RetrogeneDB ID:

retro_mmus_3530

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:X:145833316..145834131(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000080915
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Phb
Ensembl ID:ENSMUSG00000038845
Aliases:Phb, Bap32
Description:prohibitin [Source:MGI Symbol;Acc:MGI:97572]


Retrocopy-Parental alignment summary:






>retro_mmus_3530
ATGGCTGCCAAAGCTTTCAAGTCCATGGGAAAGCTCAGTCTGGTGTTAGCAGTTGCAGTAGGTGTGGTGAACTCTGCTTT
ATGTAATGTAGGTGTTGGACACAGAACTGTTTTCTCTGACAAATTCCATGGAGTACAGGACATTGTGGTAAGGAAAGGGA
TTCACTTTCTCAACCCTTGGGTAGAGAAACCAATTATCTTTGACTGCTGCTTTTGACCATGAAATGTGCCCATTGTCACC
GGGAGCAGACTTGCAGAATGTCAACATCACATTGATCATCCTCTTCTGGCTGATTGCCAGCTAGTTTCCTCATTCCTATA
CAAGCATTGGTGAGGACTATGATGAGCGAGTGTTGCCATCTATCACCACAGAGATCTTCAAGTTGGTGGTGGCTCAAATC
GATGCTGGAGAGTTAGTTACCCAGCGAGAACTGGTCTCCAGGCAGGTGAGCGATGACCTCACAGAGCAAGCAGCAACATT
TGGGCTTATCCTGGATGACATATACCTGACACATCTGACCTTCAGGAAGGAGTTCACAGAGACAATAAAAGCCAAACAGA
TGGCTCAGCAGGAAGCAAGAGAGAGCCAGATTTATGGTGGAAAAGGCTGAGCAGCAGCAGAAGGCAGCCATCATCTCTGC
TGAGAGTGACTCCAAGGAAGATGAGCTGATTGTCAATTCGCTGGCCACAGCAGATGCTGGCCTGATTGAGCTGCAAAAGC
TGGAAGCTGCTGAGGACATTGCATACCAGCACTGCCACTCTCCGAACATCATCTACCTGCCAGCAGGGCAGTCTGTGCTC
CTCCAGCTTCTCCAG

ORF - retro_mmus_3530 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.55 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAAKVFESIGKFGLALAVAGGVVNSALYNVDAGHRAVIFDRFRGVQDIVVGEGTHFLIPWVQKPIIFDCR
MAAK.F.S.GK..L.LAVA.GVVNSAL.NV..GHR.V..D.F.GVQDIVV..G.HFL.PWV.KPIIFDC.
RetrocopyMAAKAFKSMGKLSLVLAVAVGVVNSALCNVGVGHRTVFSDKFHGVQDIVVRKGIHFLNPWVEKPIIFDCC
ParentalSRPRNV-PVITGSKDLQNVNITLRILFRPVASQLPRIYTSIGEDYDERVLPSITTEILKSVVARFDAGEL
..P.NV.P...G..DLQNVNITL.ILF...AS..P..YTSIGEDYDERVLPSITTEI.K.VVA..DAGEL
RetrocopyF*P*NV>PLSPGA-DLQNVNITLIILFWLIAS*FPHSYTSIGEDYDERVLPSITTEIFKLVVAQIDAGEL
ParentalITQRELVSRQVSDDLTERAATFGLILDDVSLTHLTFGKEFTEAVEAKQVAQQEA-ERARFVVEKAEQQKK
.TQRELVSRQVSDDLTE.AATFGLILDD..LTHLTF.KEFTE...AKQ.AQQEA.ERARF.VEKAEQQ.K
RetrocopyVTQRELVSRQVSDDLTEQAATFGLILDDIYLTHLTFRKEFTETIKAKQMAQQEA>ERARFMVEKAEQQQK
ParentalAAIISAEGDSKAAELIANSLATAGDGLIELRKLEAAEDIAYQLSRSRNITYLPAGQSVLLQLPQ
AAIISAE.DSK..ELI.NSLATA..GLIEL.KLEAAEDIAYQ...S.NI.YLPAGQSVLLQL.Q
RetrocopyAAIISAESDSKEDELIVNSLATADAGLIELQKLEAAEDIAYQHCHSPNIIYLPAGQSVLLQLLQ

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






(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 17 .43 RPM
SRP007412_cerebellum 0 .00 RPM 19 .89 RPM
SRP007412_heart 0 .00 RPM 63 .66 RPM
SRP007412_kidney 0 .00 RPM 43 .68 RPM
SRP007412_liver 0 .00 RPM 25 .48 RPM
SRP007412_testis 0 .00 RPM 2 .88 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_3530 was not detected
No EST(s) were mapped for retro_mmus_3530 retrocopy.
No TSS is located nearby retro_mmus_3530 retrocopy 5' end.
retro_mmus_3530 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_3530 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Rattus norvegicus retro_rnor_2855

Parental genes homology:
Parental genes homology involve 15 parental genes, and 87 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000047971 retrocopy
Canis familiaris ENSCAFG000000169261 retrocopy
Choloepus hoffmanni ENSCHOG000000075882 retrocopies
Callithrix jacchus ENSCJAG0000000717422 retrocopies
Erinaceus europaeus ENSEEUG000000064813 retrocopies
Gorilla gorilla ENSGGOG0000002800212 retrocopies
Macropus eugenii ENSMEUG000000051221 retrocopy
Myotis lucifugus ENSMLUG000000082032 retrocopies
Macaca mulatta ENSMMUG0000000015613 retrocopies
Monodelphis domestica ENSMODG000000122101 retrocopy
Mus musculus ENSMUSG00000038845 8 retrocopies
Otolemur garnettii ENSOGAG000000270151 retrocopy
Procavia capensis ENSPCAG000000088511 retrocopy
Rattus norvegicus ENSRNOG0000004679918 retrocopies
Tursiops truncatus ENSTTRG000000108361 retrocopy



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