RetrogeneDB ID:

retro_mmus_119

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:5:97455312..97456977(-)
Located in intron of:ENSMUSG00000097516
Retrocopy
information
Ensembl ID:ENSMUSG00000050553
Aliases:Gk2, GKTA, Gk-rs2
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Gyk
Ensembl ID:ENSMUSG00000025059
Aliases:Gyk, D930012N15Rik, GK
Description:glycerol kinase [Source:MGI Symbol;Acc:MGI:106594]


Retrocopy-Parental alignment summary:






>retro_mmus_119
ATGGCAGCCTCGAAGCAAACCTCTGCGGGACCGTTGGTAGGAGCGGTGGTCCAGGGAACCAACTCCACTCGCTTTCTAGT
TTTCAATAGCAAAACAGCAGAACTAGTTTGCTCTCATCAGGTGGAACTGACACAAGAATACCCAAAAGAAGGATGGGTGG
AGCAAGACCCCAAGGAAATCCTTAAATCTGTCTATGAGTGCATAGCGAAAGCTTGTGAAAAACTTGCTGAAGTGAACATT
GATATTTCCAACATTAAAGCTATCGGCGTGAGTAACCAGCGGGAAACCACTGTGGTCTGGGACAAGTTCACGGGAGACCC
TCTGTACAATGCCGTGGTGTGGCTTGATCTCAGAACCCAGTCTACTGTGGAGACTCTCACTAAGAAAATCCCAGGAAATA
GCAACTTTGTCAAGTCTAAGACCGGCCTTCCTCTTAGCACTTACTTCAGTGCTGTGAAGCTGCGGTGGATGCTGGACAAC
CTAAGACCCATTCAAAAGGCTGTTGAGGAAGGCAGAGCCATGTTTGGAACCATCGACTCTTGGCTCATCTGGTGTATGAC
CGGAGGAGTCAATGGAGGCATCCATTGCACCGATGTAACAAATGCATGCAGAACGATGCTTTTTAACATCCACTCTTTGG
AATGGGATAAAGATCTCTGTGACTTTTTTGAAATTCCAATGAGCATCCTCCCAAATGTATGCAGTTCTTCTGAGATCTAT
GGCCTGATGACATCAGGGGCCTTGGAAGGCGTGCCAATATCTGGATGTTTGGGGGATCAGTCTGCTGCTTTAGTGGGACA
AATGTGTTTCCATGAAGGTCAAGCCAAAAACACATACGGAACAGGCTGTTTTTTACTATGTAATACAGGCCAGAAATGTG
TGTTTTCTGAACATGGCCTTCTGACCACATTGGCTTACAAACTAGGCAAAAATAAGCCAGTTTTTTATGCCTTAGAAGGT
TCTGTTGCTATAGCTGGTGCTGTTATTCGCTGGCTAAGAGACAATTTCGAAATTATAACAACCTCAGGGGAAGTTGAAAA
TCTTGCAAGAGAGGTAGGCACTTCCTATGGCTGCTACTTTGTCCCAGCCTTTTCGGGGCTGTATGCACCTTACTGGGAAC
CCAGTGCAAGAGGGATAATCTGTGGTCTCACTCAGTTCACCAACAAATGCCATATTGCCTTTGCTGCGTTAGAAGCTGTT
TGTTTCCAAACCCGAGAGATTTTGGATGCCATGAATCGCGACTGTGGAATTCCACTCAGTCATTTGCAGGTCGATGGAGG
AATGACCAACAACAGGATTCTTATGCAGCTACAGGCAGATATTCTGCACATTCCGGTAGTTAAGTCTGTCATGCCTGAAA
CGACGGCCCTGGGAGCTGCCATGGCAGCCGGAGCTGCAGAAGGGGTAAATGTTTGGAGTCTTGAACCTGAAGATTTGTCT
ACGATCTTGATGGAACGATATGAACCACAAATCCAAGCCACAGAGAGTGAAATTCGTTTTTCAACATGGAAGAGAGCAGT
GATGAAGTCAATGGGTTGGGTTACAGCAAAGGACCCTGAAAATGGCGATAACCCTGTCTTCTCTTGTCTGCCCTTGGGTT
TTTTTATAGTGAGTAGCATGACGTTATTAATTGGAGCAAGATGTGTCTCAACTGCTGAAGAGTAA

