RetrogeneDB ID:

retro_mmus_2424

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:4:147276061..147278964(+)
Located in intron of:ENSMUSG00000097168
Retrocopy
information
Ensembl ID:ENSMUSG00000082925
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Smarca5
Ensembl ID:ENSMUSG00000031715
Aliases:None
Description:SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 [Source:MGI Symbol;Acc:MGI:1935129]


Retrocopy-Parental alignment summary:






>retro_mmus_2424
GCAACAAAGGCGGCCCCGAGGGCTGCGGGCTCGTGCCCCGGCCCCGCGGACACCGAGATGGAGGAAGTATTTGATAATGG
ATCACCTGGAAAGCAAAAAGAAATCCAAGAACCAGATCCTACATATGAAGAAAAAATGCAAACTGACCGAGCAAATAGAT
TTGAGTATTTATTAAAGCAGACAGAGCTGTTCGCTCATTTCATTCAGCCTGCTGCTCAGAAGACTCCAACCTCACCCTTG
AAGATGAAACCAGGGCGCCCACGGGTAAAAAAGGATGAAAAACAGAATTTGCTTTCAGTTGGAGATTACCAACACTGTAG
AACAGAGCAAGAGGAGGATAAAGAGCTATAAACAGAAAGTTCCAAAGCAACTAATGTTTGTACTCGATTTGAAGATTCTT
CATCATATGTAAAATGGGGTAAACTGAGAGATTATCAGGTGCGAGGATTGAATTGGCTCATCTCTCTGTATGAGAATGGC
ATCAATGGGATCCTTGCAGATGAAATGGGTTTGGGAAAGACACTTCAAACAATTTCTCTTCTTGGATACAGGAAACACTA
TAGAAATATTCCTGGTCCTCATATGGTTTTGGTTCCCAAGTCTACATTGCACAACTGGATGAGTGAATTCAAGAGATGGA
TACCAACACTTAGGTCTGTTTGCTTGATAGGAGATGAAGAGCAAAGAGCTGTATTTGTCAGGGATGTTTTATTACCAGGA
GAGTAGGATGTATGTGTCACATCTTATGAAATGCTTATTAAAGAGAAAGTCTGTGTTCAAAAAAATTCAGCTGGAGATAC
TTAGTTATAGATGAAGCTCACAGGATAAAAAATGAAAAAATCTAAGTTGTCAGAAATAGTGAGAGAATTCAAGACTACAA
ATCGGCTGTTGCTAACAGGGACGCCTCTTCAGAACAACCTGCATGAGCTCTGGTCACTTCTAAACTTTTTGTTACCAGAT
GTGTTTAATTCAGCTGATGACTTTGATTCCTGGTTTGATACAAATAATTGCCTTGGGGATCAAAAGCTAGTTGAGAGGCT
TCATATGGTTTTGTGTCCATTCCTCCTTCGTCGAATTAAAGCTGATGTTGAAAAGAGTTTGCCTCCAAAAAAAGAAGTAA
AAATCTATGTGAGTCTTAGCAAAATGCAAAGACAATGGTATACTCGGATATTAATAAAGATATAGACATGTTAAACTCAG
CAGGAAAGATGGACAAAATGAGGCTATTGAACATTTTGATGCAGTTGAGGAAATGCTGCAATCATCCGTAACTCTTCGAT
GGAGCTGAACCTGGTCCACTGTACACAACAGATACGCATCTAGTTACCAACAGTGGCAAGATGGTGGTGTTAGACAAGCT
ACTCCCTAAACTGAAAGAACAAGGTTCAAGAGTACTAATCTTTAGTCAGATGACAAGAGTATTAGACATTTTGGAAGATT
ATTGCATGTGGAGAAATTATGAGTACTGCAGGTTGGATGAACAGACACCCCATGAGAGACAAGACTCCATCAATGCATAC
AATGAACCAAATAGCACAAAGTTTGTATTTATGCTAAGCACACGTGCTGGTGGTCTGGGCATCAATCTTGCAACTGCTGA
TGTAGTAATTTTATATGATTCAGATTGGAATCCTCAAGTTGATCTTCAGGCTATGGACTATGCCCATAGAATTGGACAAA
GGAAGACTGTCCGAGTGTTTCGCTTTATAACCGATAACACTGTGGAAGAAAGAATAGTGGAACGTGCTGAGATGAAACTT
AGACTGGATTCGATAGTAATTCAACAAGGGAGGCTTGTAGATCAGAACCTGAACAAAATTGGGAAAGATGAAATGCTTCA
AATGATTCGACGTGGTGCCACACATGTGTTTGCTTCAAAAGAAAGTGAAATCACTGATGAGGATATTGATGGTATTTTAG
AAAGAGGTGCAAAGAAGACTGCAGAAATGAATGAAAAGCTGTCCAAGATGGGTGAAAGTTCACTTAGAAACTTTACGATG
GATACAGAGTCCAGTGTTTATAACTTTGAAGGAGAAGACTATAGAGAAAAACAAAAGAGTGCATTCACAGAGTGGATTGA
ACCACCAAAAAGAGAAAGAAAAGCCAACTATGCTGTTGATGCATATTTCAGGGAAGCTCTCCGTGTTAGTGAGCCTAAAG
CACCCAAGGCACCTCGACCTCCAAAACAACTAAATGTTCAGGATTTCCAGTTCTTTCCTCCAGGTTTATGTGAATTACTG
GAAAAAGAAATTCTGTATTACAGGAAAACTATTGGGTATAAGGTACCTTGGAGTCCTGATCTACCTAATGCAGCACAGGC
ATAGAAAGAACAGCTAAAAATTGATGAAGCAGAGACCCTCAATGACGAGGAGTTAGAGGAAAAAGAGAAGCTTCTGACAC
AGGGGTTTACAAATTGGAATAAGAGAGATTTTAACCAGTTTATCAAGGCTAATGAGAAGTGGGGTCGTGATGATATTGAA
AATATAGCCAGAGAAGTAGAAGGAAAAACTCCAGAAGAAGTCATTGAATACTCAGCTGTGTTCTGGGAAAGATGCAATGA
GCTTCAGGACATAGAGAAGATTATGGCTCAGATTGAAAGGGGAGAGGCAAGAATTCAAAGAAGAATAAGTATCAAGAAAG
CACTAGATACAAAGATTGGACGGTACAAAGCACCCTTTCATCAGCTAAGAATATCATATGGTACTAACAAAGGAAAAAAC
TATACTGAAGAAGAGGATCATTTTCTCATTTGTATGCTGCCCAAGCTTGGCTTCGACAAGGAAAATGTGTATGATGAATT
ACGACAATGCATCCGAAACTCCCCTCAGTTTAGATTTGATTGGTTTCTCAAGTCCAGAACTGCGATGGAGCTCCAGAGGA
GGTGTAATACCTTAATTACTTTG

