RetrogeneDB ID:

retro_mmus_347

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:1:98457767..98459159(+)
Located in intron of:ENSMUSG00000026336
Retrocopy
information
Ensembl ID:ENSMUSG00000089791
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Stk38l
Ensembl ID:ENSMUSG00000001630
Aliases:Stk38l, 4930473A22Rik, B230328I19, Ndr2, Ndr54
Description:serine/threonine kinase 38 like [Source:MGI Symbol;Acc:MGI:1922250]


Retrocopy-Parental alignment summary:






>retro_mmus_347
ATGGCAATGACGGCAGGGGCAACAACTACCTTTCCTATGAGCAACCATACCCGGGAAAGAGTAACTGTGGCCAAGCTCAC
ACTGGAGAATTTTTACAGCAACCTAATTTTACAGCATGAAGAGAGAGAAACCAGGCAGAAGAAGTTAGAAGTGGCTATGG
AAGAAGAAGGATTGGCAGATGAGGAGAAAAAGTTACGTCGATCGCAGCATGCTCATAAAGAAACAGAGTTCTTACGCCTT
AAGAGGACCAGACTTGGCCTGGATGACTTTGAGTCTCTGAAGGTTATAGGAAGAGGAGCTTTCGGAGAGGTGCGGCTGGT
CCAGAAGAAAGACACGGGGCACATCTATGCCATGAAGATCCTGAGGAAAGCTGACATGCTTGAGAAAGAGCAGGTGGCTC
ATATCCAAGCAGAAAGGGACATTTTGGTGGAAGCAGATGGAGCCTGGGTGGTGAAGATGTTCTACAGTTTTCAGGACAAA
CGGAATCTCTATCTCATCATGGAATTTCTTCCTGGAGGTGACATGATGACATTGCTGATGAAGAAGGACACCTTAACAGA
AGAAGAGACACAGTTCTACATCTCAGAGACTGTCTTGGCGATAGATGCAATTCACCAGCTGGGCTTCATCCACTGGGACA
TCAAACCAGACAACCTTTTACTAGATGCCAAGGGACATGTAAAATTATCTGATTTTGGTTTGTGCACGGGGTTAAAGAAA
GCTCACAGGACTGAATTGTACAGAAACCTCACACATAACCCGCCAAGCGACTTCTCATTTCAGAACATGAATTCAAAGTG
GACAGCAGAGACATGGAAGAAGAACAGGAGACAGCTGGCTTACTCCACAGTTGGAACAGCAGACTACATTGCTCCAGAAG
TATTCATGCAGACTGGCTCTAACAAATTGTGTGACTGGTGGTCCTTGGGAGTGATTATGTACGAGATGCTAATAGGCTTT
CCACCTTTCTGCTCCGAAACACCACAAGAAACGTACAGAAAAGTTATGAGCTGGAAGGAGACGCTGGCATTTCCTCCGGA
AGTGCCCGTCTCTGAGAAAGCCAAGGACTTGATTCTCAGATTTTGTACTGATTCTGAAAACAGAATTGGGAATGGTGGTG
TGGAAGAAATCAGAGGTCATCCGTTCTTTGAGGGTGTAGACTGGGGGCACATAAGGGAAAGACCAGCAGCTATTCCTATA
GAAATCCGGAGTATAGATGACACCTCAAACTTTGATGACTTCCCCGAGTCTGATATCTTACAGCCAGTGCTGAATACCAC
AGAGCCCGACTACAAATCCAAAGACTGGGTTTTTCTCAATTACACCTACAAAAGGTTTGAAGGGCTGATCCAGAGAGGCT
CCATTCCTACATACATGAAAGCTGGGAAGTTA

