RetrogeneDB ID:

retro_mmus_3634

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:X:70420718..70422454(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000084193
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Ythdf2
Ensembl ID:ENSMUSG00000040025
Aliases:Ythdf2, 9430020E02Rik, HGRG8, NY-REN-2
Description:YTH domain family 2 [Source:MGI Symbol;Acc:MGI:2444233]


Retrocopy-Parental alignment summary:






>retro_mmus_3634
ATGTCAGCCAGCAGCCTCTTGGAGCAGAGACCAAAAGGACAAGTAAACAAAGTACGAAATGGTTCTGTGCATCAAAAGGA
TGGACTAAATGATGATGATTTTGAACGTTACTTGAGCCTACAGGCAAGGCCGAATAATGCATATACTGCCATGTCAGACT
CCTACTTACCCAGTTACTACAGCCCCTCCACTGGCTTTTCCTATTCTTTGGGTTAAGCGGCTTGGTCTACTGAAGGCAAC
ACAGCCATGCCCTATCTAACTTCTTATGGACAACTGAGCAACGGAGAGCCCCACTTTCTACCAGATGCAATGTTTGGGCA
ACCAGGAGCCCTAGGTAGCATCCCATTTCTTGGTCAGCATAGTTTTAATTTTTTTCCCAGTGGGATTGACTTCTCTGCAT
GGGGAAATAACAGTTCTCAGGGACAGTCTACTCAAAGCTCTGGATATAGTAGCAATTATGCTTATGCACCCAGCTCCTTA
GGTGGAGCCATGATTGATGGACAGTCAGCTTTTGCCAATGAGACCCTCAATAAAGCTCCTGGCATGAATACTACAGACCA
AAGGATGGCAGCACTGAAACTAGGTAGCACAGAAGTTTCAAGCAGTGTTCCAAAAGGTGTAGGCTCTGCTGTTGGTAGTG
GGTCCATCACTAGTAACATTGTGGCTTCTAGCAGTTTGCCTCCAGCTACTATTGCTCCTCCAAAACCAGCATCTTGGGCT
GATATTGCTAGCAAGCCTGCAGAATAACAACCTAAACTGAAGACCAAGAATGGCATTGCAGGATCAAGTCTTCCACCACC
CCCAATAAAGCATAACATGGATATTGGAACTTGAGATAACAAGGGTCCCATGTCAAAAGCCCCCTCACAGGCTTTGGTTC
AAAATATAGGCCAGCCAACCCAGGGATCTCCTCAGCCTGTCAGACAGCAGGTCAATAATAGCCCACCAGTGGCTCAGACA
TCAGTAGGGCAACAGACACAGCCTTTGCCTCCACCTCCACCACAGCCTGCTCAGATCTCAGTCCAGCAACAGGCAGCTCA
GCCAACTTGCTGGGTAGCACCTCGGAACCGTGGCAGTGGTTTCGGTCATAATGGGGTGGCTGGTAATGGAGTAGGACAGT
CTCAGGCAGGTTCTGATCTACTCCTTCAGAGCCTCACCCAGTGTTGGAGAAACTTCGGTCCATTAATAACTATAACACTA
AAGATTTCGACTGGAATCTGAAACATGGTCGGGTTTTCATCATTAAGAGCTACTCTGAGGATGATATCCACCTTTCCATT
AAGTATAATATCTGGTGCAGCACAGAGCAAGGTAACAAGATACTGGATGCCACCTATCGGTCCATGAATGGGAAGGGCCC
TGCGTACTTACTTTTCAGTGTCAACGGCAGTGGACACTTCTGTGGAATTTCAGAGATGAAATCTGCTGTGGACTACAACA
CGTGTGCAGGTTTGTGGTCCCAGGACAAATGGAAGGTTCGTTTCAATGTCAGATGGATTTTTGTGAAGGACATTCCCAAT
AGCCAACTGCAACACATTCGTCTAGAGAACAACGAAAATAAACCAGTGACCAACTCTAGGGACACTCAGGAAGTGCCTCT
GGAAAAAGCTAAGCAGGTGTTGAAAATCATAGCCAGCTACAAGCACACCACTTCCATTTTTGATGACTTCTCACACTATG
AGAAATGCCAAGAGGAAGAAGAAAGTGTTAAAAAGGAACGTCAAGGTCGTGGGAAA

