RetrogeneDB ID:

retro_mmul_2188

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:7:127541828..127543326(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMMUG00000000492
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.5357
Ensembl ID:ENSMMUG00000004696
Aliases:None
Description:heat shock cognate 71 kDa protein [Source:RefSeq peptide;Acc:NP_001248586]


Retrocopy-Parental alignment summary:






>retro_mmul_2188
GCCCGTGGCCCGGCTATCGGCATCGACCTGGGCACCACCTACTCGTGCGTGGGGGTCTTCCAACATGGCAAGGTGGAGAT
CATCGCCAACGACCAGGGCAACCGCACCACCCCTAGCTACGTGGCCTTCACGGACACCGAGCGCCTCATCGGCGACGCCG
CCAAGAACCAGGTGGCCATGAACCCCACCAACACCATCTTCGACGCCAAGAGGCTTATTGGACGGAAGTTCGAGGATGCC
ACAGTGCAGTCGGACATGAAACACTGGCCATTCCGGGTGGTGAGTGAGGGAGGCAAGCCCAAAGTGCAAGTGGAGTACAA
GGGGGAGACCAAGACCTTCTTCCCGGAGGAGATATCCTCCATGGTCCTCACGAAGATGAAGGAGATCGCAGAAGCCTACC
TGGGGGGCAAGGTGCACAGCGCCGTCATAACGGTCCCCGCCTATTTCAACGACTCCCAGCGCCAGGCCACCAAGGACGCT
GGCACCATCACGGGGCTCAATGTGCTGCGCATCATCAACGAGCCCACAGCGGCGGCCATCGCCTACGGCCTGGACAAGAA
GGGCTGTGCGGGCGGCGAGAAGAACGTGCTCATCTTTGACCTGGGCGGTGGCACCTTCGACGTGTCCATCCTGACCATCG
AGGACGGCATCTTCGAGGTGAAGTCCACGGCCGGCGACACTCACCTGGGCGGTGAGGACTTCGACAACCGCATGGTGAGC
CACCTGGCGGAGGAGTTCAAGCGCAAGCACAAGAAGGACATTGGGCCTAACAAGCGCGCCGTGAGGCGGCTGCGCACCGC
CTGCGAGCGCGCCAAGCGCACCCTGAGCTCGTCCACGCAGGCGAGCATCGAGATCGACTCGCTGTATGAGGGCGTGGACT
TCTATACGTCCATCACCCGCGCCCGCTTCGAGGAGCTCAATGCCGACCTCTTTCGCGGGACCCTGGAGCCGGTGGAGAAG
GCGCTGCGCGACGCCAAGCTGGACAAGGGCCAGATCCAGGAGATCGTGCTGGTGGGCGGCTCCACTCGTATCCCCAAGAT
CCAGAAGCTGCTGCAGGATTTCTTCAACGGCAAGGAGCTGAACAAGAGCATCAACCCCGACGAGGCAGTGGCCTATGGCG
CCGCGGTGCAGGCGGCCATCCTCATCGGCGACAAATCGGAGAATGTGCAGGACCTGCTGCTCCTTGACGTGACCCCGTTG
TCGCTGGGCATCGAGACAGCTGGCGGTGTCATGACCCCACTCATCAAGAGGAACACCACGATCCCCACCAAGCAGACGCA
GACCTTCACCACCTACTCGGACAATCAGAGCAGCGTGCTGGTGCAGGTATACGAGGGCGAACGGGCCATGACCAAGGACA
ATAACCTGCTGGGCAAGTTCGACCTGACCGGGATTCCCCCTGCGCCTCGCGGGGTCCCCCCAGATCGAGGTCACCTTCGA
CATTGACGCCAATGGCATCCTTAACGTTACCGCCGCCGACAAGAGCACCGGTAAGGAA

ORF - retro_mmul_2188 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.8 %
Parental protein coverage: 76.93 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDAK
..GPA.GIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNT.FDAK
RetrocopyARGPAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTIFDAK
ParentalRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTVTN
RLIGR.F.DA.VQSDMKHWPF.VV...G.PKVQVEYKGETK.F.PEE.SSMVLTKMKEIAEAYLG..V..
RetrocopyRLIGRKFEDATVQSDMKHWPFRVVSEGGKPKVQVEYKGETKTFFPEEISSMVLTKMKEIAEAYLGGKVHS
ParentalAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKK--VGAERNVLIFDLGGGTFDVSI
AV.TVPAYFNDSQRQATKDAGTI.GLNVLRIINEPTAAAIAYGLDKK...G.E.NVLIFDLGGGTFDVSI
RetrocopyAVITVPAYFNDSQRQATKDAGTITGLNVLRIINEPTAAAIAYGLDKKGCAGGEKNVLIFDLGGGTFDVSI
ParentalLTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSSTQ
LTIEDGIFEVKSTAGDTHLGGEDFDNRMV.H...EFKRKHKKDI..NKRAVRRLRTACERAKRTLSSSTQ
RetrocopyLTIEDGIFEVKSTAGDTHLGGEDFDNRMVSHLAEEFKRKHKKDIGPNKRAVRRLRTACERAKRTLSSSTQ
ParentalASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKL
ASIEIDSLYEG.DFYTSITRARFEELNADLFRGTL.PVEKALRDAKLDK.QI..IVLVGGSTRIPKIQKL
RetrocopyASIEIDSLYEGVDFYTSITRARFEELNADLFRGTLEPVEKALRDAKLDKGQIQEIVLVGGSTRIPKIQKL
ParentalLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMTVLIKRNTT
LQDFFNGKELNKSINPDEAVAYGAAVQAAIL.GDKSENVQDLLLLDVTPLSLGIETAGGVMT.LIKRNTT
RetrocopyLQDFFNGKELNKSINPDEAVAYGAAVQAAILIGDKSENVQDLLLLDVTPLSLGIETAGGVMTPLIKRNTT
ParentalIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGV-PQIEVTFDIDANGILNV
IPTKQTQTFTTYSDNQ..VL.QVYEGERAMTKDNNLLGKF.LTGIPPAPRGV.PQIEVTFDIDANGILNV
RetrocopyIPTKQTQTFTTYSDNQSSVLVQVYEGERAMTKDNNLLGKFDLTGIPPAPRGV>PQIEVTFDIDANGILNV
ParentalSAVDKSTGKE
.A.DKSTGKE
RetrocopyTAADKSTGKE

