RetrogeneDB ID:

retro_mmus_2596

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:5:108822226..108823123(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000093756
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Ccdc77
Ensembl ID:ENSMUSG00000030177
Aliases:Ccdc77, 2400002C23Rik, 2700091N06Rik, AV168274
Description:coiled-coil domain containing 77 [Source:MGI Symbol;Acc:MGI:1914450]


Retrocopy-Parental alignment summary:






>retro_mmus_2596
GCTTCCAAAGTAGATCCTGGAGTAAGCAAAAGATGAGTAAGGATAAAGGACAGAGAAGACTTTTCTGAGCACTACCAGAA
GGACATAGAGACACTCTTCCTGCAAGTGGAAGCACTTCAGACCCAACTGGGAGAGCAGACTAAGTTTTCTAGAGATCATG
TTGAATGACTCATGGAGGACAGACGGAACCCGAATTGAGGAGATCTAAGTTCAGCACCAGAGAAATCAAGAGAAAAATCA
AGGAGCTGACTAAGAATCTCCATCAAACCCAAAAACTGCTCTACCAGAGTACCAAAGACTTTCTATAACTAAAACTTGAA
AACCAAAATAAAGAGAAGGTATTTTTTGCTTGAGAAAGATCACCTGATGTCAAAGATTAAACAGTATGAAGTACTTTGCA
AGAAGAAAGAAGATAAACTTGGAAAAATAGTTCCCATTTTTCATGAAAGTCATCCTTCTCAAAATGAATATATTAAGTCT
CCTAAGGATAAGCTAATACAAGAGAAAAAGCTGTCCAACATATACCAAGAACAGTGCATCTCCCTAGAAGAAGAACTTCC
TCTTCGTAAGGAGGAAGAAGGAGTGAGGAGAGAGATCTTCACGAATCACTCCAACAAGATGGGCAAGTGGTCACATATAA
TGACAAAACACTATCAGGCCTTGGAGCATTGAAAATCCTGGGAGTAGAAGGTTTCAAGATAGACATTAAGGTTCTCTGAC
AGAAGTTGAAAGACCTGGACAAATGTTCTATAAGGCAACCATGAACACTCATGGAAATCAGGACCTGACCATGCTATGTG
AAGTCCAGATAGCAATAGAAGAACCCATAAGATACAAGGAGAACTGAAGAACCTCAACTCTAAAGTGTTTGGTCTGCAGA
ATGAGCTTAGGCTGTGT

ORF - retro_mmus_2596 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.14 %
Parental protein coverage: 61.35 %
Number of stop codons detected: 6
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalASKADPGVSKRQVRIKDKEGISERHQRDTEMLLLQVEALQAQLGEQTKLSREQVEGLMEDRR-IRVEEIQ
ASK.DPGVSKR.VRIKD.E..SE..Q.D.E.L.LQVEALQ.QLGEQTK.SR..VE.LMEDRR..R.EEI.
RetrocopyASKVDPGVSKR*VRIKDREDFSEHYQKDIETLFLQVEALQTQLGEQTKFSRDHVE*LMEDRR>TRIEEI*
ParentalVQHQRNQEK-IMELTKSLHHTQELLYESTKDFLQLKFENQNKEKVW-MLEKDHLMSKITQYRAQCKKKED
VQHQRNQEK.I.ELTK.LH.TQ.LLY.STKDFL.LK.ENQNKEKV...LEKDHLMSKI.QY...CKKKED
RetrocopyVQHQRNQEK>IKELTKNLHQTQKLLYQSTKDFL*LKLENQNKEKVF>LLEKDHLMSKIKQYEVLCKKKED
ParentalKLGKVVPILHESHHTQNEYIKSLKDKLIQEKKLSNMYQEQCISLEEELARIREEEGVRREIFKDRSNKMG
KLGK.VPI.HESH..QNEYIKS.KDKLIQEKKLSN.YQEQCISLEEEL....EEEGVRREIF...SNKMG
RetrocopyKLGKIVPIFHESHPSQNEYIKSPKDKLIQEKKLSNIYQEQCISLEEELPLRKEEEGVRREIFTNHSNKMG
ParentalKRLQIMTKRYQALEHRRALE-VEGFKTDIKSLRQKLRDLE-QMLYKATMNNTHGDQDLAMLCEVR-DSNR
K...IMTK.YQALEH....E.VEGFK.DIK.L.QKL.DL..QM.YKATM.NTHG.QDL.MLCEV..DSNR
RetrocopyKWSHIMTKHYQALEH*KSWE<VEGFKIDIKVL*QKLKDLD<QMFYKATM-NTHGNQDLTMLCEVQ<DSNR
ParentalRAHKIQGELKNLKSKVFGLENALRLC
R.HKIQGELKNL.SKVFGL.N.LRLC
RetrocopyRTHKIQGELKNLNSKVFGLQNELRLC

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 5 .98 RPM
SRP007412_cerebellum 0 .00 RPM 9 .29 RPM
SRP007412_heart 0 .00 RPM 6 .13 RPM
SRP007412_kidney 0 .00 RPM 6 .29 RPM
SRP007412_liver 0 .00 RPM 4 .10 RPM
SRP007412_testis 0 .05 RPM 29 .68 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_2596 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_2596 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_2596 retrocopy 5' end.

Lab - click to see more details

retro_mmus_2596 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2596 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Mus musculus ENSMUSG00000030177 2 retrocopies
retro_mmus_1581, retro_mmus_2596 ,


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