RetrogeneDB ID:

retro_mmus_2521

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:4:143242026..143243358(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000082575
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Eef2
Ensembl ID:ENSMUSG00000034994
Aliases:Eef2, Ef-2
Description:eukaryotic translation elongation factor 2 [Source:MGI Symbol;Acc:MGI:95288]


Retrocopy-Parental alignment summary:






>retro_mmus_2521
AGAGTGTTCTCTGGGGTGGTGTCCACAGGCCTGAAGGTCTGGATCCTGGGCCCCAACTACACGCCTGGGAAGAAAGAGGA
CCTGTACCTGAAGCCTATCCAGAGAACCATTCTGATGATGGGCCGCTATGTGGAGCTGATTGAGTATGTGCCCTGTGGAA
ACATTGTGGGGCTGGTCGGAGTGGACCAGTTCCTTGTGAAGACCGGGACCATCACCACCTTTGAGCACGCTCACAATATG
CGCGTGATGAAGTTCAGCGTCAGTCCTGTCGTCCGGGTGGCAGTGGAGGCCAAGAACCCAGCTGACCTGTCCAAGCTGGT
GGAGGGGCTGAAGCGGCTGGCTAAGTCTGATCCTATGGTGCAGTGCATCATTGAGGAGTCTGGAGAGCATATCATTGCTG
GCGCCGGTGAGCTGCACCTGGAGATCTGCCTTAAGGACCTGGAGGAGGACCATGCCTGCATCCCCATCAAGAAATCTGAC
CCTGTTGTGTCATACCGGGAGACAGTCAGTGAGGAATCCAACGTGCTGTGTCTGTCCAAGTCCCCCAATAAGCACAAGCG
GCTGTACATGAAGGCCACGCCCTTCCCTGATGGCCTGGCAGAGGACATCGATAAGGGTGAGGTGTCTGCCCGCCAGGAGC
TCAAGGCATGTGCTCACTACCTGGTCGAAAAGTATGAGTGGGACGTTGCTGAAGCCCGCAAGATCTGGTGCTTTGGCCCT
GATGGCACTGGCCCCAACATTCTCACCGACATCACCAAGGGCGTGCAGTACCTGAATGAGATCAAGGACAGTGTGGTGGC
TGGCTACCAGTGGGCTACTAAGGAGGGCGCTCTCTGTGAGGAGAACATGCGTGGTGTGCGGTTTGATGTTCATGTTGTGA
CCCTGCATGCTGATGCCATTCACCAGGGAGGTGGCCAGATCATCCCCACAGCACGCCGCTGCCTCTATGCCAGTGTGCTG
ACCGCACAGCCCTGCCTCATGGAGCCTATCTATCTGGAGGAGATCCAGTGTCCTGAGCAAGTGGTGGGTGGCATCTACGG
TGTCCTGAACAGGAAGCGTGGCCATGTGTTTGAGGAGTCCCAGGTGGCTGGTACCCACATGTTTGTGGTCAAGGCATACC
TGCCTGTCAATGAGTCTTTTGGCTTCACCGCTGATCTGTGATCCAACACTGGCGGCCAGGCCTTCCCCCAGTGCGTGTTT
GACCACTGGCAGATCCTGCTTGGGGATCCTTTTGACAACAGCAGCCGCCCCAGCCAAGCGGTAGCTGAGACCCGCAAGCG
CAAGGGCCTGAAAGAGGACATCCCAGCGCTGGACAACTTCCTGGACAAACTG