ORF - retro_mmus_2424 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.86 %
Parental protein coverage: 92.01 %
Number of stop codons detected: 4
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalAAPAAPCAAGS--GPADTEMEEVFDHGSPGKQKEIQEPDPTYEEKMQTDRANRFEYLLKQTELFAHFIQP
A..AAP.AAGS..GPADTEMEEVFD.GSPGKQKEIQEPDPTYEEKMQTDRANRFEYLLKQTELFAHFIQP
RetrocopyATKAAPRAAGSCPGPADTEMEEVFDNGSPGKQKEIQEPDPTYEEKMQTDRANRFEYLLKQTELFAHFIQP
ParentalAAQKTPTSPLKMKPGRPRVKKDEKQNLLSVGDYRHRRTEQEEDEELLTESSKATNVCTRFEDSPSYVKWG
AAQKTPTSPLKMKPGRPRVKKDEKQNLLSVGDY.H.RTEQEED.EL.TESSKATNVCTRFEDS.SYVKWG
RetrocopyAAQKTPTSPLKMKPGRPRVKKDEKQNLLSVGDYQHCRTEQEEDKEL*TESSKATNVCTRFEDSSSYVKWG
ParentalKLRDYQVRGLNWLISLYENGINGILADEMGLGKTLQTISLLGYMKHYRNIPGPHMVLVPKSTLHNWMSEF
KLRDYQVRGLNWLISLYENGINGILADEMGLGKTLQTISLLGY.KHYRNIPGPHMVLVPKSTLHNWMSEF
RetrocopyKLRDYQVRGLNWLISLYENGINGILADEMGLGKTLQTISLLGYRKHYRNIPGPHMVLVPKSTLHNWMSEF
ParentalKKWVPTLRSVCLIGDKEQRAAFVRDVLLPGEWDVCVTSYEMLIKEK-SVFKK-FNWRYLVIDEAHRIKNE
K.W.PTLRSVCLIGD.EQRA.FVRDVLLPGE.DVCVTSYEMLIKEK.SVFKK.F.WRYLVIDEAHR....
RetrocopyKRWIPTLRSVCLIGDEEQRAVFVRDVLLPGE*DVCVTSYEMLIKEK>SVFKK>FSWRYLVIDEAHRXXXX
ParentalK-SKLSEIVREFKTTNRLLLTGTPLQNNLHELWSLLNFLLPDVFNSADDFDSWFDTNNCLGDQKLVERLH
..SKLSEIVREFKTTNRLLLTGTPLQNNLHELWSLLNFLLPDVFNSADDFDSWFDTNNCLGDQKLVERLH
RetrocopyX>SKLSEIVREFKTTNRLLLTGTPLQNNLHELWSLLNFLLPDVFNSADDFDSWFDTNNCLGDQKLVERLH
ParentalMVLRPFLLRRIKADVEKSLPPKKEVKIYVGLSKMQREWYTRILMK-DIDILNSAGKMDKMRLLNILMQLR
MVL.PFLLRRIKADVEKSLPPKKEVKIYV.LSKMQR.WYTRIL.K.DID.LNSAGKMDKMRLLNILMQLR
RetrocopyMVLCPFLLRRIKADVEKSLPPKKEVKIYVSLSKMQRQWYTRILIK<DIDMLNSAGKMDKMRLLNILMQLR
ParentalKCCNHPYLFDGAEPGPPYTTDMHLVTNSGKMVVLDKLLPKLKEQGSRVLIFSQMTRVLDILEDYCMWRNY
KCCNHP.LFDGAEPGP.YTTD.HLVTNSGKMVVLDKLLPKLKEQGSRVLIFSQMTRVLDILEDYCMWRNY
RetrocopyKCCNHP*LFDGAEPGPLYTTDTHLVTNSGKMVVLDKLLPKLKEQGSRVLIFSQMTRVLDILEDYCMWRNY
ParentalEYCRLDGQTPHDERQDSINAYNEPNSTKFVFMLSTRAGGLGINLATADVVILYDSDWNPQVDLQAMDRAH
EYCRLD.QTPH.ERQDSINAYNEPNSTKFVFMLSTRAGGLGINLATADVVILYDSDWNPQVDLQAMD.AH
RetrocopyEYCRLDEQTPH-ERQDSINAYNEPNSTKFVFMLSTRAGGLGINLATADVVILYDSDWNPQVDLQAMDYAH
ParentalRIGQTKTVRVFRFITDNTVEERIVERAEMKLRLDSIVIQQGRLVDQNLNKIGKDEMLQMIRHGATHVFAS
RIGQ.KTVRVFRFITDNTVEERIVERAEMKLRLDSIVIQQGRLVDQNLNKIGKDEMLQMIR.GATHVFAS