ORF - retro_mmus_3634 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.93 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSASSLLEQRPKGQGNKVQNGSVHQKDGLNDDDFEPYLSPQARPNNAYTAMSDSYLPSYYSPSIGFSYSL
MSASSLLEQRPKGQ.NKV.NGSVHQKDGLNDDDFE.YLS.QARPNNAYTAMSDSYLPSYYSPS.GFSYSL
RetrocopyMSASSLLEQRPKGQVNKVRNGSVHQKDGLNDDDFERYLSLQARPNNAYTAMSDSYLPSYYSPSTGFSYSL
ParentalGEAAWSTGGDTAMPYLTSYGQLSNGEPHFLPDAMFGQPGALGSTPFLGQHGFNFFPSGIDFSAWGNNSSQ
G.AAWST.G.TAMPYLTSYGQLSNGEPHFLPDAMFGQPGALGS.PFLGQH.FNFFPSGIDFSAWGNNSSQ
RetrocopyG*AAWSTEGNTAMPYLTSYGQLSNGEPHFLPDAMFGQPGALGSIPFLGQHSFNFFPSGIDFSAWGNNSSQ
ParentalGQSTQSSGYSSNYAYAPSSLGGAMIDGQSAFANETLNKAPGMNTIDQGMAALKLGSTEVASSVPKVVGSA
GQSTQSSGYSSNYAYAPSSLGGAMIDGQSAFANETLNKAPGMNT.DQ.MAALKLGSTEV.SSVPK.VGSA
RetrocopyGQSTQSSGYSSNYAYAPSSLGGAMIDGQSAFANETLNKAPGMNTTDQRMAALKLGSTEVSSSVPKGVGSA
ParentalVGSGSITSNIVASSSLPPATIAPPKPASWADIASKPAKQQPKLKTKNGIAGSSLPPPPIKHNMDIGTWDN
VGSGSITSNIVASSSLPPATIAPPKPASWADIASKPA..QPKLKTKNGIAGSSLPPPPIKHNMDIGT.DN
RetrocopyVGSGSITSNIVASSSLPPATIAPPKPASWADIASKPAE*QPKLKTKNGIAGSSLPPPPIKHNMDIGT*DN
ParentalKGPVAKAPSQALVQNIGQPTQGSPQPVGQQANNSPPVAQASVGQQTQPLPPPPPQPAQLSVQQQAAQPTR
KGP..KAPSQALVQNIGQPTQGSPQPV.QQ.NNSPPVAQ.SVGQQTQPLPPPPPQPAQ.SVQQQAAQPT.
RetrocopyKGPMSKAPSQALVQNIGQPTQGSPQPVRQQVNNSPPVAQTSVGQQTQPLPPPPPQPAQISVQQQAAQPTC
ParentalWVAPRNRGSGFGHNGVDGNGVGQSQAGSG-STPSEPHPVLEKLRSINNYNPKDFDWNLKHGRVFIIKSYS
WVAPRNRGSGFGHNGV.GNGVGQSQAGS..STPSEPHPVLEKLRSINNYN.KDFDWNLKHGRVFIIKSYS
RetrocopyWVAPRNRGSGFGHNGVAGNGVGQSQAGSD<STPSEPHPVLEKLRSINNYNTKDFDWNLKHGRVFIIKSYS
ParentalEDDIHRSIKYNIWCSTEHGNKRLDAAYRSMNGKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCAGVWSQD
EDDIH.SIKYNIWCSTE.GNK.LDA.YRSMNGKGP.YLLFSVNGSGHFCG..EMKSAVDYNTCAG.WSQD
RetrocopyEDDIHLSIKYNIWCSTEQGNKILDATYRSMNGKGPAYLLFSVNGSGHFCGISEMKSAVDYNTCAGLWSQD
ParentalKWKGRFDVRWIFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKIIASYKHTTSIFDDFSH
KWK.RF.VRWIFVKD.PNSQL.HIRLENNENKPVTNSRDTQEVPLEKAKQVLKIIASYKHTTSIFDDFSH
RetrocopyKWKVRFNVRWIFVKDIPNSQLQHIRLENNENKPVTNSRDTQEVPLEKAKQVLKIIASYKHTTSIFDDFSH
ParentalYEKRQEEEESVKKERQGRGK
YEK.QEEEESVKKERQGRGK
RetrocopyYEKCQEEEESVKKERQGRGK

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 31 .80 RPM
SRP007412_cerebellum 0 .00 RPM 25 .01 RPM
SRP007412_heart 0 .00 RPM 17 .99 RPM
SRP007412_kidney 0 .00 RPM 25 .31 RPM
SRP007412_liver 0 .00 RPM 21 .52 RPM
SRP007412_testis 0 .00 RPM 26 .85 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_3634 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_3634 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_3634 retrocopy 5' end.

Lab - click to see more details

retro_mmus_3634 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_3634 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 ENSMUSG00000040025 2 retrocopies
retro_mmus_3463, retro_mmus_3634 ,


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