RetrogeneDB ID:

retro_mmus_2006

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:2:181897179..181898380(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000083397
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Pabpc4
Ensembl ID:ENSMUSG00000011257
Aliases:None
Description:poly(A) binding protein, cytoplasmic 4 [Source:MGI Symbol;Acc:MGI:2385206]


Retrocopy-Parental alignment summary:






>retro_mmus_2006
TCTAAGGGCTATGCTTTTGTTCACTTCGAGACCCAAGAGGCCGCCGACAAGGTCATCGAGAAGATGAACGGCATGCTTCT
CAATGACCGTAAAGTGTTTGTGGGTAGATTCAAGTCTCGCAAAGAGCGGAAGCGGAGCTTGGAGCCAAGGCCAAGGAATT
CACCAATGTTTATATCAAAAACTTCGGAGAAGAGGTGGATGATGGGAATCTGAAAGAGCTCTTCAGCCAGTTTGGTAAGA
CCCTAAGTGTCAAGGTGATGAGAGACTCCAGTGGGAAGTCCAAAGGCTTTGGCTTTGTAAGTTATGAGAAACATGAGGAT
GTCAATAAGGCTGTGGAAGAAATGAAAGGAAAAGAAATGAGCGGGAAAGCCATATTTGTAGGCCACGCACAGAAAAAGGT
AGAACAGCAGGCTGAGTTAAAGCGGAAGTTTGAGTAGCTGAAGCAGGAGACGATTAGCCAGCACCAGGAAGTGAATCTCT
ACAGTAAGAACTTGGATGACACCATTGATGATGAGAAATTAAGGAAAGAGTTTTCTCCTTTTGGATCAATCACTAGTGCG
AAGGTGATGCTAGAAGACGAAAGAAGCAAAGGGTTTGGCTTTGTCTCTTTCTCCTCTCCTGAAGAGGCGACCAAAGCTGT
CGGCGAGATGAACGGAAGCATTGTGGGCTCCAAGCCTCTGTAAGTCGCCCTGGCCCAGAGGAAGAGGGGAAGGCTCACCT
GACTAATCAGTACATGCAGCGTGTGGTGGGGATGAGAGCACTCCCTGCCAAGTGCCATCTTAAATCAGTTCCAGCCTGCA
GCTGGTGGCTACTTTGTGCCCGCAGTTCCGCAGGCTCAGGCAAGACCCCATATTACACGCCTAACCAGTTAGCACAGATG
AGGCCTAACCCACGCTGGCAGCAAGGCGGGAGACCTCAAGGCTTCCAAGGAATGCCAAGTCCTCTGCAGCAGTCTGGGCC
TCGTCCAGCTCTTCCACATCTGGCTCCAACTGGGTCTGAGTGCCCGGACCGTTTGGCTATGGACTTTGATGGGGCTGGTG
CCGCCCAGCAAGGGCTGACTGACAGCTGCCAGTCTGGAGGCGTCCCTACAGCTGTGTCAAACCTTGCACCTCCTGCTCCC
AGGGCTGTGGCTCCATACAAGTACACCTCCAGTGTCCACAGGCCGCACCCTGCCATCCAGCCGCTGCAGGCCCCCCAGCC
T

ORF - retro_mmus_2006 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.17 %
Parental protein coverage: 62.42 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalSKGYAFVHFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKER-EAELGAKAKEFTNVYIKNFGEEVDDG
SKGYAFVHFETQEAADK.IEKMNGMLLNDRKVFVGRFKSRKER.EAELGAKAKEFTNVYIKNFGEEVDDG
RetrocopySKGYAFVHFETQEAADKVIEKMNGMLLNDRKVFVGRFKSRKER<EAELGAKAKEFTNVYIKNFGEEVDDG
ParentalNLKELFSQFGKTLSVKVMRDSSGKSKGFGFVSYEKHEDANKAVEEMNGKEMSGKAIFVGRAQKKVERQAE
NLKELFSQFGKTLSVKVMRDSSGKSKGFGFVSYEKHED.NKAVEEM.GKEMSGKAIFVG.AQKKVE.QAE
RetrocopyNLKELFSQFGKTLSVKVMRDSSGKSKGFGFVSYEKHEDVNKAVEEMKGKEMSGKAIFVGHAQKKVEQQAE
ParentalLKRKFEQLKQERISRYQGVNLYIKNLDDTIDDEKLRREFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEE
LKRKFE.LKQE.IS..Q.VNLY.KNLDDTIDDEKLR.EFSPFGSITSAKVMLED.RSKGFGFV.FSSPEE
RetrocopyLKRKFE*LKQETISQHQEVNLYSKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDERSKGFGFVSFSSPEE
ParentalATKAVTEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQRVAGMRALPASAILNQFQPAAGGYFVPAVPQ
ATKAV.EMNG.IVGSKPL.VALAQRK..R...L.............LP..AILNQFQPAAGGYFVPAVPQ
RetrocopyATKAVGEMNGSIVGSKPL*VALAQRKRGRLT*LISTCSVWWG*EHSLPS-AILNQFQPAAGGYFVPAVPQ
ParentalAQGRP-PYYTPNQLAQMRPNPRWQQGGRPQGFQGMPSALRQSGPRPALRHLAPTGSECPDRLAMDFGGAG
AQ.RP.PYYTPNQLAQMRPNPRWQQGGRPQGFQGMPS.L.QSGPRPAL.HLAPTGSECPDRLAMDF.GAG
RetrocopyAQARP<PYYTPNQLAQMRPNPRWQQGGRPQGFQGMPSPLQQSGPRPALPHLAPTGSECPDRLAMDFDGAG
ParentalAAQQGLTDSCQSGGVPTAVPNLAPRAAVAAAAPRAVAPYKYASSVRSPHPAIQP
AAQQGLTDSCQSGGVPTAV.NLAP.A..A.A................P..A.QP
RetrocopyAAQQGLTDSCQSGGVPTAVSNLAPPAPRAVAPYKYTSSVHRPHPAIQPLQAPQP

