RetrogeneDB ID:

retro_mmus_284

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:1:175686487..175688353(-)
Located in intron of:ENSMUSG00000026525
Retrocopy
information
Ensembl ID:ENSMUSG00000078185
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Chm
Ensembl ID:ENSMUSG00000025531
Aliases:Chm, Rep-1
Description:choroidermia [Source:MGI Symbol;Acc:MGI:892979]


Retrocopy-Parental alignment summary:






>retro_mmus_284
ATGGCGGAGAAGCTTCCCACAGAGTTTGATGTGGTAATAATAGGGACAGGCTTGCCGGAGTCCATCCTGGCAGCTGCATG
TTCAAGAAGTGGACAGAGAGTTCTGCATGTTGACTCAAGGAGTTACTATGGAGGGAATTGGGCGAGTTTCAGCTTTACAG
GTTTGCAGTCCTGGCTGAAGGACTATCAACAGAACCATGACAGCGAGGAAGGCGTGACCGCCACATGGCAAGACCTGATC
CATGAAACAGAAGAAGCCATCTCTCTTCGCAAGAAGGATGAAACTATTCAGCACACAGAAGTCTTCTGTTATGCTAGTCA
AGATGTGGAGGACAGCGTGCAAGACACCGAGACTCTGCAGAGAAGTTCCCCCCTAGAGGCATCTGCTACTCCGGCTGACT
CTCTGGATTCTGCAAGCTTGCCCAAAGAAAGGCAGTCAGCTTACTCTACAAGCTATGAAGTGCCTTCTAGACATACAGAG
GAAAGTGATAGAGAGCTTTCACTACCCTCAGCTAATGTGGAGGACTCACTGGAGAAAGAAAAGTACTGTGGCGATAAGAC
GGATATGCACACAGTTTCAGGTGAAGATAAAGGTGAACACAAACTTGTTGTACAAGACAGCATTGAACAACCAAAGAGAA
ATAGGATTACTTACTCTCAAATGGTTAAGGAGAGCCGGAGATTTAATATTGACTTGGTATCAAAGCCGCTGTATTCTCAA
GGGTCACTGATTGATCTTCTAATCAAATCAAATGTTAGTCGTTATGCAGAATTTAAGAATGTCACTAGGATCCTTGCATT
TTGGGAAGGGAAGGTAGAACAGGTGCCTTGCTCCAGAGCAGATGTCTTTAATAGTAAAGAGCTCAGTATGGTTGAAAAGA
GAATGCTAATGAAGTTTCTTACATTCTGTTTAGACTATGAACAACATTCTGATGAATACCAAGATTTCAAACAGTGTTCA
TTTTCTGACTACTTAAAAACTAAAAAACTAACACCTAATCTCCAGCACTTCATACTACACTCAATTGCAATGACATCAGA
ATCATCTTGCACTACATTAGATGGCCTTCAAGCAACAAAAACCTTTCTTCAGTGTCTTGGACGGTTTGGCAATACTCCCT
TTATATTTCCTTTATACGGCCACGGAGAAATTCCCCAGTGTTTCTGCAGGATGTGTGCAGTTTTTGGTGGAGTCTATTGT
CTTCGCCATAAAGTACAATGCCTTGTAGTTGACAAAGACTCTGGAAGATGTAAAGGAATCATAGATGCCTTTGGTCAGAG
AATAAGTGCCAACTACTTTATTGTGGAGGACAGTTATCTTCCTAAGGAAACATGTTCAAACGTGCAATATAAGCAGATCT
CAAGGGCAGTGCTCATCACAGATCAGTCCATCCTGAAGACAGATTCGGACCAGCAGATTTCCATTTTGGTAGTGCCTCCT
CTGGAGCCAGGAACCACTTCTGTTCGGGTCATGGAATTATGTTCGTCAACCATGACATGCATGAAGGACAGCTATCTGGT
CCACCTGACCTGTTCCTCTTCAAAAACAGCCAGAGAAGACTTGGAACCTGTGGTGAAGCAGTTATTCATTCCTGAAGCAG
AAGCAGAAGCAGGCAAAGATGAACTCCGAAAACCAAGACTCTTGTGGGCTCTTTATTTTAATATGAGAGATTCCTCAGGA
GTGAGCCGAAGCTCATACTGTGGCTTACCTTCCAATGTGTACATCTGCTCTGGGCCTGACTGGGGACTGGGGAGTGAGCA
TGCAGTCAAGCAGGCGGAAACACTGTTCCAAGAGATTTTTCCCAGTGAAGAGTTCTGCCCTCCTCCACCAAACCCTGAAG
ACATCATCTTTGAAGCTGAGGGTTAG

