RetrogeneDB ID:

retro_mmus_26

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:12:76404533..76406435(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000059970
Aliases:Hspa2, 70kDa, HSP70.2, HSP70A2, Hsp70-2
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Hspa8
Ensembl ID:ENSMUSG00000015656
Aliases:Hspa8, 2410008N15Rik, Hsc70, Hsc71, Hsc73, Hsp73, Hspa10
Description:heat shock protein 8 [Source:MGI Symbol;Acc:MGI:105384]


Retrocopy-Parental alignment summary:






>retro_mmus_26
ATGTCTGCCCGCGGCCCGGCTATCGGCATCGACCTGGGCACCACTTACTCGTGCGTGGGGGTATTCCAACATGGCAAGGT
GGAGATCATCGCCAACGACCAGGGTAACCGCACCACCCCCAGCTACGTGGCCTTCACTGACACCGAGCGTCTCATCGGCG
ACGCCGCCAAGAACCAAGTGGCCATGAACCCCACAAACACCATCTTCGACGCCAAGCGGCTGATCGGACGGAAGTTCGAG
GACGCCACAGTGCAGTCCGATATGAAGCACTGGCCGTTCCGAGTGGTGAGCGAAGGTGGGAAGCCCAAAGTGCAGGTGGA
ATATAAAGGGGAGATGAAGACCTTCTTCCCTGAGGAGATTTCTTCCATGGTCCTCACTAAGATGAAGGAGATCGCCGAAG
CCTACCTGGGGGGCAAGGTGCAGAGCGCAGTCATCACTGTTCCTGCCTATTTCAACGACTCGCAGCGCCAGGCCACCAAG
GATGCGGGCACCATCACCGGCCTCAACGTGTTGCGCATCATCAATGAGCCCACAGCAGCGGCCATCGCCTACGGCCTGGA
TAAGAAGGGCTGTGCGGGCGGCGAGAAGAACGTGCTCATCTTTGACCTGGGCGGGGGCACCTTCGATGTGTCCATCCTGA
CCATCGAGGATGGCATCTTTGAGGTGAAGTCCACGGCCGGCGATACCCACCTGGGTGGCGAAGACTTCGACAACCGTATG
GTCAGCCACCTGGCGGAGGAGTTCAAGCGCAAACACAAGAAGGACATTGGGCCCAACAAGCGCGCTGTGCGCCGGCTGCG
CACCGCCTGCGAGCGCGCTAAGCGCACCCTGAGCTCGTCCACGCAGGCCAGCATAGAGATCGACTCGCTCTACGAGGGCG
TGGATTTCTACACGTCCATCACCCGCGCCCGCTTCGAGGAGCTCAACGCCGATCTCTTCCGAGGGACCCTGGAGCCGGTG
GAAAAGGCGCTGCGCGATGCCAAGCTAGACAAGGGCCAGATCCAGGAGATAGTGCTGGTGGGCGGCTCAACCCGCATCCC
TAAGATCCAGAAGCTCCTGCAAGATTTCTTCAACGGCAAGGAGCTGAACAAGAGCATTAATCCCGACGAGGCGGTGGCCT
ACGGCGCCGCTGTGCAGGCGGCTATCCTCATCGGCGACAAGTCGGAAAATGTGCAGGATCTGCTGTTACTCGACGTGACT
CCATTGTCGCTCGGCATCGAAACAGCTGGCGGTGTCATGACCCCACTCATCAAGAGAAACACCACGATCCCCACCAAGCA
GACGCAGACCTTCACTACCTACTCAGACAACCAGAGCAGCGTGCTGGTGCAAGTGTACGAGGGCGAACGGGCCATGACCA
AGGACAATAACCTCTTGGGCAAGTTCGACCTGACTGGGATCCCCCCAGCACCCCGTGGGGTCCCCCAGATCGAGGTCACC
TTTGACATCGATGCCAACGGCATCCTTAACGTCACTGCTGCCGACAAGAGCACCGGTAAAGAAAATAAAATCACCATAAC
CAACGACAAGGGTCGGCTGAGCAAAGACGACATTGACCGGATGGTGCAGGAGGCGGAGCGGTACAAATCGGAAGATGAAG
CAAATCGCGATCGCGTGGCAGCCAAAAATGCGGTGGAGTCCTATACCTACAACATCAAGCAGACCGTGGAAGACGAGAAA
CTGAGGGGCAAGATTAGCGAGCAGGACAAAAACAAGATCCTCGACAAGTGTCAGGAGGTGATCAACTGGCTTGACCGAAA
CCAGATGGCAGAGAAAGATGAGTACGAACACAAGCAGAAAGAGCTTGAGAGAGTGTGCAACCCCATCATCAGCAAACTTT
ACCAAGGCGGTCCAGGCGGCGGCGGCTCCTCTGGAGGGCCCACCATCGAGGAAGTGGACTAG

