RetrogeneDB ID:

retro_mmus_2776

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:6:112563641..112565078(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000083443
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Arfgap2
Ensembl ID:ENSMUSG00000027255
Aliases:Arfgap2, 2310032E02Rik, Zfp289
Description:ADP-ribosylation factor GTPase activating protein 2 [Source:MGI Symbol;Acc:MGI:1924288]


Retrocopy-Parental alignment summary:






>retro_mmus_2776
ATGGCGTCGAGCCCGAGCAAGACCGAAATCCAGACTATTTTTAAGAGGCTTCGCGCAATTCCCACCAACAAGGCCTGTTT
CGATTGTGGTGCCAAGAGACCTAGTTGGGCCAGCATCACTTACGGTGTATTTTTGTGTATTGACTGCTCCGGAGTGCATC
GCTCCTTGGGTGTCCATCTCAGCTTTATCAGGTCCACAGAGTTGGATTCGAACTGGAGCTGGTTGCAGCTGAGGTGTATG
CAGGTCGGCGGGAATGCCAATGCGACTGCTTTTTTCCGCCAACACGGATGTATGGCCAATGATGCTAACACCAAATATAC
GAGCCGAGCTGCCCAGATGTACCGAGAGAAGATCCGGCAGTTAGGGAGTGCAGCTCTGACTAGGCATGGTACTGATCTTT
GGATGGACAGTATGAACAGTGTTCCAAGTCACTCTCCAGGGAAGAAAGACTCTGATTTCTTCACAGAACATACTCAGGCC
CCTGCTTGAGATACAGCAGCCACTGATCCTTCAGGGACCCAGCAACCAGCCCTACCTTCAGAGAGCAGTAGCCTGGCACA
ACCTGAACAAGGCCCTAACACTGATCTGCTCAGAACCTCACCCCAAGCCTCTCTGGAACTGAAAAGCTCCATTATTGGCA
AGAAGAAGCCAGCAGCCGCTAAGAAAGGGCTGGGTGCCAAGAAAGGCCTGGGAGCTCAGAAGGTGAGCAACCAGAGCTTT
ACTGAGATTGAGCGGCAGGCCCAGGTGGCAGAGAAGCTCCGAGAGCAGCAGGAAGCTGATGCCAAGAAGCAGGCAGAAGA
GTCCATGGTTGCCTCCATGCGTCTGGCCTACCAGGAGCTCCAGATTGATCGCAAGGAGGAGGAGAAAAAGCTCCAGAATC
TTGAAGGAAGGAATCGAGAGCAGGCTGAAAGGCTGGGCATGGGCTTGGTGTCCCGAAGCTCCATCTCCCGCTCTGTGCTG
TCTGAGATGCAGATAATTGAGCAGGAAACCCCGCTGAGTGCGAAATCCTCCCGTTCACAGCTTGACTTGTTTGATGATGT
TGGAACATTTGCACCTGGACCCCCAAAGTACAAGGACAACCCCTTTACCTTGTGAGAAACTTTTGGTTCCCGCTGGGATT
CAGATGCAGCCTGGGGCGTGGACAGGGTAGAAGAGAAGGAACCTGAAGTTACCATCTCCAGCATCCGGCCTATTTCAGAA
AGAACTGCGAGTCAGAGGTAAGTGGAGACTCGGAGCTCAGGCCTTGAGTCCAGTGAAGCACGGCAGAAGTTTGCAGGAGC
CAAAGCCATCTCGTCCGACATGTTCTTTGGTCGTGAGGTGGATTCTGAGTATGAAGCTAGGTCTCGGTTACAGCAGCTTT
CAGGCAGCAGTGCCATCACCTCTTCAGACCTTTTTGGAGACATGGATGGAGCTCATGGAGGAAGAACTGTATGTATC

