGAGGAGGATCCTTTTGGTTTGGACAAGTTTTTAGAAG
AAGCAAAACAGCACTGTGGCTCTAAAAGACGCTTGGATAGCAGTCACACCAAGGTAGATGAGAATGAAGGCAAGAAGCAG
AGGAAGGAG

ORF - retro_mmus_1022 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.92 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMALTSFLPAPTQLSQDQLEAEERARSQRSLQTSLVSSRREPPPYGYRKGWIPRLLEDFGDGGAFPEIHVA
M.LTSFLPA.TQLSQDQLEAEERARSQRS..TSLVS.RREPP.YG.RKGWIPR.LEDFGDGG.FPEIHVA
RetrocopyMSLTSFLPALTQLSQDQLEAEERARSQRSQWTSLVSFRREPPSYGFRKGWIPRVLEDFGDGGSFPEIHVA
ParentalQYPLDMGRKKKM-SNALAIQVDPEGKIKYDAIARQGQSKDKVIYSKYTDLVPKEVMNADDPDLQRPDEEA
QYPLDMG......SNALAIQ.D.EGKIKYD.IARQG.SK.KVIYSKYTDL.PKEVMN.DDPDLQRPD.E.
RetrocopyQYPLDMGNQXXX>SNALAIQLDHEGKIKYDIIARQGHSKGKVIYSKYTDLIPKEVMNPDDPDLQRPDKET
ParentalIKEITEKTRVALEKSVSQKVAAAMPVRAADKLAPAQYIRYTPSQQGVAFNSGAKQRVIRMVEMQKDPMEP
.KEITE.TR.ALEK..S.KV.AA.PV.AA.K..P..YI.YTPSQQG..FN.G.KQRVIR..EMQKD.MEP
RetrocopyVKEITERTRIALEKIISRKVDAARPVHAAEKYTPDKYIHYTPSQQGGTFNYGPKQRVIRIIEMQKDLMEP
ParentalPRFKINKKIPRGPPSPPAPVMHSPSRKMTVKEQQEWKIPPCISNWKNAKGYTIPLDKRLAADGRGLQTVH
PRF.INKKIPRGPPSP..PVMHSP.RK.TVKEQ.EW.IPPCIS.WKN.KGYTIPLDKRLAADGRGLQTVH
RetrocopyPRFRINKKIPRGPPSPTVPVMHSPPRKNTVKEQHEWEIPPCISRWKNSKGYTIPLDKRLAADGRGLQTVH
ParentalINENFAKLAEALYIADRKAREAVEMRAQVERKMAQKEKEKHEEKLREMAQKARERRAGIKTHVEKEDGEA
INE.F.KLAE.LYI..RKAREAVE.RAQVERK.AQKEKEKHEEKLREMAQKARERRAGIKTH.EKEDGEA
RetrocopyINEKFVKLAEVLYIGERKAREAVETRAQVERKVAQKEKEKHEEKLREMAQKARERRAGIKTHTEKEDGEA
ParentalRERDEIRHDRRKERQHDRNLSRAAPDKRSKLQRNENRDISEVIALGVPNPRTSNEVQYDQRLFNQSKGMD
RERDEIRHDRRKERQHDR.LSRAAPDKRS.LQRNENRDISEVIALGVPNPRTSNEVQYDQRLFNQSKGM.
RetrocopyRERDEIRHDRRKERQHDRKLSRAAPDKRSRLQRNENRDISEVIALGVPNPRTSNEVQYDQRLFNQSKGMG
ParentalSGFAGGEDEIYNVYDQAWRGGKDMAQSIYRPSKNLDKDMYGDDLEARIKTNRFVPDKEFSGSDRKQRGRE
SGFAGGEDEIYNVYDQAW.GGKDMAQSIYRPSK.LDKDMYGDDLE.RIKTNRFVPDK.FSGSD..QRGRE
RetrocopySGFAGGEDEIYNVYDQAWKGGKDMAQSIYRPSKSLDKDMYGDDLETRIKTNRFVPDKAFSGSDLRQRGRE
ParentalGPVQFEEDPFGLDKFLEEAKQHGGSKRPSDSSRPKEHEHEGKKRRKE
GPVQFEEDPFGLDKFLEEAKQH.GSKR..DSS..K..E.EGKK.RKE
RetrocopyGPVQFEEDPFGLDKFLEEAKQHCGSKRRLDSSHTKVDENEGKKQRKE

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(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
SRP007412_brain 0 .19 RPM 29 .90 RPM
SRP007412_cerebellum 0 .00 RPM 36 .91 RPM
SRP007412_heart 0 .00 RPM 22 .54 RPM
SRP007412_kidney 0 .02 RPM 33 .90 RPM
SRP007412_liver 0 .00 RPM 22 .37 RPM
SRP007412_testis 3 .70 RPM 41 .71 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_mmus_1022 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_1022 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_1022 retrocopy 5' end.

Lab - click to see more details

retro_mmus_1022 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_1022 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 21 parental genes, and 33 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000039762 retrocopies
retro_amel_163, retro_amel_912,
Canis familiaris ENSCAFG000000304091 retrocopy
retro_cfam_195,
Callithrix jacchus ENSCJAG000000169472 retrocopies
retro_cjac_2932, retro_cjac_576,
Dipodomys ordii ENSDORG000000123803 retrocopies
retro_dord_693, retro_dord_781, retro_dord_782,
Felis catus ENSFCAG000000016371 retrocopy
retro_fcat_635,
Homo sapiens ENSG000001006031 retrocopy
retro_hsap_174,
Gorilla gorilla ENSGGOG000000260161 retrocopy
retro_ggor_257,
Loxodonta africana ENSLAFG000000034822 retrocopies
retro_lafr_474, retro_lafr_787,
Myotis lucifugus ENSMLUG000000052282 retrocopies
retro_mluc_387, retro_mluc_805,
Monodelphis domestica ENSMODG000000052521 retrocopy
retro_mdom_1841,
Mustela putorius furoENSMPUG000000087241 retrocopy
retro_mputfur_551,
Mus musculus ENSMUSG00000021039 2 retrocopies
retro_mmus_1022 , retro_mmus_387,
Nomascus leucogenys ENSNLEG000000167711 retrocopy
retro_nleu_982,
Otolemur garnettii ENSOGAG000000298251 retrocopy
retro_ogar_1404,
Ochotona princeps ENSOPRG000000075681 retrocopy
retro_opri_737,
Pongo abelii ENSPPYG000000060311 retrocopy
retro_pabe_454,
Pan troglodytes ENSPTRG000000065871 retrocopy
retro_ptro_165,
Sorex araneus ENSSARG000000022793 retrocopies
retro_sara_403, retro_sara_568, retro_sara_727,
Tupaia belangeri ENSTBEG000000140743 retrocopies
retro_tbel_2575, retro_tbel_2927, retro_tbel_3536,
Taeniopygia guttata ENSTGUG000000123402 retrocopies
retro_tgut_15, retro_tgut_30,
Tarsius syrichta ENSTSYG000000109511 retrocopy
retro_tsyr_1871,


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