ORF - retro_mmus_2521 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.5 %
Parental protein coverage: 51.75 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRVFSGVVSTGLKVRIMGPNYTPGKKEDLYLKPIQRTILMMGRYVEPIEDVPCGNIVGLVGVDQFLVKTGT
RVFSGVVSTGLKV.I.GPNYTPGKKEDLYLKPIQRTILMMGRYVE.IE.VPCGNIVGLVGVDQFLVKTGT
RetrocopyRVFSGVVSTGLKVWILGPNYTPGKKEDLYLKPIQRTILMMGRYVELIEYVPCGNIVGLVGVDQFLVKTGT
ParentalITTFEHAHNMRVMKFSVSPVVRVAVEAKNPADLPKLVEGLKRLAKSDPMVQCIIEESGEHIIAGAGELHL
ITTFEHAHNMRVMKFSVSPVVRVAVEAKNPADL.KLVEGLKRLAKSDPMVQCIIEESGEHIIAGAGELHL
RetrocopyITTFEHAHNMRVMKFSVSPVVRVAVEAKNPADLSKLVEGLKRLAKSDPMVQCIIEESGEHIIAGAGELHL
ParentalEICLKDLEEDHACIPIKKSDPVVSYRETVSEESNVLCLSKSPNKHNRLYMKARPFPDGLAEDIDKGEVSA
EICLKDLEEDHACIPIKKSDPVVSYRETVSEESNVLCLSKSPNKH.RLYMKA.PFPDGLAEDIDKGEVSA
RetrocopyEICLKDLEEDHACIPIKKSDPVVSYRETVSEESNVLCLSKSPNKHKRLYMKATPFPDGLAEDIDKGEVSA
ParentalRQELKARARYLAEKYEWDVAEARKIWCFGPDGTGPNILTDITKGVQYLNEIKDSVVAGFQWATKEGALCE
RQELKA.A.YL.EKYEWDVAEARKIWCFGPDGTGPNILTDITKGVQYLNEIKDSVVAG.QWATKEGALCE
RetrocopyRQELKACAHYLVEKYEWDVAEARKIWCFGPDGTGPNILTDITKGVQYLNEIKDSVVAGYQWATKEGALCE
ParentalENMRGVRFDVHDVTLHADAIHRGGGQIIPTARRCLYASVLTAQPRLMEPIYLVEIQCPEQVVGGIYGVLN
ENMRGVRFDVH.VTLHADAIH.GGGQIIPTARRCLYASVLTAQP.LMEPIYL.EIQCPEQVVGGIYGVLN
RetrocopyENMRGVRFDVHVVTLHADAIHQGGGQIIPTARRCLYASVLTAQPCLMEPIYLEEIQCPEQVVGGIYGVLN
ParentalRKRGHVFEESQVAGTPMFVVKAYLPVNESFGFTADLRSNTGGQAFPQCVFDHWQILPGDPFDNSSRPSQV
RKRGHVFEESQVAGT.MFVVKAYLPVNESFGFTADL.SNTGGQAFPQCVFDHWQIL.GDPFDNSSRPSQ.
RetrocopyRKRGHVFEESQVAGTHMFVVKAYLPVNESFGFTADL*SNTGGQAFPQCVFDHWQILLGDPFDNSSRPSQA
ParentalVAETRKRKGLKEGIPALDNFLDKL
VAETRKRKGLKE.IPALDNFLDKL
RetrocopyVAETRKRKGLKEDIPALDNFLDKL

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 .72 RPM 937 .34 RPM
SRP007412_cerebellum 0 .78 RPM 1260 .65 RPM
SRP007412_heart 1 .96 RPM 1758 .70 RPM
SRP007412_kidney 1 .85 RPM 1893 .36 RPM
SRP007412_liver 0 .96 RPM 1725 .35 RPM
SRP007412_testis 1 .33 RPM 1854 .12 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_2521 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_2521 retrocopy.

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_102669236 libraries434 libraries387 libraries11 libraries4 libraries

The graphical summary, for retro_mmus_2521 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_2521 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2521 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000042582 retrocopies
retro_btau_1809, retro_btau_539,
Canis familiaris ENSCAFG000000191581 retrocopy
retro_cfam_1503,
Latimeria chalumnae ENSLACG000000111241 retrocopy
retro_lcha_83,
Macaca mulatta ENSMMUG000000227671 retrocopy
retro_mmul_2026,
Monodelphis domestica ENSMODG000000007501 retrocopy
retro_mdom_223,
Mus musculus ENSMUSG00000034994 1 retrocopy
retro_mmus_2521 ,


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