ORF - retro_mmus_119 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.64 %
Parental protein coverage: 99.46 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAAAKKAVLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVEIKQEFPREGWVEQDPKEILQSVYECIEK
MAA.K....GPLVGAV.QGT.STRFLVFNSKTAEL...HQVE..QE.P.EGWVEQDPKEIL.SVYECI.K
RetrocopyMAASKQTSAGPLVGAVVQGTNSTRFLVFNSKTAELVCSHQVELTQEYPKEGWVEQDPKEILKSVYECIAK
ParentalTCEKLGQLNIDISNIKAIGVSNQRETTVVWDKVTGEPLYNAVVWLDLRTQSTVENLSKRIPGNNNFVKSK
.CEKL...NIDISNIKAIGVSNQRETTVVWDK.TG.PLYNAVVWLDLRTQSTVE.L.K.IPGN.NFVKSK
RetrocopyACEKLAEVNIDISNIKAIGVSNQRETTVVWDKFTGDPLYNAVVWLDLRTQSTVETLTKKIPGNSNFVKSK
ParentalTGLPLSTYFSAVKLRWLLDNVKKVQEAVEENRALFGTIDSWLIWSLTGGIHGGVHCTDVTNASRTMLFNI
TGLPLSTYFSAVKLRW.LDN....Q.AVEE.RA.FGTIDSWLIW..TGG..GG.HCTDVTNA.RTMLFNI
RetrocopyTGLPLSTYFSAVKLRWMLDNLRPIQKAVEEGRAMFGTIDSWLIWCMTGGVNGGIHCTDVTNACRTMLFNI
ParentalHSLEWDKELCEFFGIPMEILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG
HSLEWDK.LC.FF.IPM.ILPNV.SSSEIYGLM..GALEGVPISGCLGDQSAALVGQMCF..GQAKNTYG
RetrocopyHSLEWDKDLCDFFEIPMSILPNVCSSSEIYGLMTSGALEGVPISGCLGDQSAALVGQMCFHEGQAKNTYG
ParentalTGCFLLCNTGHKCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVIRWLRDNLGIIKSSEEIEKLAK
TGCFLLCNTG.KCVFSEHGLLTT.AYKLG..KPV.YALEGSVAIAGAVIRWLRDN..II..S.E.E.LA.
RetrocopyTGCFLLCNTGQKCVFSEHGLLTTLAYKLGKNKPVFYALEGSVAIAGAVIRWLRDNFEIITTSGEVENLAR
ParentalEVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFQTREILDAMNRDCGIPLS
EVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFQTREILDAMNRDCGIPLS
RetrocopyEVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFQTREILDAMNRDCGIPLS
ParentalHLQVDGGMTSNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSLEPEDLSAVTMERFEPQ
HLQVDGGMT.N.ILMQLQADIL.IPVVK..MPETTALGAAMAAGAAEGV.VWSLEPEDLS...MER.EPQ
RetrocopyHLQVDGGMTNNRILMQLQADILHIPVVKSVMPETTALGAAMAAGAAEGVNVWSLEPEDLSTILMERYEPQ
ParentalINAEESEIRYSTWKKAVMKSIGWVTTQSPESGDPSIFCSLPLGFFIVSSMVMLIGARYIS
I.A.ESEIR.STWK.AVMKS.GWVT...PE.GD...F..LPLGFFIVSSM..LIGAR..S
RetrocopyIQATESEIRFSTWKRAVMKSMGWVTAKDPENGDNPVFSCLPLGFFIVSSMTLLIGARCVS

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 .09 RPM 18 .83 RPM
SRP007412_cerebellum 0 .00 RPM 15 .68 RPM
SRP007412_heart 0 .00 RPM 23 .60 RPM
SRP007412_kidney 0 .00 RPM 331 .61 RPM
SRP007412_liver 0 .11 RPM 75 .92 RPM
SRP007412_testis 401 .68 RPM 1 .56 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_119 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_119 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_1167581061 libraries4 libraries1 library0 libraries6 libraries

The graphical summary, for retro_mmus_119 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_119 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_119 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_70
Callithrix jacchus retro_cjac_125
Rattus norvegicus retro_rnor_34
Sus scrofa retro_sscr_59
Canis familiaris retro_cfam_19
Parental genes homology:
Parental genes homology involve 14 parental genes, and 25 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000076333 retrocopies
retro_cjac_125, retro_cjac_3161, retro_cjac_4035,
Cavia porcellus ENSCPOG000000032612 retrocopies
retro_cpor_11, retro_cpor_20,
Echinops telfairi ENSETEG000000082792 retrocopies
retro_etel_2000, retro_etel_247,
Felis catus ENSFCAG000000042641 retrocopy
retro_fcat_140,
Homo sapiens ENSG000001988144 retrocopies
retro_hsap_3087, retro_hsap_3120, retro_hsap_4885, retro_hsap_70,
Loxodonta africana ENSLAFG000000076321 retrocopy
retro_lafr_30,
Monodelphis domestica ENSMODG000000024171 retrocopy
retro_mdom_234,
Mus musculus ENSMUSG00000025059 2 retrocopies
retro_mmus_119 , retro_mmus_97,
Nomascus leucogenys ENSNLEG000000101022 retrocopies
retro_nleu_1650, retro_nleu_771,
Oryctolagus cuniculus ENSOCUG000000130232 retrocopies
retro_ocun_2, retro_ocun_81,
Rattus norvegicus ENSRNOG000000341162 retrocopies
retro_rnor_114, retro_rnor_34,
Sarcophilus harrisii ENSSHAG000000064701 retrocopy
retro_shar_35,
Ictidomys tridecemlineatus ENSSTOG000000087321 retrocopy
retro_itri_1436,
Tarsius syrichta ENSTSYG000000082491 retrocopy
retro_tsyr_29,


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