RetrogeneDB ID:

retro_mmus_924

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:12:21776101..21776818(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000091105
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Mrto4
Ensembl ID:ENSMUSG00000028741
Aliases:Mrto4, 2610012O22Rik, Mg684, Mrt4
Description:MRT4, mRNA turnover 4, homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1917152]


Retrocopy-Parental alignment summary:






>retro_mmus_924
ATGCCCAAATCCAAGCGAGACAAGAAAGTTTCTTTAACAAAAACTGCCAAGAAAGGCTTGGAACTGAAGCAGAACCTGAT
AGAAGAGCTTCGGAAATGTGTGGACACCTACAAGTACCTTTTCATCTTCTCTGTGGCCAACATGAGGAACAGCAAACTGA
AGGACATCCGGAACGCCTGGAAGCACAGCCGGATGTTCTTTGGCAAAAACAAGGTGATGATGGTGGCCTTGGGTCGAAGC
CCATCTGATGAATACAAAGACGACCTACATCAGGTCAGCAAGAAGTTGAGAGGTGAAGTTGGGCTGCTGTTTACCAACCG
CACGAAGGAGGAGGTGAATGAGTGGTTCACAAAGTATACAGAAATGGATTTTGCTCGAGCGGGGAACAAAGCAACTCTAA
CTGTGAGCCTGGATCCAGGGCCCCTGAAGCAATTCCCTCACTCCATGGAGCTACAACTGAGGCAGCTGGGGCTGCCCACT
GCCCTCGAGAAAGGTGTGGTGACCCTGCTGTCTGACTATGAAGTATGCAAAGAGGGTGACGTGCTGACCCCAGAGCAGGC
CCGGATCCTGAAGCTGTTTGGGTATGAGATGGCTGAATTCAAAGTGACCATCAAATACATGTGGGACGCCCAGTCGGGAC
AATTCCAGCAGATGGACGATGACCTGCCTGAGAGCGCGCCTGAGTCTGAGGGAGAGTCTGAGGAGGAGGATGACAGC

ORF - retro_mmus_924 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.91 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMPKSKRDKKVSLTKTAKKGLELKQNLIEELRKCVDTYKYLFIFSVANMRNSKLKDIRNAWKHSRMFFGKN
MPKSKRDKKVSLTKTAKKGLELKQNLIEELRKCVDTYKYLFIFSVANMRNSKLKDIRNAWKHSRMFFGKN
RetrocopyMPKSKRDKKVSLTKTAKKGLELKQNLIEELRKCVDTYKYLFIFSVANMRNSKLKDIRNAWKHSRMFFGKN
ParentalKVMMVALGRSPSDEYKDNLHQVSKKLRGEVGLLFTNRTKEEVNEWFTKYTEMDFARAGNKATLTVSLDPG
KVMMVALGRSPSDEYKD.LHQVSKKLRGEVGLLFTNRTKEEVNEWFTKYTEMDFARAGNKATLTVSLDPG
RetrocopyKVMMVALGRSPSDEYKDDLHQVSKKLRGEVGLLFTNRTKEEVNEWFTKYTEMDFARAGNKATLTVSLDPG
ParentalPLKQFPHSMEPQLRQLGLPTALKKGVVTLLSDYEVCKEGDVLTPEQARILKLFGYEMAEFKVIIKYMWDA
PLKQFPHSME.QLRQLGLPTAL.KGVVTLLSDYEVCKEGDVLTPEQARILKLFGYEMAEFKV.IKYMWDA
RetrocopyPLKQFPHSMELQLRQLGLPTALEKGVVTLLSDYEVCKEGDVLTPEQARILKLFGYEMAEFKVTIKYMWDA
ParentalQSGRFQQMDDDLPESAPESEGESEEEDDS
QSG.FQQMDDDLPESAPESEGESEEEDDS
RetrocopyQSGQFQQMDDDLPESAPESEGESEEEDDS

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 .00 RPM 13 .76 RPM
SRP007412_cerebellum 0 .00 RPM 13 .68 RPM
SRP007412_heart 0 .06 RPM 11 .80 RPM
SRP007412_kidney 0 .02 RPM 11 .03 RPM
SRP007412_liver 0 .00 RPM 13 .22 RPM
SRP007412_testis 0 .00 RPM 27 .40 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_924 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_924 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_924 retrocopy 5' end.

Lab - click to see more details

retro_mmus_924 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_924 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 20 parental genes, and 47 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000151891 retrocopy
retro_cfam_1353,
Callithrix jacchus ENSCJAG000000068123 retrocopies
retro_cjac_1146, retro_cjac_1834, retro_cjac_3791,
Dasypus novemcinctus ENSDNOG000000101196 retrocopies
retro_dnov_1051, retro_dnov_1545, retro_dnov_170, retro_dnov_1890, retro_dnov_2044, retro_dnov_2255,
Echinops telfairi ENSETEG000000016755 retrocopies
retro_etel_1080, retro_etel_1162, retro_etel_1172, retro_etel_1887, retro_etel_2177,
Homo sapiens ENSG000000533722 retrocopies
retro_hsap_1766, retro_hsap_1914,
Gorilla gorilla ENSGGOG000000005332 retrocopies
retro_ggor_1400, retro_ggor_2244,
Macropus eugenii ENSMEUG000000000271 retrocopy
retro_meug_1606,
Microcebus murinus ENSMICG000000040192 retrocopies
retro_mmur_1235, retro_mmur_733,
Myotis lucifugus ENSMLUG000000015661 retrocopy
retro_mluc_374,
Macaca mulatta ENSMMUG000000066951 retrocopy
retro_mmul_107,
Monodelphis domestica ENSMODG000000158741 retrocopy
retro_mdom_1694,
Mustela putorius furoENSMPUG000000161812 retrocopies
retro_mputfur_1177, retro_mputfur_1430,
Mus musculus ENSMUSG00000028741 2 retrocopies
retro_mmus_852, retro_mmus_924 ,
Oryctolagus cuniculus ENSOCUG000000002742 retrocopies
retro_ocun_1191, retro_ocun_951,
Otolemur garnettii ENSOGAG000000107132 retrocopies
retro_ogar_1826, retro_ogar_2060,
Pongo abelii ENSPPYG000000017952 retrocopies
retro_pabe_1535, retro_pabe_1548,
Pan troglodytes ENSPTRG000000002622 retrocopies
retro_ptro_1182, retro_ptro_1248,
Rattus norvegicus ENSRNOG000000179791 retrocopy
retro_rnor_2967,
Ictidomys tridecemlineatus ENSSTOG000000281121 retrocopy
retro_itri_1551,
Tupaia belangeri ENSTBEG000000065028 retrocopies
retro_tbel_1020, retro_tbel_1189, retro_tbel_1210, retro_tbel_1873, retro_tbel_1945, retro_tbel_2665, retro_tbel_394, retro_tbel_559,




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