RetrogeneDB ID:

retro_mmus_3652

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:X:80533744..80535034(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000083367
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Nono
Ensembl ID:ENSMUSG00000031311
Aliases:Nono, AA407051, AV149256, NRB54, P54NRB, nonA
Description:non-POU-domain-containing, octamer binding protein [Source:MGI Symbol;Acc:MGI:1855692]


Retrocopy-Parental alignment summary:






>retro_mmus_3652
CCTGCAAATGGCCAGTAGGCCAGCAGCCAGAATGAAGGCTTGACTATTGACCTTAAGAATTTTAGGAAACCAGGAGAGAA
GACCTTTACACAGCGTAGCCGTCTCTTTGTGGACAATCTTCCCCTTGATATCACTGAGGAGGATATGAGGAAACTATTTG
AGAAATATGGAAAAGCAGGCGAAGTTTTCATTCATAAGGATAAAGGCTTTGGTTTTATTCGCTTGGAAACACGAACCCTA
GCGGAAATTGCCAAAGTGGAGCTGGACAACATGCCCCTCCGTGGGAAGCAGCTGCGAGTGCGCTTTGCCTGTCACAGTGC
ATCCCTTACAGTCCGCAACCTTCCTCAGTACGTGTCGAATGAACTGCTGGAAGAAGCCTTTTCTGTGTTCGGCCAGGTGG
AGAGGGCTGTAGTCATTGTGGATGACCTAGGAAGGCCCTCAGGGAAAGGCATTGTTGAGTTCTCAGGGAAGCCAGCTGCT
CCGAAAGCTCTGGACAGATGCAGTGAAGGCTCCTTCTTGCTGACCACGTTTCCTCGGCCTGTGACTGTGGAGCCTATGGA
CCAGTTAGATGATGAAGAGGGACTTCCAGAGAAACTGGTTATAAAAAACCAGCAATTCCACAAGGTGAGAGAACAGCCAC
CCAGATTTGCACAACCTGGGTCCTTTGAGTATGAGTATGCCATGCGCTGGAAGGCACTCATTGAGATGGAGAAGCAACAG
CAGGATCAAGTGGATCGGAACATCAAGGAGGCTCGTGAGAAGCTGGAGATGGAGATGGAGGCAGCACGCCATGAGCACCA
GGTTATGCTAATGAGGCAGGATTTGATGAGGCGTCAAGAAGAGCTTCGGAGAATGGAGGAGCTGCATAACCAAGAGGTTC
AGAAGCGAAAGCAGTTAGAACTCAGGCAGGAAGAGGAACGCAGGCACTGTGAGGAAGAGATGCGGCGACAGCAAGAGGAA
ATGATGCGCCGACAGCAGGAAGGATTCAAGGGAACCTTCCCTGATGAGAGAGAACAAGAGATACTGATGGGACAAATGGC
TATGGGAGGTGCTATGGGCATAAACAATAGAGGTGCCATGCCCCCTGCTCCTGTGCCACCTGGTACTCCAGCTCCTCCAG
GACCTGCCACTCTGATGCCCGATGGAACCCTTGGATTGACCCCATCAACAACTGAACAGTTTGGCCAAGCTGCAACAATG
GAAGGAATTGGAGCAATTGGTGGAACTCCTCCTGCATTCAACCGTCCAGCTCCGGGAGCTGAATTTGCTCCAAATAAACG
CCGCCGATAT