RetrocopyRIGQRKTVRVFRFITDNTVEERIVERAEMKLRLDSIVIQQGRLVDQNLNKIGKDEMLQMIRRGATHVFAS
ParentalKESEITDEDIDGILERGAKKTAEMNEKLSKMGESSLRNFTMDTESSVYNFEGEDYREKQKIAFTEWIEPP
KESEITDEDIDGILERGAKKTAEMNEKLSKMGESSLRNFTMDTESSVYNFEGEDYREKQK.AFTEWIEPP
RetrocopyKESEITDEDIDGILERGAKKTAEMNEKLSKMGESSLRNFTMDTESSVYNFEGEDYREKQKSAFTEWIEPP
ParentalKRERKANYAVDAYFREALRVSEPKAPKAPRPPKQPNVQDFQFFPPRLFELLEKEILYYRKTIGYKVPRSP
KRERKANYAVDAYFREALRVSEPKAPKAPRPPKQ.NVQDFQFFPP.L.ELLEKEILYYRKTIGYKVP.SP
RetrocopyKRERKANYAVDAYFREALRVSEPKAPKAPRPPKQLNVQDFQFFPPGLCELLEKEILYYRKTIGYKVPWSP
ParentalDLPNAAQAQKEEQLKIDEAEPLNDEELEEKEKLLTQGFTNWNKRDFNQFIKANEKWGRDDIENIAREVEG
DLPNAAQA.K.EQLKIDEAE.LNDEELEEKEKLLTQGFTNWNKRDFNQFIKANEKWGRDDIENIAREVEG
RetrocopyDLPNAAQA*K-EQLKIDEAETLNDEELEEKEKLLTQGFTNWNKRDFNQFIKANEKWGRDDIENIAREVEG
ParentalKTPEEVIEYSAVFWERCNELQDIEKIMAQIERGEARIQRRISIKKALDTKIGRYKAPFHQLRISYGTNKG
KTPEEVIEYSAVFWERCNELQDIEKIMAQIERGEARIQRRISIKKALDTKIGRYKAPFHQLRISYGTNKG
RetrocopyKTPEEVIEYSAVFWERCNELQDIEKIMAQIERGEARIQRRISIKKALDTKIGRYKAPFHQLRISYGTNKG
ParentalKNYTEEEDRFLICMLHKLGFDKENVYDELRQCIRNSPQFRFDWFLKSRTAMELQRRCNTLITL
KNYTEEED.FLICML.KLGFDKENVYDELRQCIRNSPQFRFDWFLKSRTAMELQRRCNTLITL
RetrocopyKNYTEEEDHFLICMLPKLGFDKENVYDELRQCIRNSPQFRFDWFLKSRTAMELQRRCNTLITL

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 .00 RPM 40 .79 RPM
SRP007412_cerebellum 0 .00 RPM 35 .21 RPM
SRP007412_heart 0 .06 RPM 25 .40 RPM
SRP007412_kidney 0 .00 RPM 33 .40 RPM
SRP007412_liver 0 .00 RPM 24 .50 RPM
SRP007412_testis 0 .37 RPM 69 .43 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_2424 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_mmus_2424 retrocopy
EST ID Start End Identity Match Mis-match Score
CB233168 147278619 147278795 99.5 173 1 170

TSS - click to see more details

No TSS is located nearby retro_mmus_2424 retrocopy 5' end.

Lab - click to see more details

retro_mmus_2424 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2424 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Mus musculus ENSMUSG00000031715 5 retrocopies
retro_mmus_2406, retro_mmus_2413, retro_mmus_2419, retro_mmus_2424 , retro_mmus_2533,


Copyright © RetrogeneDB 2014-2017