RetrogeneDB ID:

retro_mmus_3686

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:X:109388743..109390503(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000082189
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Eif4b
Ensembl ID:ENSMUSG00000058655
Aliases:Eif4b, 2310046H11Rik, AL024095, C85189, Eif4a2
Description:eukaryotic translation initiation factor 4B [Source:MGI Symbol;Acc:MGI:95304]


Retrocopy-Parental alignment summary:






>retro_mmus_3686
GGAACCTGTAGAGGAAGCACCTATGTCCCCAAACCAGTCAGCTGGGCTGATGAAACAGACGATTTGGAAGGAGATGTGTC
AACAACTTGGCATAGTAACAATAATGATGTGTACAGGGCGCCTCCAATTGACCGTTCCATCCTTCCCACTGCTCCAAGGG
CTGCTCAGGAACCCAATATTGACCGGAGCCGTCTTCCAAGTCGCCACCCTACACTGCTTTCCTAGAGAATCTGCCCTACA
ATGTGACAGAAGACTCCATTAAGGATTTCTTTAGAGGATTAAATATCAGCGCTGTAAGCTTACCACGGGAACCCGGAAAT
CCAGACAGGTTGAAAGGTTTCGGCTATGCAGAATTTGAGGACCTGGATTCTCTGCTCAGTACTCTGAGTCTCAATGAAGA
GTCTCTTGGTAACAGGAGAATTCGTGTGGATGTTGCTGGTCAAGCACAGGATAAAGACAGGGATGACCGTTCTTTTGGTC
GAGATAGAAATCGGGATTCTGACAAAACAGACACAGACTGGAGGGCCTGTCCCGCCACAGACAGTTTTGATGACTACACA
CCTAGAAGAGGGGATGATAGCTTTGGGGAGAAGTATCGAGATCATTATGATTCAGACCAGTATCGGGATGGGTATAGGGA
CGGATATCGGGATGGCCCACATAGAGACATGGACCACTATGGGAGCTGGGATCGCTATGGTGACCAAGGCATCAGAGACT
ATGACCGAGGCTATGACTCCAGGATAGGCAGTGGCAGAAGAGCATTTGGAAGTGAGTACCTGAGAGATGATGACTACAGA
GGACATGGGGATCACTATGAAGACCGCTATGACAGACGAGATGATCGGTCCTGGAGCTCCAGGAATGATTACTCTCGGGA
CAATTATAGGCATGATGACAGAGCCCCCCCCCCCCAGAGACCCAGACTGAACCTCAAGCCTCGCAGTGCTCCTAAGGAGG
ATGATGCCTCCGTCAGCACCTCCCAGTCCAGCCGGGTGGCCTCCATCTTTGGAGGAGCGAAGCCTGTTGACACAGCTTTT
AGGGAAAGAGAAGTAGAGAAGTGGCTACAGAAGGAGCAGGAGAAGCTGCAGCATCAGCTGGATGAGCCAAAACTAGACCG
CCAGCCCCGGGAGAGACACCAAAGTTGGCGAAGTGAAGAAACTCAGGAAAGAGAATGGTCGAGGACAGGAAGTGAGTCAT
CGCAGACTGGGGCCTCGGCCACATCTGGCAGAAATACACGATGCAGAGAGAGTGAGAACTCTCTAGAAAATGAAACCCTC
AATAAAGAAGAAGACTGTCACTCTCCGACCTCTAAGCCTCCTAAACCTGACCAGCCTCTAAAGGTAGTGTCAGCCCCTCC
ACCAAAGGAGAATGTGTGGGTGAAGCGAAGCTCTAACCCTCCTGCTCAATCTCAGAACTCAGACACAGAGCAGACGTCCC
CTACAAGTGGTGGAGGGAAAGTAGCTCCAGTCCAGCCCTCTGAGGAAGGACCATCAAGGAAAGATGGAAATAAAGTGGAT
GTGGTGAGTGCCACACAAGGCCAAACTGGAAGCTCCAACCGTGGTCCCGGGGATAGAGGGAACAGAGACCACTGGAAGGA
GTTGGATAGGAAGGATGGCAAAAAAGATCAAGACTCCAGATCTGCACCTTAGCCAAAGAAACCTGAGGAGAATCTGGCCT
CTAAGTTCAATTCTGCAAGCAACTATGTTGCTCTGTCTGTGGACGGTGAGGATGAGGATGAAGGAGACGACTGCACTGAG

