RetrogeneDB ID:

retro_ogar_3417

Retrocopy
location
Organism:Bushbaby (Otolemur garnettii)
Coordinates:GL873824.1:94173..96469(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOGAG00000028065
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MATR3
Ensembl ID:ENSOGAG00000010607
Aliases:None
Description:matrin 3 [Source:HGNC Symbol;Acc:6912]


Retrocopy-Parental alignment summary:






>retro_ogar_3417
CTTCTTCCCATATTTAACATTGGAAGTAGAGGTTCACTCCCTTTATCTTCTCAACACCGTGGAGATGTAGACCAAGCCAG
TAACATTTTGGCCAGCTTTGGTCTGTCTGCTAGAGACTTAGATGAACTGAGTTGTTATCCAGAGGACAAGATTACTCCTG
AGAATTTGCCCCAGATCCTTCTACAGCGTAAAAGGAGGAGAACTGAAGAAGGCCCTACATTGAGTTATGGTAGAGATGGC
AGATCTGCTACATGGAGCCACCATACAGAGTACCTAGGGATGACTGGGAAGAAAAAAGTCACTTTAGAAGAGATAGTTTT
GATGATCATGGTCCTAGTCTCAACCCAGTGCTTGATTATGACCATGGAAGTCATTCTCAAGAATCTGGTTATTATGACAG
AATGGATTATGAAGATGACAGATTAAGAGATGGAGAAAGGTTTAAGGATGATTCTTTTTTTGGTGAGACCTCGCATAACT
ATCATAAATTTGACAGTGAGTATGAGAGAATGGGACATGGTCCTGGCCCCTTACAAGAGAGATCTCTCTTTGAGAAAAAG
AGGGGTGCTCCTCCAAGTAGCAATATTGAAGACTTCCATGGACTCTTACCGAAGGGTTATCCCCATCTGTGCTCTATATG
TGATTTGCCAGTTCATTCTAATAAGGAGTGGAGTCAACATATCAATGGAGCAATTCACAGTCGTCGATGCCAGCTTCTTC
TTGAAATCTATCCAGAATAGAATCCTGACAATGATACAGGACACACAATGGGTGATCCCTTCATGTTGCAGCAGTCCACA
AACCCAGGGCCAGGAATTCTGGGACCTCCACCTCCCTCATTCCATCTTGGGCGACCAGCAGTTGGACCAAGAGGAAATCT
GGTTACTGGAAATGGGAACCTGCAAGGACCTAGACACATGCAGAAAGGCAGAGTAGAAACTAGCCGAGTTGTTCACATCA
TGGATTTTCAATGAGGGAAAAACTTGAGATACCAACTATTACAGCTTGTGGAACCATCTGAAGTCATTTCAAATCATCTG
ATTCTAAATAAAATTAATGAGGCTTTTATTGAAATGGCAACTACAGAGGATGCTCAGGCTGCAGTGGATTATTATACAAC
CACGCCAGCATTAGTGTTTAGCAAGCCAGTGAGAGTCCATTTATCCCAGAAGTATAAAAGAATAAAGAAGCCCAAGGGGA
AGCCAGATCAGAAGTTTGATCAAAAGCAAGAGCTTGGACATGTAATACATCTTAGCAATTTGCCCCATTCTGGCTATTCT
GATAGTGCTATTCTAAAGCTTGCTGAGCTTTATGGAAAAATAAAAAATTATATATTGATGAGGATGAAGAGTCAGGCCTT
CATTGAGATGGAGACAAGAGAAGATGCAATGGCAATGGTTGACCATTGTTTGAAAAAAGCCCTTTGCTTTCAGGGGAGAG
ATGTATAAAGGTTGACCTTTCTGAAAAATACAAAAAACTGGTACTGAGGATTCCTAACACAGGCATTGACTTACTGAAAA
AAGATAAATCCCGAAAAAGGTCTTATTCTCCAGATGGCAAAGAATCTCTAAGTGATAAGAAATCTAAAACTGATGGTTCC
AGAAGACTTAAAGTACAACTGAAGGTAAAGAACAAGAAGAAAAGTCAGGTGAAGATGGTGACAAAGATACAAAGGATGAC
CAGACAGAACAGGAACCCAGTATGCTTCTCGAATCTGAAGATGAGCTGGTTGTAGATGAAGAAGAAGCAGCTGCATTATT
AGAAAGTGGCAGTTCAGTGGGAGATGAGACTGATCTTGCTAATTTAGGTGATGTGGCTTCTGATGGGAAAAAAGGAGGCT
TCAGATAAAGCTGTGAAAAAAGATGCAACTGCTTCAGCAGCAGCAAAGAAAAAGCTTAAAAAGGTGGACAAGATCAAGGA
ACTTGATCAAGAAAATGAAGCAGCGTTGGAAAATGGAATTAAAAATGAGGAAAATACAGAACCAGGTGCAGAATCTGCTG
AGAATGCTGATAATCCCAACAAAGATACAAGTGAAAATGCAGATGGACAAAGTGATGAAAACAAGGAGGACTATACAATC
CCAGATGAGTATAGACTTGGACCACATCAGCCCAATGTTCTTGTTGGTATAGACTATGTGATACCTAAAACAGGGTTTTA
CTATAAGCTGTGTTCGCTCTGTTATACAAATGAAGAAGTTGCAAAGAAAACTCATTGCAGCAGCCTTCCTCATTATCAGA
AATTAAAGAAATTTCTGAATAAATTGGCAGAGGAATGCAGACAAAAGAAGGAAACA

