RetrogeneDB ID:

retro_mmus_121

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:4:88720148..88722002(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000070923
Aliases:Klhl9, 8030469P05, C530050O22Rik, ENSMUSG00000070923, mKIAA1354
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Klhl13
Ensembl ID:ENSMUSG00000036782
Aliases:Klhl13, 1200009K10Rik, AI451128, Bklhd2, D130072F20Rik, mKIAA1309
Description:kelch-like 13 [Source:MGI Symbol;Acc:MGI:1914705]


Retrocopy-Parental alignment summary:






>retro_mmus_121
ATGAAGGTGTCTCTGGGTAACGGCGACATGGGCGTCTCTGCCCACCTGCAGCCTTGCAAGTCTGGAACTACGCGGTTTTT
TACCAGCAACACGCACAGTTCGGTTGTATTGCAAGGCTTTGATCAGCTCAGAATAGAGGGCCTACTTTGTGACGTGACGC
TGGTACCTGGCGATGGAGAGGAAATCTTCCCGGTTCATAGAGCCATGATGGCGTCTGCCAGTGATTATTTCAAGGCCATG
TTCACTGGAGGAATGAAAGAGAAAGATTTGATGTGCATCAAGCTTCATGGGGTGAACAAAGTTGGTCTGAAGAAAATCAT
TGATTTTATTTATACTGCAAAACTGTCTCTTAATATGGACAATCTTCAGGACACTCTTGAAGCTGCCAGCTTTCTACAGA
TCTTGCCGGTTTTGGATTTTTGTAAAGTATTTCTTATATCAGGCGTCTCTTTGGATAACTGTGTGGAGGTTGGCCGGATT
GCTAACACCTACAATCTTATAGAAGTGGATAAATACGTAAATAATTTCATCCTGAAGAACTTTCCTGCCTTGTTGAATAC
TGGGGAGTTTCTGAAACTCCCCTTTGAACGGCTTGCCTTTGTGCTTTCCAGCAATAGTCTCAAGCACTGTTCGGAACTTG
AGCTCTTCAAGGCAGCCTGCCGCTGGCTGAGGCTGGAAGACCCTCGGATGGACTATGCCGCAAAATTAATGAAGAATATT
CGCTTTCCACTGATGACACCACAGGATCTCATCAACTATGTGCAGACAGTAGATTTCATGAGAACAGACAATACCTGTGT
GAATTTACTTTTGGAAGCAAGCAATTACCAAATGATGCCGTATATGCAGCCGGTGATGCAGTCGGACAGAACTGCCATTC
GATCTGATTCTACTCATTTGGTTACCTTAGGAGGAGTTTTGAGACAACAGCTAGTTGTCAGTAAAGAGTTACGAATGTAC
GACGAAAGGGCGCAGGAGTGGAAGTCGTTAGCGCCCATGGATGCTCCTCGATACCAGCATGGCATTGCTGTTATTGGAAA
TTTCCTTTATGTAGTTGGTGGCCAGAGTAATTATGATACAAAAGGAAAAACGGCTGTTGATACAGTTTTCAGATTTGATC
CTCGTTATAATAAGTGGATGCAGGTGGCATCATTAAACGAAAAGCGCACATTCTTTCACCTGAGTGCCCTCAAAGGACAT
TTATATGCAGTTGGTGGGCGCAGTGCAGCTGGTGAACTGGCCACAGTAGAATGTTACAACCCAAGAATGAATGAATGGAG
CTACGTTGCAAAGATGAGTGAACCCCACTATGGCCATGCTGGAACAGTATATGGGGGTTTAATGTATATTTCCGGAGGAA
TCACTCATGACACTTTCCAAAATGAGCTCATGTGTTTTGACCCAGATACAGACAAATGGACACAGAAGGCTCCTATGACT
ACAGTCCGAGGTCTGCATTGCATGTGTACAGTTGGAGACAAGCTGTATGTCATCGGTGGCAACCACTTCAGAGGAACAAG
TGATTATGATGATGTCCTAAGCTGCGAATACTATTCGCCAACTCTTGACCAGTGGACACCAATTGCTGCTATGCTGAGAG
GTCAGAGTGATGTTGGAGTTGCAGTCTTTGAAAACAAAATCTATGTTGTTGGTGGATATTCTTGGAATAACCGGTGCATG
GTAGAAATTGTCCAGAAATATGACCCAGAAAAAGACGAGTGGCATAAAGTTTTTGATCTTCCTGAGTCGCTGGGTGGCAT
TCGGGCTTGCACTCTCACAGTTTTTCCACCTGAAGAAAACCCTGGGTCACCTTCTAGAGAATCACCTCTTTCAGCACCTT
CAGATCATTCTTAG

