RetrogeneDB ID:

retro_mmus_2053

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:2:83744483..83745211(-)
Located in intron of:ENSMUSG00000085335
Retrocopy
information
Ensembl ID:ENSMUSG00000081801
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Dnmt3l
Ensembl ID:ENSMUSG00000000730
Aliases:Dnmt3l, D6Ertd14e, ecat7
Description:DNA (cytosine-5-)-methyltransferase 3-like [Source:MGI Symbol;Acc:MGI:1859287]


Retrocopy-Parental alignment summary:






>retro_mmus_2053
CTTCCTCTGCCTTTCTCTCAAAGCAGCCTGCTGCAGAGGCGGAGGACATGGCACCACCAGCTAAAGGCCTTCCATCACCT
GGATGGGGCAAACCTCGGGGAGATGTGCAAGGCAGTGCCTATGTGGAAGGATGAGGCAGGGCATGTGCTGACACATGGGA
GGATATTGAACATGAGCTAAAGAGTTTGGGCTTTGGGGAAGTGGATCTGGTTTTGAGGGAGAAAGATGGAAGAACTCAGA
AGCTGTCACAAACATCGCAAGGAGAGACATGGAAGGATGGGGCCCCTTTGACTTCGTGTAAATGGCTCAACACAACCCCT
AGTCTACTGCTGTGACCACTGCCCTGGCTGGTGCCAGTTCCAATTCCACCGGGTCCTACAGTACACATGACCGCACCCAG
GTTGACTGCAGCCCTTCTTCTGGATGTTTGTCAGCAACCCACTGCTGACTAAGAATGACCAAACCTCAGCAGCCTAACTC
GAGATGGAGGCTATGACCTTCAGGATGTCTGCTGCAGATCCTCCAGAATGCTGTATGGGTGTGCAGCGACATGGGGGTGA
GAGGGAGCAAGCATGCACGAGACACTGACACCAGGGAAGGAACAGTTCCTGAAAGCCCAAGTCAGTACAAGAGCCACGCT
GGTACCCAGAGCCTGGAGCTCCTGGAGAACTGCCTTCTCCCCCCTACCAGAATACTTCAGATATTTTTCTCAGAGCTCAC
TTCCTCTT

ORF - retro_mmus_2053 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 50.79 %
Parental protein coverage: 57.96 %
Number of stop codons detected: 4
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalLCLPFSRSGLLQRRKRWRHQLKAFHDQEGAGPMEIYKTVSAWKRQPVRVLS-LFRNIDKVLKSLGFLE-S
L.LPFS.S.LLQRR..W.HQLKAFH...GA...E..K.V..WK.....VL......I...LKSLGF.E.S
RetrocopyLPLPFSQSSLLQRRRTWHHQLKAFHHLDGANLGEMCKAVPMWKDEAGHVLT<TWEDIEHELKSLGFGE<S
ParentalGSGSGGGTLKYVEDVTNVVRRDVEKW-GPFDL-VYGSTQPLGSSCDRCPGWYMFQFHRILQYALPRQESQ
GSG..G...K..E.VTN..RRD.E.W.GP..L.V.GSTQPL...CD.CPGW..FQFHR.LQY..P.....
RetrocopyGSGFEGERWKNSEAVTNIARRDMEGW<GPL*LRVNGSTQPLVYCCDHCPGWCQFQFHRVLQYT*PHPG*L
ParentalRPFFWIFMDNLLLTEDDQETTTRFLQTEAVT-LQDVRGRD-YQNAMRVWSNIPGLKSKHAPLTPKEEEYL
.PFFW.F..N.LLT..DQ.T....L..EA.T.LQDV..R...QNA..V.S......SKHA..T...E...
RetrocopyQPFFWMFVSNPLLTKNDQ-TSAA*LEMEAMT<LQDVCCRS<LQNAVWVCSDMGVRGSKHARDTDTREGTV
Parental-QAQVRSRSKLDAPKVDLLVKNCLL-PLREYFKYFSQNSLPL
........S........LL..NCLL.PL.EYF.YFSQ.SLPL
RetrocopyPESPSQYKSHAGTQSLELL-ENCLL>PLPEYFRYFSQSSLPL

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 .02 RPM 0 .12 RPM
SRP007412_cerebellum 0 .04 RPM 0 .09 RPM
SRP007412_heart 0 .00 RPM 0 .12 RPM
SRP007412_kidney 0 .13 RPM 0 .33 RPM
SRP007412_liver 0 .05 RPM 0 .05 RPM
SRP007412_testis 0 .00 RPM 3 .16 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_2053 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_2053 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_2053 retrocopy 5' end.

Lab - click to see more details

retro_mmus_2053 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2053 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Mus musculus ENSMUSG00000000730 1 retrocopy
retro_mmus_2053 ,


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