ORF - retro_mmus_3686 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.39 %
Parental protein coverage: 95.91 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalGTGGGSTYVPKPVSWADETDDLEGDVSTTWHSNDDDVYRAPPIDRSILPTAPRAAREPNIDRSRLP-KSP
GT..GSTYVPKPVSWADETDDLEGDVSTTWHSN..DVYRAPPIDRSILPTAPRAA.EPNIDRSRLP.KSP
RetrocopyGTCRGSTYVPKPVSWADETDDLEGDVSTTWHSNNNDVYRAPPIDRSILPTAPRAAQEPNIDRSRLP<KSP
ParentalPYTAFLGNLPYDVTEDSIKDFFRGLNISAVRLPREPSNPDRLKGFGYAEFEDLDSLLSALSLNEESLGNR
PYTAFL.NLPY.VTEDSIKDFFRGLNISAV.LPREP.NPDRLKGFGYAEFEDLDSLLS.LSLNEESLGNR
RetrocopyPYTAFLENLPYNVTEDSIKDFFRGLNISAVSLPREPGNPDRLKGFGYAEFEDLDSLLSTLSLNEESLGNR
ParentalRIRVDVADQAQDKDRDDRSFGRDRNRDSDKTDTDWRARPTTDSFDDYPPRRGDDSFGDKYRDRYDSDRYR
RIRVDVA.QAQDKDRDDRSFGRDRNRDSDKTDTDWRA.P.TDSFDDY.PRRGDDSFG.KYRD.YDSD...
RetrocopyRIRVDVAGQAQDKDRDDRSFGRDRNRDSDKTDTDWRACPATDSFDDYTPRRGDDSFGEKYRDHYDSDXXX
ParentalDGYRDGYRDGPRRDMDRYGGRDRYDDRGSRDYDRGYDSRIGSGRRAFGSGYRRDDDYRGGGDRYEDRYDR
..........P.RDMD.YG..DRY.D.G.RDYDRGYDSRIGSGRRAFGS.Y.RDDDYRG.GD.YEDRYDR
RetrocopyXXXXXXXXXXPHRDMDHYGSWDRYGDQGIRDYDRGYDSRIGSGRRAFGSEYLRDDDYRGHGDHYEDRYDR
ParentalRDDRSWSSRDDYSRDDYRRDDRGPPQ-RPRLNLKPRSAPKEDDASASTSQSSRAASIFGGAKPVDTAARE
RDDRSWSSR.DYSRD.YR.DDR.....RPRLNLKPRSAPKEDDAS.STSQSSR.ASIFGGAKPVDTA.RE
RetrocopyRDDRSWSSRNDYSRDNYRHDDRXXXXXRPRLNLKPRSAPKEDDASVSTSQSSRVASIFGGAKPVDTAFRE
ParentalREVEERLQKEQEKLQRQLDEPKLDRRPRERHPSWRSEETQERERSRTGSESSQTGASATSGRNTRRRESE
REVE..LQKEQEKLQ.QLDEPKLDR.PRERH.SWRSEETQERE.SRTGSESSQTGASATSGRNTR.RESE
RetrocopyREVEKWLQKEQEKLQHQLDEPKLDRQPRERHQSWRSEETQEREWSRTGSESSQTGASATSGRNTRCRESE
ParentalKSLENETLNKEEDCHSPTSKPPKPDQPLKVMPAPPPKENAWVKRSSNPPARSQSSDTEQPSPTSGGGKVA
.SLENETLNKEEDCHSPTSKPPKPDQPLKV..APPPKEN.WVKRSSNPPA.SQ.SDTEQ.SPTSGGGKVA
RetrocopyNSLENETLNKEEDCHSPTSKPPKPDQPLKVVSAPPPKENVWVKRSSNPPAQSQNSDTEQTSPTSGGGKVA
ParentalAVQPPEEGPSRKDGNKVDVVGATQGQAGSCSRGPGDGGSRDHWKDLDRKDGKKDQDSRSAPEPKKPEENP
.VQP.EEGPSRKDGNKVDVV.ATQGQ.GS..RGPGD.G.RDHWK.LDRKDGKKDQDSRSAP.PKKPEEN.
RetrocopyPVQPSEEGPSRKDGNKVDVVSATQGQTGSSNRGPGDRGNRDHWKELDRKDGKKDQDSRSAP*PKKPEENL
ParentalASKFSSASKYAALSVDGEDEDEGDDCTE
ASKF.SAS.Y.ALSVDGEDEDEGDDCTE
RetrocopyASKFNSASNYVALSVDGEDEDEGDDCTE