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 .26 RPM 13 .06 RPM
SRP007412_cerebellum 0 .69 RPM 9 .60 RPM
SRP007412_heart 0 .19 RPM 120 .01 RPM
SRP007412_kidney 0 .10 RPM 35 .50 RPM
SRP007412_liver 0 .00 RPM 16 .19 RPM
SRP007412_testis 0 .55 RPM 3 .06 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_2006 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_2006 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_2006 retrocopy 5' end.

Lab - click to see more details

retro_mmus_2006 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2006 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 29 parental genes, and 64 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000115352 retrocopies
retro_amel_107, retro_amel_676,
Bos taurus ENSBTAG000000171253 retrocopies
retro_btau_1492, retro_btau_28, retro_btau_656,
Canis familiaris ENSCAFG000000030812 retrocopies
retro_cfam_45, retro_cfam_837,
Choloepus hoffmanni ENSCHOG000000053273 retrocopies
retro_chof_1150, retro_chof_1182, retro_chof_1274,
Callithrix jacchus ENSCJAG000000025123 retrocopies
retro_cjac_214, retro_cjac_2722, retro_cjac_284,
Cavia porcellus ENSCPOG000000095522 retrocopies
retro_cpor_1330, retro_cpor_77,
Equus caballus ENSECAG000000093962 retrocopies
retro_ecab_2, retro_ecab_502,
Felis catus ENSFCAG000000152542 retrocopies
retro_fcat_116, retro_fcat_545,
Homo sapiens ENSG000000906212 retrocopies
retro_hsap_109, retro_hsap_74,
Gorilla gorilla ENSGGOG000000040023 retrocopies
retro_ggor_2127, retro_ggor_87, retro_ggor_916,
Loxodonta africana ENSLAFG000000001513 retrocopies
retro_lafr_1144, retro_lafr_390, retro_lafr_597,
Microcebus murinus ENSMICG000000166331 retrocopy
retro_mmur_675,
Myotis lucifugus ENSMLUG000000120682 retrocopies
retro_mluc_228, retro_mluc_397,
Macaca mulatta ENSMMUG000000074971 retrocopy
retro_mmul_178,
Monodelphis domestica ENSMODG000000176572 retrocopies
retro_mdom_1090, retro_mdom_1805,
Mustela putorius furoENSMPUG000000144142 retrocopies
retro_mputfur_152, retro_mputfur_546,
Mus musculus ENSMUSG00000011257 7 retrocopies
retro_mmus_2006 , retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Mus musculus ENSMUSG000000222832 retrocopies
retro_mmus_102, retro_mmus_2164,
Mus musculus ENSMUSG000000400431 retrocopy
retro_mmus_1530,
Nomascus leucogenys ENSNLEG000000119282 retrocopies
retro_nleu_1517, retro_nleu_62,
Oryctolagus cuniculus ENSOCUG000000005622 retrocopies
retro_ocun_153, retro_ocun_792,
Otolemur garnettii ENSOGAG000000040671 retrocopy
retro_ogar_71,
Ochotona princeps ENSOPRG000000119841 retrocopy
retro_opri_1133,
Pongo abelii ENSPPYG000000015062 retrocopies
retro_pabe_190, retro_pabe_2563,
Pan troglodytes ENSPTRG000000005733 retrocopies
retro_ptro_101, retro_ptro_2093, retro_ptro_8,
Rattus norvegicus ENSRNOG000000156422 retrocopies
retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii ENSSHAG000000181391 retrocopy
retro_shar_823,
Sus scrofa ENSSSCG000000036603 retrocopies
retro_sscr_1210, retro_sscr_974, retro_sscr_975,
Tursiops truncatus ENSTTRG000000143402 retrocopies
retro_ttru_1117, retro_ttru_246,


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