ORF - retro_mmus_2776 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.86 %
Parental protein coverage: 92.12 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAASPSKTEIQTIFKRLRAIPTNKACFDCGAKSPSWASITYGVFLCIDCSGVHRSLGVHLSFIRSTELDS
MA.SPSKTEIQTIFKRLRAIPTNKACFDCGAK.PSWASITYGVFLCIDCSGVHRSLGVHLSFIRSTELDS
RetrocopyMASSPSKTEIQTIFKRLRAIPTNKACFDCGAKRPSWASITYGVFLCIDCSGVHRSLGVHLSFIRSTELDS
ParentalNWSWLQLRCMQVGGNANATAFFRQHGCMANDANTKYTSRAAQMYREKIRQLGSAALTRHGTDLWIDSMNS
NWSWLQLRCMQVGGNANATAFFRQHGCMANDANTKYTSRAAQMYREKIRQLGSAALTRHGTDLW.DSMNS
RetrocopyNWSWLQLRCMQVGGNANATAFFRQHGCMANDANTKYTSRAAQMYREKIRQLGSAALTRHGTDLWMDSMNS
ParentalAPSHSPEKKDSDFFTEHTQAPAWDTAATDPSGTQQPALPSESSSLAQPEQGPNTDLLGTSPQASLELKSS
.PSHSP.KKDSDFFTEHTQAPA.DTAATDPSGTQQPALPSESSSLAQPEQGPNTDLL.TSPQASLELKSS
RetrocopyVPSHSPGKKDSDFFTEHTQAPA*DTAATDPSGTQQPALPSESSSLAQPEQGPNTDLLRTSPQASLELKSS
ParentalIIGKKKPAAAKKGLGAKKGLGAQKVSNQSFTEIERQAQVAEKLREQQAADAKKQAEESMVASMRLAYQEL
IIGKKKPAA...............VSNQSFTEIERQAQVAEKLREQQ.ADAKKQAEESMVASMRLAYQEL
RetrocopyIIGKKKPAAXXXXXXXXXXXXXXXVSNQSFTEIERQAQVAEKLREQQEADAKKQAEESMVASMRLAYQEL
ParentalQIDRKKEEKKLQNLEGKKREQAERLGMGLVSRSSISHSVLSEMQMIEQETPLSAKSSRSQLDLFDDVGTF
QIDRK.EEKKLQNLEG..REQAERLGMGLVSRSSIS.SVLSEMQ.IEQETPLSAKSSRSQLDLFDDVGTF
RetrocopyQIDRKEEEKKLQNLEGRNREQAERLGMGLVSRSSISRSVLSEMQIIEQETPLSAKSSRSQLDLFDDVGTF
ParentalASGPPKYKDNPFSLGETFGSRWDSDAAWGMDRVEEKEPEVTISSIRPISERTASRREVETRSSGLESSEA
A.GPPKYKDNPF.L.ETFGSRWDSDAAWG.DRVEEKEPEVTISSIRPISERTAS.R.VETRSSGLESSEA
RetrocopyAPGPPKYKDNPFTL*ETFGSRWDSDAAWGVDRVEEKEPEVTISSIRPISERTASQR*VETRSSGLESSEA
ParentalRQKFAGAKAISSDMFFGREVDSEYEARSRLQQLSGSSAISSSDLFGNMDGAHGGGTVSL
RQKFAGAKAISSDMFFGREVDSEYEARSRLQQLSGSSAI.SSDLFG.MDGAHGG.TV..
RetrocopyRQKFAGAKAISSDMFFGREVDSEYEARSRLQQLSGSSAITSSDLFGDMDGAHGGRTVCI

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 .16 RPM 21 .19 RPM
SRP007412_cerebellum 0 .13 RPM 28 .40 RPM
SRP007412_heart 0 .09 RPM 25 .56 RPM
SRP007412_kidney 0 .17 RPM 22 .33 RPM
SRP007412_liver 0 .14 RPM 46 .10 RPM
SRP007412_testis 0 .46 RPM 34 .44 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_2776 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_2776 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_2776 retrocopy 5' end.

Lab - click to see more details

retro_mmus_2776 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2776 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000199651 retrocopy
retro_cjac_415,
Macropus eugenii ENSMEUG000000049841 retrocopy
retro_meug_1841,
Microcebus murinus ENSMICG000000070191 retrocopy
retro_mmur_51,
Mus musculus ENSMUSG00000027255 1 retrocopy
retro_mmus_2776 ,
Oryctolagus cuniculus ENSOCUG000000020732 retrocopies
retro_ocun_1769, retro_ocun_599,


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