ORF - retro_mmus_347 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.41 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAMTAGATTTFPMSNHTRERVTVAKLTLENFYSNLILQHEERETRQKKLEVAMEEEGLADEEKKLRRSQH
MAMTAGATTTFPMSNHTRERVTVAKLTLENFYSNLILQHEERETRQKKLEVAMEEEGLADEEKKLRRSQH
RetrocopyMAMTAGATTTFPMSNHTRERVTVAKLTLENFYSNLILQHEERETRQKKLEVAMEEEGLADEEKKLRRSQH
ParentalARKETEFLRLKRTRLGLDDFESLKVIGRGAFGEVRLVQKKDTGHIYAMKILRKADMLEKEQVAHIRAERD
A.KETEFLRLKRTRLGLDDFESLKVIGRGAFGEVRLVQKKDTGHIYAMKILRKADMLEKEQVAHI.AERD
RetrocopyAHKETEFLRLKRTRLGLDDFESLKVIGRGAFGEVRLVQKKDTGHIYAMKILRKADMLEKEQVAHIQAERD
ParentalILVEADGAWVVKMFYSFQDKRNLYLIMEFLPGGDMMTLLMKKDTLTEEETQFYISETVLAIDAIHQLGFI
ILVEADGAWVVKMFYSFQDKRNLYLIMEFLPGGDMMTLLMKKDTLTEEETQFYISETVLAIDAIHQLGFI
RetrocopyILVEADGAWVVKMFYSFQDKRNLYLIMEFLPGGDMMTLLMKKDTLTEEETQFYISETVLAIDAIHQLGFI
ParentalHRDVKPDNLLLDAKGHVKLSDFGLCTGLKKAHRTEFYRNLTHNPPSDFSFQNMNSKRKAETWKKNRRQLA
H.D.KPDNLLLDAKGHVKLSDFGLCTGLKKAHRTE.YRNLTHNPPSDFSFQNMNSK..AETWKKNRRQLA
RetrocopyHWDIKPDNLLLDAKGHVKLSDFGLCTGLKKAHRTELYRNLTHNPPSDFSFQNMNSKWTAETWKKNRRQLA
ParentalYSTVGTPDYIAPEVFMQTGYNKLCDWWSLGVIMYEMLIGFPPFCSETPQETYRKVMSWKETLAFPPEVPV
YSTVGT.DYIAPEVFMQTG.NKLCDWWSLGVIMYEMLIGFPPFCSETPQETYRKVMSWKETLAFPPEVPV
RetrocopyYSTVGTADYIAPEVFMQTGSNKLCDWWSLGVIMYEMLIGFPPFCSETPQETYRKVMSWKETLAFPPEVPV
ParentalSEKAKDLILRFCTDSENRIGNGGVEEIKGHPFFEGVDWGHIRERPAAIPIEIRSIDDTSNFDDFPESDIL
SEKAKDLILRFCTDSENRIGNGGVEEI.GHPFFEGVDWGHIRERPAAIPIEIRSIDDTSNFDDFPESDIL
RetrocopySEKAKDLILRFCTDSENRIGNGGVEEIRGHPFFEGVDWGHIRERPAAIPIEIRSIDDTSNFDDFPESDIL
ParentalQPVPNTTEPDYKSKDWVFLNYTYKRFEGLTQRGSIPTYMKAGKL
QPV.NTTEPDYKSKDWVFLNYTYKRFEGL.QRGSIPTYMKAGKL
RetrocopyQPVLNTTEPDYKSKDWVFLNYTYKRFEGLIQRGSIPTYMKAGKL

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 .12 RPM 25 .30 RPM
SRP007412_cerebellum 0 .13 RPM 21 .97 RPM
SRP007412_heart 0 .03 RPM 16 .78 RPM
SRP007412_kidney 0 .37 RPM 17 .98 RPM
SRP007412_liver 0 .08 RPM 16 .28 RPM
SRP007412_testis 0 .69 RPM 8 .51 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_347 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_347 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_67957284 libraries427 libraries336 libraries21 libraries4 libraries

The graphical summary, for retro_mmus_347 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_347 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_347 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000255731 retrocopy
retro_dnov_1680,
Monodelphis domestica ENSMODG000000166361 retrocopy
retro_mdom_1913,
Mus musculus ENSMUSG00000001630 2 retrocopies
retro_mmus_3100, retro_mmus_347 ,


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