ORF - retro_mmus_121 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.23 %
Parental protein coverage: 94.44 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLKLCLGS-EMGLSSHLQSCKAGSTRIFTSNSHSSVVLQGFDQLRLDGLLCDVTLMPGDTDDAYPVHRVMM
.K..LG...MG.S.HLQ.CK.G.TR.FTSN.HSSVVLQGFDQLR..GLLCDVTL.PGD.....PVHR.MM
RetrocopyMKVSLGNGDMGVSAHLQPCKSGTTRFFTSNTHSSVVLQGFDQLRIEGLLCDVTLVPGDGEEIFPVHRAMM
ParentalASASDYFKAMFTGGMKEQELMCIKLHGVSRVGLRKIIDFIYTAKLSLNMDTLQDTLEAASFLQILPVLDF
ASASDYFKAMFTGGMKE..LMCIKLHGV..VGL.KIIDFIYTAKLSLNMD.LQDTLEAASFLQILPVLDF
RetrocopyASASDYFKAMFTGGMKEKDLMCIKLHGVNKVGLKKIIDFIYTAKLSLNMDNLQDTLEAASFLQILPVLDF
ParentalCKVFLISGVTLDNCVEVGRIANTYHLTEVDKYVNSFVLKNFAALLSTGEFLKLPFERLAFVLSSNSLKRC
CKVFLISGV.LDNCVEVGRIANTY.L.EVDKYVN.F.LKNF.ALL.TGEFLKLPFERLAFVLSSNSLK.C
RetrocopyCKVFLISGVSLDNCVEVGRIANTYNLIEVDKYVNNFILKNFPALLNTGEFLKLPFERLAFVLSSNSLKHC
ParentalTELDLFKATCRWLRLEEPRMDVAAKLMKNIRFPLMTPQELINYVQTVDFMRTDNTCVNLLLEASNYQMMP
.EL.LFKA.CRWLRLE.PRMD.AAKLMKNIRFPLMTPQ.LINYVQTVDFMRTDNTCVNLLLEASNYQMMP
RetrocopySELELFKAACRWLRLEDPRMDYAAKLMKNIRFPLMTPQDLINYVQTVDFMRTDNTCVNLLLEASNYQMMP
ParentalFMQPVMQSDRTAIRSDTTRLVTLGGVLRQQLVVSKELRMYDEKTHEWKSLAPMDAPRYQHGIAVIGNFLY
.MQPVMQSDRTAIRSD.T.LVTLGGVLRQQLVVSKELRMYDE...EWKSLAPMDAPRYQHGIAVIGNFLY
RetrocopyYMQPVMQSDRTAIRSDSTHLVTLGGVLRQQLVVSKELRMYDERAQEWKSLAPMDAPRYQHGIAVIGNFLY
ParentalVVGGQSNYDTKGKTAVDTVFRFDPRYNKWIQVASLNEKRTFFHLSALKGFLYAVGGRNAAGELPTVECYN
VVGGQSNYDTKGKTAVDTVFRFDPRYNKW.QVASLNEKRTFFHLSALKG.LYAVGGR.AAGEL.TVECYN
RetrocopyVVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSALKGHLYAVGGRSAAGELATVECYN
ParentalPRTNEWTYVAKMNEPHYGHAGTVYGGVMYISGGITHDTFQKELMCFDPDTDKWTQKAPMTTVRGLHCMCT
PR.NEW.YVAKM.EPHYGHAGTVYGG.MYISGGITHDTFQ.ELMCFDPDTDKWTQKAPMTTVRGLHCMCT
RetrocopyPRMNEWSYVAKMSEPHYGHAGTVYGGLMYISGGITHDTFQNELMCFDPDTDKWTQKAPMTTVRGLHCMCT
ParentalVGDRLYVIGGNHFRGTSDYDDVLSCEYYSPILDQWTPIASMLRGQSDVGVAVFENKIYVVGGYSWNNRCM
VGD.LYVIGGNHFRGTSDYDDVLSCEYYSP.LDQWTPIA.MLRGQSDVGVAVFENKIYVVGGYSWNNRCM
RetrocopyVGDKLYVIGGNHFRGTSDYDDVLSCEYYSPTLDQWTPIAAMLRGQSDVGVAVFENKIYVVGGYSWNNRCM
ParentalVEIVQKYDPEKNEWHKVFDLPESLGGIRACTLTVYPPEEATPSPSRESPLSGP
VEIVQKYDPEK.EWHKVFDLPESLGGIRACTLTV.PPEE...SPSRESPLS.P
RetrocopyVEIVQKYDPEKDEWHKVFDLPESLGGIRACTLTVFPPEENPGSPSRESPLSAP