ORF - retro_mmus_284 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.96 %
Parental protein coverage: 64.65 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalSTEQSSEILPKVQDNTETPKRNVITYSQIIKEGRRFNIDLVSKLLYSRGLLIDLLIKSNVSRYAEFKNIT
S.E...E....VQD..E.PKRN.ITYSQ..KE.RRFNIDLVSK.LYS.G.LIDLLIKSNVSRYAEFKN.T
RetrocopySGEDKGEHKLVVQDSIEQPKRNRITYSQMVKESRRFNIDLVSKPLYSQGSLIDLLIKSNVSRYAEFKNVT
ParentalRILAFREGTVEQVPCSRADVFNSKQLTMVEKRMLMKFLTFCVEYEDHPDEYKAYEETTFSEYLKTQKLTP
RILAF.EG.VEQVPCSRADVFNSK.L.MVEKRMLMKFLTFC..YE.H.DEY.......FS.YLKT.KLTP
RetrocopyRILAFWEGKVEQVPCSRADVFNSKELSMVEKRMLMKFLTFCLDYEQHSDEYQDFKQCSFSDYLKTKKLTP
ParentalNLQYFVLHSIAMTSETTSSTVDGLKATKKFLQCLGRYGNTPFLFPLYGQGELPQCFCRMCAVFGGIYCLR
NLQ.F.LHSIAMTSE....T.DGL.ATK.FLQCLGR.GNTPF.FPLYG.GE.PQCFCRMCAVFGG.YCLR
RetrocopyNLQHFILHSIAMTSESSCTTLDGLQATKTFLQCLGRFGNTPFIFPLYGHGEIPQCFCRMCAVFGGVYCLR
ParentalHSVQCLVVDKESRKCKAIVDQFGQRIISKHFVIEDSYLSENTCSGVQYRQISRAVLITDGSVLKPDSDQQ
H.VQCLVVDK.S..CK.I.D.FGQRI....F..EDSYL...TCS.VQY.QISRAVLITD.S.LK.DSDQQ
RetrocopyHKVQCLVVDKDSGRCKGIIDAFGQRISANYFIVEDSYLPKETCSNVQYKQISRAVLITDQSILKTDSDQQ
ParentalVSILTVPAEESGSFAVRVIELCSSTMTCMKGTYLVHLTCMSSKTAREDLERVVQKLFTPYTEIEAENEQV
.SIL.VP..E.G...VRV.ELCSSTMTCMK..YLVHLTC.SSKTAREDLE.VV..LF.P..E.EA.....
RetrocopyISILVVPPLEPGTTSVRVMELCSSTMTCMKDSYLVHLTCSSSKTAREDLEPVVKQLFIPEAEAEAGKDEL
ParentalEKPRILWALYFNMRDSSDISRDCYNDLPSNVYVCSGPDCNLGNDNAVQQAETVFQKICPNEDFCPAPPNP
.KPR.LWALYFNMRDSS..SR..Y..LPSNVY.CSGPD..LG...AV.QAET.FQ.I.P.E.FCP.PPNP
RetrocopyRKPRLLWALYFNMRDSSGVSRSSYCGLPSNVYICSGPDWGLGSEHAVKQAETLFQEIFPSEEFCPPPPNP
ParentalEDIILDGD
EDII....
RetrocopyEDIIFEAE

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 4 .56 RPM 40 .42 RPM
SRP007412_cerebellum 3 .52 RPM 23 .36 RPM
SRP007412_heart 3 .70 RPM 10 .90 RPM
SRP007412_kidney 2 .27 RPM 16 .07 RPM
SRP007412_liver 0 .52 RPM 9 .15 RPM
SRP007412_testis 5 .72 RPM 1 .65 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity may be related with retro_mmus_284 in 2 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001YJZ POLR2A 1:175682346..175693367
ENCFF001YKA POLR2A 1:175682205..175691265

EST - click to see more details

No EST(s) were mapped for retro_mmus_284 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_284 retrocopy 5' end.

Lab - click to see more details

retro_mmus_284 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_284 has 10 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_56
Pan troglodytes retro_ptro_400
Gorilla gorilla retro_ggor_488
Pongo abelii retro_pabe_215
Macaca mulatta retro_mmul_460
Rattus norvegicus retro_rnor_981
Oryctolagus cuniculus retro_ocun_893
Bos taurus retro_btau_227
Canis familiaris retro_cfam_1873
Equus caballus retro_ecab_36
Parental genes homology:
Parental genes homology involve 22 parental genes, and 23 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000101901 retrocopy
retro_amel_733,
Bos taurus ENSBTAG000000095981 retrocopy
retro_btau_227,
Canis familiaris ENSCAFG000000174061 retrocopy
retro_cfam_1873,
Equus caballus ENSECAG000000192011 retrocopy
retro_ecab_36,
Felis catus ENSFCAG000000306521 retrocopy
retro_fcat_1744,
Homo sapiens ENSG000001884191 retrocopy
retro_hsap_56,
Gorilla gorilla ENSGGOG000000229121 retrocopy
retro_ggor_488,
Loxodonta africana ENSLAFG000000005231 retrocopy
retro_lafr_441,
Myotis lucifugus ENSMLUG000000112861 retrocopy
retro_mluc_138,
Macaca mulatta ENSMMUG000000167761 retrocopy
retro_mmul_460,
Monodelphis domestica ENSMODG000000143641 retrocopy
retro_mdom_1776,
Mustela putorius furoENSMPUG000000011941 retrocopy
retro_mputfur_831,
Mus musculus ENSMUSG000000212182 retrocopies
retro_mmus_2971, retro_mmus_360,
Mus musculus ENSMUSG00000025531 1 retrocopy
retro_mmus_284 ,
Nomascus leucogenys ENSNLEG000000027621 retrocopy
retro_nleu_120,
Oryctolagus cuniculus ENSOCUG000000128191 retrocopy
retro_ocun_893,
Pongo abelii ENSPPYG000000205201 retrocopy
retro_pabe_215,
Pan troglodytes ENSPTRG000000220711 retrocopy
retro_ptro_400,
Rattus norvegicus ENSRNOG000000001611 retrocopy
retro_rnor_981,
Sarcophilus harrisii ENSSHAG000000175681 retrocopy
retro_shar_127,
Ictidomys tridecemlineatus ENSSTOG000000221111 retrocopy
retro_itri_870,
Vicugna pacos ENSVPAG000000019631 retrocopy
retro_vpac_231,


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