ORF - retro_mmus_3652 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.02 %
Parental protein coverage: 90.91 %
Number of stop codons detected: 1
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalPANGQQASSQNEGLTIDLKNFRKPGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGF
PANGQ.ASSQNEGLTIDLKNFRKPGEKTFTQRSRLFV.NLP.DITEE.MRKLFEKYGKAGEVFIHKDKGF
RetrocopyPANGQ*ASSQNEGLTIDLKNFRKPGEKTFTQRSRLFVDNLPLDITEEDMRKLFEKYGKAGEVFIHKDKGF
ParentalGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIV
GFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIV
RetrocopyGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIV
ParentalDDRGRPSGKGIVEFSGKPAARKALDRCSEGSFLLTTFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFHKER
DD.GRPSGKGIVEFSGKPAA.KALDRCSEGSFLLTTFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFHK.R
RetrocopyDDLGRPSGKGIVEFSGKPAAPKALDRCSEGSFLLTTFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFHKVR
ParentalEQPPRFAQPGSFEYEYAMRWKALIEMEKQQQDQVDRNIKEAREKLEMEMEAARHEHQVMLMRQDLMRRQE
EQPPRFAQPGSFEYEYAMRWKALIEMEKQQQDQVDRNIKEAREKLEMEMEAARHEHQVMLMRQDLMRRQE
RetrocopyEQPPRFAQPGSFEYEYAMRWKALIEMEKQQQDQVDRNIKEAREKLEMEMEAARHEHQVMLMRQDLMRRQE
ParentalELRRMEELHNQEVQKRKQLELRQEEERRRREEEMRRQQEEMMRRQQEGFKGTFPDAREQEIRMGQMAMGG
ELRRMEELHNQEVQKRKQLELRQEEERR..................EGFKGTFPD.REQEI.MGQMAMGG
RetrocopyELRRMEELHNQEVQKRKQLELRQEEERRHCXXXXXXXXXXXXXXXXEGFKGTFPDEREQEILMGQMAMGG
ParentalAMGINNRGAMPPAPVPPGTPAPPGPATMMPDGTLGLTPPTTERFGQAATMEGIGAIGGTPPAFNRPAPGA
AMGINNRGAMPPAPVPPGTPAPPGPAT.MPDGTLGLTP.TTE.FGQAATMEGIGAIGGTPPAFNRPAPGA
RetrocopyAMGINNRGAMPPAPVPPGTPAPPGPATLMPDGTLGLTPSTTEQFGQAATMEGIGAIGGTPPAFNRPAPGA
ParentalEFAPNKRRRY
EFAPNKRRRY
RetrocopyEFAPNKRRRY

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 .05 RPM 77 .12 RPM
SRP007412_cerebellum 0 .17 RPM 100 .30 RPM
SRP007412_heart 0 .09 RPM 62 .51 RPM
SRP007412_kidney 0 .13 RPM 106 .84 RPM
SRP007412_liver 0 .14 RPM 73 .60 RPM
SRP007412_testis 0 .14 RPM 16 .65 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_mmus_3652 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_3652 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_3652 retrocopy 5' end.

Lab - click to see more details

retro_mmus_3652 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_3652 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 21 parental genes, and 31 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000160572 retrocopies
retro_amel_1438, retro_amel_795,
Bos taurus ENSBTAG000000121522 retrocopies
retro_btau_1027, retro_btau_313,
Canis familiaris ENSCAFG000000170711 retrocopy
retro_cfam_98,
Callithrix jacchus ENSCJAG000000367441 retrocopy
retro_cjac_3990,
Equus caballus ENSECAG000000085022 retrocopies
retro_ecab_357, retro_ecab_427,
Felis catus ENSFCAG000000148072 retrocopies
retro_fcat_1219, retro_fcat_147,
Homo sapiens ENSG000001471401 retrocopy
retro_hsap_1699,
Gorilla gorilla ENSGGOG000000061941 retrocopy
retro_ggor_1273,
Microcebus murinus ENSMICG000000002321 retrocopy
retro_mmur_569,
Myotis lucifugus ENSMLUG000000024891 retrocopy
retro_mluc_622,
Mustela putorius furoENSMPUG000000049371 retrocopy
retro_mputfur_937,
Mus musculus ENSMUSG00000031311 2 retrocopies
retro_mmus_3652 , retro_mmus_632,
Nomascus leucogenys ENSNLEG000000012781 retrocopy
retro_nleu_1344,
Oryctolagus cuniculus ENSOCUG000000218482 retrocopies
retro_ocun_1317, retro_ocun_1804,
Otolemur garnettii ENSOGAG000000048343 retrocopies
retro_ogar_1525, retro_ogar_546, retro_ogar_593,
Pongo abelii ENSPPYG000000204511 retrocopy
retro_pabe_1398,
Pan troglodytes ENSPTRG000000220101 retrocopy
retro_ptro_1150,
Pteropus vampyrus ENSPVAG000000165031 retrocopy
retro_pvam_444,
Rattus norvegicus ENSRNOG000000036892 retrocopies
retro_rnor_1178, retro_rnor_1503,
Sorex araneus ENSSARG000000079592 retrocopies
retro_sara_661, retro_sara_663,
Drosophila melanogaster FBgn00042271 retrocopy
retro_dmel_11,


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