ORF - retro_mmus_26 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.72 %
Parental protein coverage: 96.44 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDAK
..GPA.GIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNT.FDAK
RetrocopyARGPAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTIFDAK
ParentalRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTVTN
RLIGR.F.DA.VQSDMKHWPF.VV...G.PKVQVEYKGE.K.F.PEE.SSMVLTKMKEIAEAYLG..V..
RetrocopyRLIGRKFEDATVQSDMKHWPFRVVSEGGKPKVQVEYKGEMKTFFPEEISSMVLTKMKEIAEAYLGGKVQS
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
ParentalIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDIDANGILNVS
IPTKQTQTFTTYSDNQ..VL.QVYEGERAMTKDNNLLGKF.LTGIPPAPRGVPQIEVTFDIDANGILNV.
RetrocopyIPTKQTQTFTTYSDNQSSVLVQVYEGERAMTKDNNLLGKFDLTGIPPAPRGVPQIEVTFDIDANGILNVT
ParentalAVDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLESYAFNMKATVEDEKLQ
A.DKSTGKENKITITNDKGRLSK.DI.RMVQEAE.YK.EDE..RD.V..KN..ESY..N.K.TVEDEKL.
RetrocopyAADKSTGKENKITITNDKGRLSKDDIDRMVQEAERYKSEDEANRDRVAAKNAVESYTYNIKQTVEDEKLR
ParentalGKINDEDKQKILDKCNEIISWLDKNQTAEKEEFEHQQKELEKVCNPIITKLYQSAGGMPGGMPGG
GKI...DK.KILDKC.E.I.WLD.NQ.AEK.E.EH.QKELE.VCNPII.KLYQ...G..GG..GG
RetrocopyGKISEQDKNKILDKCQEVINWLDRNQMAEKDEYEHKQKELERVCNPIISKLYQGGPG-GGGSSGG

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 30 .49 RPM 636 .03 RPM
SRP007412_cerebellum 18 .58 RPM 538 .64 RPM
SRP007412_heart 9 .31 RPM 516 .11 RPM
SRP007412_kidney 25 .12 RPM 730 .22 RPM
SRP007412_liver 7 .92 RPM 613 .92 RPM
SRP007412_testis 1497 .91 RPM 60 .19 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_mmus_26 in 4 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001XVA POLR2A 12:76403425..76404826
ENCFF001YIJ POLR2A 12:76403115..76404645
ENCFF001YJZ POLR2A 12:76402920..76404662
ENCFF001YKA POLR2A 12:76403270..76404875

EST - click to see more details

10 EST(s) were mapped to retro_mmus_26 retrocopy
EST ID Start End Identity Match Mis-match Score
BG803868 76404445 76405045 100 600 0 600
BI082332 76404442 76405223 99.7 778 1 773
BI651863 76404441 76405222 99.2 777 2 770
BI987250 76404434 76405034 100 600 0 600
BQ944352 76404918 76405755 97.4 823 4 804
BY353835 76405068 76405358 98.7 286 4 282
BY713605 76404411 76405080 99.6 663 3 660
CA531828 76404836 76405283 99.8 446 1 445
CA883929 76404442 76404938 100 496 0 496
CN683380 76404431 76405024 100 593 0 593

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_24553336 libraries456 libraries254 libraries11 libraries15 libraries
TSS #2 TSS_24554960 libraries100 libraries7 libraries1 library4 libraries
TSS #3 TSS_24555235 libraries420 libraries387 libraries30 libraries0 libraries
TSS #4 TSS_2455669 libraries85 libraries459 libraries219 libraries240 libraries
TSS #5 TSS_245571058 libraries9 libraries2 libraries2 libraries1 library
TSS #6 TSS_245581042 libraries26 libraries3 libraries0 libraries1 library

The graphical summary, for retro_mmus_26 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_26 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_26 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Macaca mulatta retro_mmul_2188
Parental genes homology:
Parental genes homology involve 30 parental genes, and 89 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,
Callithrix jacchus ENSCJAG000000076485 retrocopies
retro_cjac_2388, retro_cjac_3306, retro_cjac_3898, retro_cjac_4057, retro_cjac_721,
Cavia porcellus ENSCPOG000000041693 retrocopies
retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi ENSCSAVG000000085881 retrocopy
retro_csav_3,
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,
Gallus gallus ENSGALG000000065121 retrocopy
retro_ggal_8,
Gorilla gorilla ENSGGOG000000083818 retrocopies
retro_ggor_1053, retro_ggor_1810, retro_ggor_1888, retro_ggor_1918, retro_ggor_2501, retro_ggor_3054, retro_ggor_3057, retro_ggor_360,
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,
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,
Mus musculus ENSMUSG00000015656 8 retrocopies
retro_mmus_2244, retro_mmus_2584, retro_mmus_26 , retro_mmus_2621, retro_mmus_2840, retro_mmus_316, retro_mmus_351, retro_mmus_620,
Mus musculus ENSMUSG000000243591 retrocopy
retro_mmus_3624,
Mus musculus ENSMUSG000000268641 retrocopy
retro_mmus_1299,
Oryctolagus cuniculus ENSOCUG000000155334 retrocopies
retro_ocun_1308, retro_ocun_53, retro_ocun_584, retro_ocun_753,
Oreochromis niloticus ENSONIG000000047591 retrocopy
retro_onil_2,
Pongo abelii ENSPPYG000000039879 retrocopies
retro_pabe_183, retro_pabe_2193, retro_pabe_2254, retro_pabe_2260, retro_pabe_2261, retro_pabe_3153, retro_pabe_355, retro_pabe_3804, retro_pabe_3808,
Pelodiscus sinensis ENSPSIG000000124502 retrocopies
retro_psin_17, retro_psin_5,
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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