RetrogeneDB ID:

retro_mmus_1826

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:19:37784265..37785584(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Psmc1
Ensembl ID:ENSMUSG00000021178
Aliases:Psmc1, AI325227, P26s4, S4
Description:protease (prosome, macropain) 26S subunit, ATPase 1 [Source:MGI Symbol;Acc:MGI:106054]


Retrocopy-Parental alignment summary:






>retro_mmus_1826
ATGGGTCAAAGTCAGAGTGGTGGCCATGGTCCTGGGGGTGGCAAGAAGGATGACAAGGACAAGAAAAAGGAATATGAACC
TCCTGTCCCAACTAGAGTGGGGAAAAAGAAGAAGAAAACGAAGGGACCAGCTGCTGCCAGCAAACTTCCACTGGTAACAA
CTCACACCCAGTGCCACCTGAAATTACTAAAGCTAGAGAGAATAAAAGACTATCTTCTCATGGAGGAGGAATTCATTAGA
AATCAGGAACAGATGAAACCATTAGAAGAAAAGCAAGAAGAGGAAAGATCAAAAATGGATGATCCCAGGGGGACCCCCAT
GTCTGTAGGAACCTTGGAAGAGATCATTGATGATAATCATGCCATTGTGTCCACATCTGTGGGCTCAGAACACTACAGTC
AGCATCCTGCCATTTGTAGACAAGGATCTGCTGGAACCAGGCTGTTCAGTCCTGCTCAACCACAAGGTGCATGCTGTGAT
AGGGGTGCTAATGGATGACACGGATCCCCTGATCACGGTGATGAAGGTGGAAAAGGACCCCCAGGAAACCTATGCAGATA
TTGGGGGACTGGACAACCAGATCCAAGAAATTAAGGAGTCTGTGGAGCTTGCTCTTACCCATCCTGGCTATTACGAAGAG
ATGGGGATAAAGCCCCCTAAGGGGGTCATTCTCTACGGTCCACCAGGAACAGGTAAAGCTCTATTGGCCAAAGCAGTAGC
GAACCAGACTTCAGCCATTCTCTTGCGAGTGGTTGGCTCAGAGCTTATCCAGAAGTATGTAGGTGACGCGGCCCAAACTT
GTCCGGGAGCTCTTCCGGGTTGCTGAGGAGCACACACCGTCCATCGTGTTCATTGATGAGATCGACACCATTGGGACCAA
AAGATATGATTCAAACTCTGGAGGTGAGAGAGAAATTCGACGAACAATGTTGGAACTGTTGAACCAGTTGGATGGATTTG
ATTCAAGGGGAGATGTAAAAGTTATCACGGCCACAAACCAAATAGAAACTTTGGATCCAGCACTTATCAGGCCAGGCCCC
ATTGACAGAAAGATCGAGTTCCCCCTGCCTGATGAGACCAAGAAGCATATCTTCCAGATTCACACCAGCAGGATGACACT
GGCTGATGATGTAACCTTGGATGACTTGATCATGGCAAAGGATGACCTCTCTGGGGCCGACATCAAGGCAATCTGTACAG
AAGCTGGCTTGATGGCCTTACGGGGACGCAGAATGAAAGTAACAAATGAAGACTACAAAAAATCTAAAGAGAATGTTCTT
TATAAAAAACAAGAAGGCACCCCCAAGGGATTCGGTCTC

