RetrogeneDB ID:

retro_mmus_2833

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:6:68387563..68388365(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Cttn
Ensembl ID:ENSMUSG00000031078
Aliases:Cttn, 1110020L01Rik, Ems1
Description:cortactin [Source:MGI Symbol;Acc:MGI:99695]


Retrocopy-Parental alignment summary:






>retro_mmus_2833
CAGACAGACAGACAGGACAAGTGTGCCCTTGGCTGGGATAATCAGGAGAAGCGGCAGCTGCATGAATCTCAAAACAACTA
TGCCAAAGGATTTGGAGGGAAGTACGGGGTACAGAAGGATCGATGGACAAGAACTCACCCACCTTTGAAGAAGTGGTCCA
GGTGCCATCTGCCTATCAGACTGTCCCAATTGAGGCTGTAACCTGCAAAACCACTGATATTCGTGCTTTGAAAACCTGGC
AAAGGGAAGAGAACAGGAGGGCAGGGAGAAGGCAGAAACTGAGAGAGTTCAGCATATTACCAAAGAAAATCAGGAGCAGG
AAGAAGTGTGAAGGAAGCTGGAAGAACAAGCCAGAGACAAGAAACAGACTCCCCCTGCATCCTCTAATCCTCAGACAGCT
GAAGACAGACCACCCTCCAGTCCCATCTATGAGGATGCAACTCCATTCAAGAAAGATCCAAGCTACTAGGGTAGTGAGCC
TGAACCTAAGTACAGCATGGCGGCAGATGTTCCTGGGGCTGAGGAGACAGCAAGGCATAGTCTACACATTAGAGCTGTGA
ACAAGACCACGGAGGCTCCTGTGTACTACCAAGGAAACAATGACACCAACAATGGGTATGAGAGGGACCTGGGCATCACA
GCCGTCGCCCTATATGACTACCAGGCTGAGGGTAGTGGTGTGATCTCTTTTGACCCTGATGACATCATCACCAACGTAGA
AATGATTGGAGATATCTGGTGATTTGAGGTGTGCAAGCACAGAAATGGGCTTTTCCAGGCCAACTATGTGGAACTGCAGC
AA

ORF - retro_mmus_2833 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.18 %
Parental protein coverage: 53.24 %
Number of stop codons detected: 3
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalQTDRQDKCALGWDHQEKLQLHESQKDYAKGFGGKYGVQKDR-MDKNASTFEEVVQVPSAYQKTVPIEAVT
QTDRQDKCALGWD.QEK.QLHESQ..YAKGFGGKYGVQKDR.MDKN..TFEEVVQVPSAYQ.TVPIEAVT
RetrocopyQTDRQDKCALGWDNQEKRQLHESQNNYAKGFGGKYGVQKDR<MDKNSPTFEEVVQVPSAYQ-TVPIEAVT
ParentalSKTSNIRANFENLAKEREQEDRRK-AEAERAQRMAKERQEQEEARRKLEEQARAKKQTPPASPSPQPIED
.KT..IRA.......E......R..AE.ER.Q...KE.QEQEE..RKLEEQAR.KKQTPPAS..PQ..ED
RetrocopyCKTTDIRA-LKTWQREENRRAGRR<AETERVQHITKENQEQEEV*RKLEEQARDKKQTPPASSNPQTAED
ParentalRPPSSPIYEDAAPFKAEPSYRGSEPEPEYSIEAAGIPEAGS-QQGLTYTSE-PVYETTEAPGHYQAEDDT
RPPSSPIYEDA.PFK..PSY.GSEPEP.YS..AA..P.A...QQG..YT.E..V..TTEAP..YQ...DT
RetrocopyRPPSSPIYEDATPFKKDPSY*GSEPEPKYSM-AADVPGAEE>QQGIVYTLE<AVNKTTEAPVYYQGNNDT
ParentalYDGYESDLGITAIALYDYQAAGDDEISFDPDDIITNIEMIDDGWWRGVCKGRYGLFPANYVELRQ
..GYE.DLGITA.ALYDYQA.G...ISFDPDDIITN.EMI.D.W...VCK.R.GLF.ANYVEL.Q
RetrocopyNNGYERDLGITAVALYDYQAEGSGVISFDPDDIITNVEMIGDIW*FEVCKHRNGLFQANYVELQQ

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 104 .83 RPM
SRP007412_cerebellum 0 .00 RPM 91 .97 RPM
SRP007412_heart 0 .00 RPM 57 .22 RPM
SRP007412_kidney 0 .00 RPM 127 .49 RPM
SRP007412_liver 0 .00 RPM 56 .80 RPM
SRP007412_testis 0 .00 RPM 47 .29 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_2833 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_2833 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_2833 retrocopy 5' end.

Lab - click to see more details

retro_mmus_2833 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2833 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 ENSMUSG00000031078 2 retrocopies
retro_mmus_1099, retro_mmus_2833 ,




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