RetrogeneDB ID:

retro_mmus_483

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:1:128520075..128521460(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Eef1a1
Ensembl ID:ENSMUSG00000037742
Aliases:None
Description:eukaryotic translation elongation factor 1 alpha 1 [Source:MGI Symbol;Acc:MGI:1096881]


Retrocopy-Parental alignment summary:






>retro_mmus_483
ATGGGAAAGGAAAAGACTCACATCAACATTGTCATAATCGGACACGTAGATTCCTGCAAGTCCACCACAACCGGCCACCT
GATCTACAAATGTGGTGGAATCAACAAGCGAACCATCAAAAAGTTTGAGAAGGAGGCTGCTGAGATGGAAAAGGGCTCCT
TTAAGTACGCCTGGGTCTTAGACAAACTGAAAGCTGAGCGTGAGCATGGTATCACTATTGACATCTCCCTGTGGAAATTC
GAGACCAGCAAATACTATGTGACCATCATTGATGCCCAGGACATAGAGACTTCGTCAAAAACATGATTACAGGCACATCC
CAGGCTGACTGTGCTGTCCTGATTGTTGCTGCTGGTGTTGGTGAATTTGAAGCTGGTATCTCCAAGAACGGGCAGACCCA
TGAGCATGCTCTTCTGGCTTACACCCTGGGTGTGAAACAGCTGATTGTTGGTGTCAACAAAATGGATTCCACCGAGCCAC
CATACAGTCAGAAGAGATACGAGGAAATCATTAAGGAAGTCAGCACCTACATTAAGAAAATTGGCTACAACCCTGACACA
GTAGCATTTGTGCCGATTTTAGGTTGGAATGGTGACAACATGCTGGAGCCAAGTGCTAATATGCCTTGGTTCAAGGGATG
GAAAGTCACCTGCAAAGATGGCAGTGCCAGTGGCACCACGGTGCTGGAAGCTTTGGATTGTATCCTACCACCAACTTGTC
CAACTTGTCCAACTCTGCGACTGCCCCTTTAGGATGTCTATAAAATTGGAGGCATTGGCACTGTCCCTGTGGGCCGAGTG
GAGACTGGTGTTCTCAAACCTGGGATGGTGGTTACCTTTGCTCCAGTCAATGTAACAACTGAAGTCAAGTCTGTTGAAAT
GCACCATGAAGCTTTGAGTGAAGCTCTTCCTGGGGACAATGTGGGCTTCAATGTAAAGAATGTGTCGGTCAAAGATGTTA
GATAAGGCAATGTTGCTTGTGACAGCAAAAACAACCCACCAATGGAAGCAGCTGGCTTCACTGCTCAGGTGATTATCCTG
AACCATCCAGGCCAAATCAGTGCTGGCTATGCTCCTGTTCTGGATTGTCACACAGCCCACATAGCATGCAAGTTTGCTGA
GCTTAAAGAAAAGATCGGTCGTCGTTCTGGTAAGAAGCTGGAAGATGGCCCCAAATTCCTGAAGTCTGGTGATGCTGCCA
TTGTTGATATGGTCCCTGGCAAGCCCATGTGTGTTGAGAGCTTCTCTGGCTATCCTCCACTTGGTCGTTTTGCTGTTCGT
GACATGAGGCAGAGAGTTGCTGTGGGTGTCATCAAAGCTGTGGACAAGAAGGCTGCTGGAGCTGGCAAAGTCACCAAGTC
TGCCCAGAAAGCTCAGAAGGCTAAA