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 55 .23 RPM 46 .82 RPM
SRP007412_cerebellum 49 .02 RPM 25 .27 RPM
SRP007412_heart 39 .63 RPM 20 .23 RPM
SRP007412_kidney 47 .66 RPM 11 .99 RPM
SRP007412_liver 31 .19 RPM 7 .73 RPM
SRP007412_testis 12 .76 RPM 0 .82 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_mmus_121 in 3 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001XVA POLR2A 4:88721749..88722764
ENCFF001YIJ POLR2A 4:88721747..88722936
ENCFF001YKA POLR2A 4:88721622..88722894

EST - click to see more details

No EST(s) were mapped for retro_mmus_121 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_1068316 libraries1 library4 libraries40 libraries1021 libraries

The graphical summary, for retro_mmus_121 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_121 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_121 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Rattus norvegicus retro_rnor_154
Parental genes homology:
Parental genes homology involve 21 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000017821 retrocopy
retro_amel_749,
Bos taurus ENSBTAG000000005011 retrocopy
retro_btau_44,
Canis familiaris ENSCAFG000000182721 retrocopy
retro_cfam_422,
Callithrix jacchus ENSCJAG000000024471 retrocopy
retro_cjac_3406,
Cavia porcellus ENSCPOG000000112681 retrocopy
retro_cpor_590,
Equus caballus ENSECAG000000082371 retrocopy
retro_ecab_622,
Loxodonta africana ENSLAFG000000081221 retrocopy
retro_lafr_1018,
Myotis lucifugus ENSMLUG000000273931 retrocopy
retro_mluc_204,
Macaca mulatta ENSMMUG000000022931 retrocopy
retro_mmul_42,
Mustela putorius furoENSMPUG000000017301 retrocopy
retro_mputfur_169,
Mus musculus ENSMUSG00000036782 1 retrocopy
retro_mmus_121 ,
Nomascus leucogenys ENSNLEG000000147361 retrocopy
retro_nleu_1031,
Oryctolagus cuniculus ENSOCUG000000019931 retrocopy
retro_ocun_254,
Pongo abelii ENSPPYG000000206581 retrocopy
retro_pabe_60,
Pteropus vampyrus ENSPVAG000000159891 retrocopy
retro_pvam_1485,
Rattus norvegicus ENSRNOG000000140291 retrocopy
retro_rnor_154,
Sus scrofa ENSSSCG000000126371 retrocopy
retro_sscr_51,
Ictidomys tridecemlineatus ENSSTOG000000120351 retrocopy
retro_itri_124,
Tarsius syrichta ENSTSYG000000025211 retrocopy
retro_tsyr_19,
Tursiops truncatus ENSTTRG000000140981 retrocopy
retro_ttru_26,
Vicugna pacos ENSVPAG000000030911 retrocopy
retro_vpac_8,




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