ORF - retro_mmus_1826 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.99 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMGQSQSGGHGPGGGKKDDKDKKKKYEPPVPTRVGKKKKKTKGPDAASKLPLVTPHTQCRLKLLKLERIKD
MGQSQSGGHGPGGGKKDDKDKKK.YEPPVPTRVGKKKKKTKGP.AASKLPLVT.HTQC.LKLLKLERIKD
RetrocopyMGQSQSGGHGPGGGKKDDKDKKKEYEPPVPTRVGKKKKKTKGPAAASKLPLVTTHTQCHLKLLKLERIKD
ParentalYLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSVGTLEEIIDDNHAIVSTSVGSEHY-VSILSFV
YLLMEEEFIRNQEQMKPLEEKQEEERSK.DD.RGTPMSVGTLEEIIDDNHAIVSTSVGSEHY.VSIL.FV
RetrocopyYLLMEEEFIRNQEQMKPLEEKQEEERSKMDDPRGTPMSVGTLEEIIDDNHAIVSTSVGSEHY>VSILPFV
ParentalDKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKAPQETYADIGGLDNQIQEIKESVELPLTHPE
DKDLLEPGCSVLLNHKVHAVIGVLMDDTDPL.TVMKVEK.PQETYADIGGLDNQIQEIKESVEL.LTHP.
RetrocopyDKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLITVMKVEKDPQETYADIGGLDNQIQEIKESVELALTHPG
ParentalYYEEMGIKPPKGVILYGPPGTGKTLLAKAVANQTSATFLRVVGSELIQKYLGDG-PKLVRELFRVAEEHA
YYEEMGIKPPKGVILYGPPGTGK.LLAKAVANQTSA..LRVVGSELIQKY.GD..PKLVRELFRVAEEH.
RetrocopyYYEEMGIKPPKGVILYGPPGTGKALLAKAVANQTSAILLRVVGSELIQKYVGDA>PKLVRELFRVAEEHT
ParentalPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRID
PSIVFIDEID.IGTKRYDSNSGGEREI.RTMLELLNQLDGFDSRGDVKVI.ATN.IETLDPALIRPG.ID
RetrocopyPSIVFIDEIDTIGTKRYDSNSGGEREIRRTMLELLNQLDGFDSRGDVKVITATNQIETLDPALIRPGPID
ParentalRKIEFPLPDEKTKKRIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALRERRMKVTNED
RKIEFPLPDE.TKK.IFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALR.RRMKVTNED
RetrocopyRKIEFPLPDE-TKKHIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALRGRRMKVTNED
ParentalFKKSKENVLYKKQEGTPEGLYL
.KKSKENVLYKKQEGTP.G..L
RetrocopyYKKSKENVLYKKQEGTPKGFGL

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 .02 RPM 96 .00 RPM
SRP007412_cerebellum 0 .09 RPM 109 .38 RPM
SRP007412_heart 0 .09 RPM 87 .29 RPM
SRP007412_kidney 0 .08 RPM 101 .66 RPM
SRP007412_liver 0 .00 RPM 96 .81 RPM
SRP007412_testis 0 .09 RPM 60 .28 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_mmus_1826 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_1826 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_64288319 libraries 234 libraries 455 libraries 55 libraries 9 libraries

The graphical summary, for retro_mmus_1826 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_mmus_1826 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_1826 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 17 parental genes, and 48 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000018394 retrocopies
retro_amel_1536, retro_amel_1886, retro_amel_405, retro_amel_962,
Canis familiaris ENSCAFG000000175102 retrocopies
retro_cfam_1238, retro_cfam_1562,
Choloepus hoffmanni ENSCHOG000000135951 retrocopy
retro_chof_1954,
Dasypus novemcinctus ENSDNOG000000064581 retrocopy
retro_dnov_2162,
Equus caballus ENSECAG000000036011 retrocopy
retro_ecab_355,
Echinops telfairi ENSETEG000000026611 retrocopy
retro_etel_580,
Felis catus ENSFCAG000000113108 retrocopies
retro_fcat_1444, retro_fcat_1559, retro_fcat_2015, retro_fcat_344, retro_fcat_614, retro_fcat_691, retro_fcat_713, retro_fcat_924,
Macropus eugenii ENSMEUG000000015261 retrocopy
retro_meug_623,
Myotis lucifugus ENSMLUG000000074712 retrocopies
retro_mluc_2490, retro_mluc_508,
Macaca mulatta ENSMMUG000000229901 retrocopy
retro_mmul_255,
Mustela putorius furoENSMPUG000000081504 retrocopies
retro_mputfur_1602, retro_mputfur_409, retro_mputfur_654, retro_mputfur_815,
Mus musculus ENSMUSG00000021178 3 retrocopies
retro_mmus_1517, retro_mmus_1826 , retro_mmus_812,
Oryctolagus cuniculus ENSOCUG000000062314 retrocopies
retro_ocun_1135, retro_ocun_1212, retro_ocun_1654, retro_ocun_411,
Otolemur garnettii ENSOGAG000000323432 retrocopies
retro_ogar_3014, retro_ogar_367,
Pongo abelii ENSPPYG000000259489 retrocopies
retro_pabe_1059, retro_pabe_153, retro_pabe_2379, retro_pabe_2408, retro_pabe_2737, retro_pabe_2832, retro_pabe_3099, retro_pabe_825, retro_pabe_907,
Pteropus vampyrus ENSPVAG000000100203 retrocopies
retro_pvam_1190, retro_pvam_350, retro_pvam_500,
Tursiops truncatus ENSTTRG000000135821 retrocopy
retro_ttru_239,


Copyright © RetrogeneDB 2014-2017