ORF - retro_mmus_483 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.95 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERG
MGKEKTHINIV.IGHVDS.KSTTTGHLIYKCGGI.KRTI.KFEKEAAEM.KGSFKYAWVLDKLKAERE.G
RetrocopyMGKEKTHINIVIIGHVDSCKSTTTGHLIYKCGGINKRTIKKFEKEAAEMEKGSFKYAWVLDKLKAEREHG
ParentalITIDISLWKFETSKYYVTIIDA-PGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALL
ITIDISLWKFETSKYYVTIIDA.PGHRDF.KNMITGTSQADCAVLIVAAGVGEFEAGISKNGQT.EHALL
RetrocopyITIDISLWKFETSKYYVTIIDA<PGHRDFVKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTHEHALL
ParentalAYTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANMP
AYTLGVKQLIVGVNKMDSTEPPYSQKRYEEI.KEVSTYIKKIGYNPDTVAFVPI.GWNGDNMLEPSANMP
RetrocopyAYTLGVKQLIVGVNKMDSTEPPYSQKRYEEIIKEVSTYIKKIGYNPDTVAFVPILGWNGDNMLEPSANMP
ParentalWFKGWKVTRKDGSASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVT
WFKGWKVT.KDGSASGTT.LEALDCILP........LRLPL.DVYKIGGIGTVPVGRVETGVLKPGMVVT
RetrocopyWFKGWKVTCKDGSASGTTVLEALDCILPXXXXXXXXLRLPL*DVYKIGGIGTVPVGRVETGVLKPGMVVT
ParentalFAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNH
FAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVR.GNVA.DSKN.PPMEAAGFTAQVIILNH
RetrocopyFAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVR*GNVACDSKNNPPMEAAGFTAQVIILNH
ParentalPGQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSDYP
PGQISAGYAPVLDCHTAHIACKFAELKEKI.RRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFS.YP
RetrocopyPGQISAGYAPVLDCHTAHIACKFAELKEKIGRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSGYP
ParentalPLGRFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK
PLGRFAVRDMRQ.VAVGVIKAVDKKAAGAGKVTKSAQKAQKAK
RetrocopyPLGRFAVRDMRQRVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 .23 RPM 938 .67 RPM
SRP007412_cerebellum 0 .13 RPM 652 .71 RPM
SRP007412_heart 0 .22 RPM 465 .27 RPM
SRP007412_kidney 1 .15 RPM 1781 .75 RPM
SRP007412_liver 1 .42 RPM 2430 .48 RPM
SRP007412_testis 0 .32 RPM 1060 .92 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_483 was not detected
No EST(s) were mapped for retro_mmus_483 retrocopy.
No TSS is located nearby retro_mmus_483 retrocopy 5' end.
retro_mmus_483 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_483 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 29 parental genes, and 226 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000000778614 retrocopies
Bos taurus ENSBTAG000000145343 retrocopies
Canis familiaris ENSCAFG000000122221 retrocopy
Canis familiaris ENSCAFG000000132491 retrocopy
Callithrix jacchus ENSCJAG000000100516 retrocopies
Cavia porcellus ENSCPOG0000000406715 retrocopies
Dipodomys ordii ENSDORG000000096291 retrocopy
Equus caballus ENSECAG000000203632 retrocopies
Equus caballus ENSECAG000000222601 retrocopy
Erinaceus europaeus ENSEEUG000000003423 retrocopies
Echinops telfairi ENSETEG0000000423614 retrocopies
Felis catus ENSFCAG0000003097714 retrocopies
Gorilla gorilla ENSGGOG0000002567520 retrocopies
Loxodonta africana ENSLAFG000000280811 retrocopy
Microcebus murinus ENSMICG0000001531921 retrocopies
Myotis lucifugus ENSMLUG0000001353724 retrocopies
Macaca mulatta ENSMMUG0000000485215 retrocopies
Monodelphis domestica ENSMODG000000185334 retrocopies
Mustela putorius furoENSMPUG000000038166 retrocopies
Mustela putorius furoENSMPUG0000000427110 retrocopies
Mus musculus ENSMUSG00000037742 15 retrocopies
Nomascus leucogenys ENSNLEG000000014766 retrocopies
Oryctolagus cuniculus ENSOCUG000000084813 retrocopies
Otolemur garnettii ENSOGAG0000000915210 retrocopies
Pongo abelii ENSPPYG000000167771 retrocopy
Pan troglodytes ENSPTRG000000183471 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000076874 retrocopies
Vicugna pacos ENSVPAG000000076379 retrocopies
Drosophila melanogaster FBgn00005571 retrocopy



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