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 165 .60 RPM
SRP007412_cerebellum 0 .04 RPM 193 .66 RPM
SRP007412_heart 0 .06 RPM 211 .19 RPM
SRP007412_kidney 0 .08 RPM 349 .79 RPM
SRP007412_liver 0 .03 RPM 287 .97 RPM
SRP007412_testis 0 .91 RPM 180 .07 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_mmus_3686 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_3686 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_3686 retrocopy 5' end.

Lab - click to see more details

retro_mmus_3686 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_3686 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 18 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000120232 retrocopies
retro_amel_1107, retro_amel_559,
Canis familiaris ENSCAFG000000071172 retrocopies
retro_cfam_1447, retro_cfam_936,
Choloepus hoffmanni ENSCHOG000000016082 retrocopies
retro_chof_1310, retro_chof_366,
Callithrix jacchus ENSCJAG000000181762 retrocopies
retro_cjac_1717, retro_cjac_2001,
Cavia porcellus ENSCPOG000000055953 retrocopies
retro_cpor_278, retro_cpor_752, retro_cpor_937,
Homo sapiens ENSG000000630467 retrocopies
retro_hsap_1686, retro_hsap_2639, retro_hsap_2698, retro_hsap_3767, retro_hsap_4196, retro_hsap_4848, retro_hsap_4891,
Gorilla gorilla ENSGGOG000000136955 retrocopies
retro_ggor_1233, retro_ggor_1263, retro_ggor_1882, retro_ggor_1883, retro_ggor_3024,
Loxodonta africana ENSLAFG000000095341 retrocopy
retro_lafr_294,
Macropus eugenii ENSMEUG000000123412 retrocopies
retro_meug_1054, retro_meug_585,
Macaca mulatta ENSMMUG000000010625 retrocopies
retro_mmul_1428, retro_mmul_2384, retro_mmul_2589, retro_mmul_731, retro_mmul_783,
Mus musculus ENSMUSG000000407311 retrocopy
retro_mmus_3659,
Mus musculus ENSMUSG00000058655 1 retrocopy
retro_mmus_3686 ,
Nomascus leucogenys ENSNLEG000000177273 retrocopies
retro_nleu_2371, retro_nleu_2601, retro_nleu_721,
Pongo abelii ENSPPYG000000258487 retrocopies
retro_pabe_1388, retro_pabe_1560, retro_pabe_2283, retro_pabe_260, retro_pabe_3532, retro_pabe_3768, retro_pabe_506,
Rattus norvegicus ENSRNOG000000101032 retrocopies
retro_rnor_2467, retro_rnor_2972,
Ictidomys tridecemlineatus ENSSTOG000000068001 retrocopy
retro_itri_604,
Tupaia belangeri ENSTBEG000000054232 retrocopies
retro_tbel_2363, retro_tbel_4167,
Tarsius syrichta ENSTSYG000000128801 retrocopy
retro_tsyr_452,


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