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 6 .50 RPM 1399 .06 RPM
SRP007412_brain_prefrontal_cortex 12 .93 RPM 1177 .02 RPM
SRP007412_cerebellum 3 .87 RPM 1090 .15 RPM
SRP007412_heart 6 .60 RPM 748 .79 RPM
SRP007412_kidney 5 .16 RPM 1404 .90 RPM
SRP007412_liver 0 .36 RPM 789 .22 RPM
SRP007412_testis 373 .77 RPM 185 .00 RPM

ChIP-Seq - click to see more details

Macaca mulatta was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mmul_2188 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_2188 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_2188 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Mus musculus retro_mmus_26
Parental genes homology:
Parental genes homology involve 27 parental genes, and 74 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000048842 retrocopies
retro_acar_21, retro_acar_6,
Ailuropoda melanoleuca ENSAMEG000000084251 retrocopy
retro_amel_126,
Anas platyrhynchos ENSAPLG000000106671 retrocopy
retro_apla_6,
Bos taurus ENSBTAG000000131621 retrocopy
retro_btau_354,
Canis familiaris ENSCAFG000000116663 retrocopies
retro_cfam_140, retro_cfam_191, retro_cfam_509,
Ciona intestinalis ENSCING000000096651 retrocopy
retro_cint_12,
Cavia porcellus ENSCPOG000000041693 retrocopies
retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi ENSCSAVG000000085881 retrocopy
retro_csav_3,
Dipodomys ordii ENSDORG000000154671 retrocopy
retro_dord_16,
Echinops telfairi ENSETEG000000109961 retrocopy
retro_etel_43,
Ficedula albicollis ENSFALG000000058121 retrocopy
retro_falb_18,
Felis catus ENSFCAG000000011326 retrocopies
retro_fcat_132, retro_fcat_1331, retro_fcat_1571, retro_fcat_1775, retro_fcat_556, retro_fcat_79,
Homo sapiens ENSG000001099718 retrocopies
retro_hsap_2384, retro_hsap_2710, retro_hsap_2758, retro_hsap_340, retro_hsap_3698, retro_hsap_4892, retro_hsap_4896, retro_hsap_68,
Gallus gallus ENSGALG000000065121 retrocopy
retro_ggal_8,
Loxodonta africana ENSLAFG000000303124 retrocopies
retro_lafr_1218, retro_lafr_391, retro_lafr_790, retro_lafr_797,
Meleagris gallopavo ENSMGAG000000019291 retrocopy
retro_mgal_9,
Myotis lucifugus ENSMLUG000000048343 retrocopies
retro_mluc_1800, retro_mluc_2300, retro_mluc_777,
Macaca mulatta ENSMMUG00000004696 7 retrocopies
retro_mmul_1536, retro_mmul_2188 , retro_mmul_2628, retro_mmul_2632, retro_mmul_580, retro_mmul_778, retro_mmul_963,
Monodelphis domestica ENSMODG000000129582 retrocopies
retro_mdom_127, retro_mdom_99,
Mustela putorius furoENSMPUG000000058109 retrocopies
retro_mputfur_1048, retro_mputfur_1056, retro_mputfur_1144, retro_mputfur_131, retro_mputfur_188, retro_mputfur_309, retro_mputfur_627, retro_mputfur_694, retro_mputfur_958,
Oreochromis niloticus ENSONIG000000047591 retrocopy
retro_onil_2,
Pelodiscus sinensis ENSPSIG000000124502 retrocopies
retro_psin_17, retro_psin_5,
Pan troglodytes ENSPTRG000000044045 retrocopies
retro_ptro_1743, retro_ptro_2507, retro_ptro_272, retro_ptro_3259, retro_ptro_3264,
Taeniopygia guttata ENSTGUG000000004911 retrocopy
retro_tgut_7,
Takifugu rubripes ENSTRUG000000052651 retrocopy
retro_trub_30,
Tursiops truncatus ENSTTRG000000111396 retrocopies
retro_ttru_1507, retro_ttru_1650, retro_ttru_1696, retro_ttru_35, retro_ttru_741, retro_ttru_808,
Xiphophorus maculatus ENSXMAG000000016021 retrocopy
retro_xmac_20,


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