ORF - retro_ogar_3417 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.25 %
Parental protein coverage: 90.32 %
Number of stop codons detected: 3
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalLQSIFNIGSRGPLPLSSQHRGDADQASNILASFGLSARDLDELSRYPEDKITPENLPQILLQLKRRRTEE
L..IFNIGSRG.LPLSSQHRGD.DQASNILASFGLSARDLDELS.YPEDKITPENLPQILLQ.KRRRTEE
RetrocopyLLPIFNIGSRGSLPLSSQHRGDVDQASNILASFGLSARDLDELSCYPEDKITPENLPQILLQRKRRRTEE
ParentalGPTLSYGRDGRSAT-REPPYRVPRDDWEEKRHFRRDSFDDRGPSLNPVLDYDHGSRSQESGYYDRMDYED
GPTLSYGRDGRSAT..EPPYRVPRDDWEEK.HFRRDSFDD.GPSLNPVLDYDHGS.SQESGYYDRMDYED
RetrocopyGPTLSYGRDGRSAT<MEPPYRVPRDDWEEKSHFRRDSFDDHGPSLNPVLDYDHGSHSQESGYYDRMDYED
ParentalDRLRDGERCRDDSFFGETSHNYHKFDSEYERMGRGPGPLQERSLFEKKRGAPPSSNIEDFHGLLPKGYPH
DRLRDGER..DDSFFGETSHNYHKFDSEYERMG.GPGPLQERSLFEKKRGAPPSSNIEDFHGLLPKGYPH
RetrocopyDRLRDGERFKDDSFFGETSHNYHKFDSEYERMGHGPGPLQERSLFEKKRGAPPSSNIEDFHGLLPKGYPH
ParentalLCSICDLPVHSNKEWSQHINGASHSRRCQLLLEIYPEWNPDNDTGHTMGDPFMLQQSTNPAPGILGPPPP
LCSICDLPVHSNKEWSQHINGA.HSRRCQLLLEIYPE.NPDNDTGHTMGDPFMLQQSTNP.PGILGPPPP
RetrocopyLCSICDLPVHSNKEWSQHINGAIHSRRCQLLLEIYPE*NPDNDTGHTMGDPFMLQQSTNPGPGILGPPPP
ParentalSFHLGGPAVGPRGNLGAGNGNLQGPRHMQKGRVETSRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL
SFHLG.PAVGPRGNL..GNGNLQGPRHMQKGRVETSRVVHIMDFQ.GKNLRYQLLQLVEP..VISNHLIL
RetrocopySFHLGRPAVGPRGNLVTGNGNLQGPRHMQKGRVETSRVVHIMDFQ*GKNLRYQLLQLVEPSEVISNHLIL
ParentalNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKKPEGKPDQKFDQKQELGRVIHLS
NKINEAFIEMATTEDAQAAVDYYTTTPALVF.KPVRVHLSQKYKRIKKP.GKPDQKFDQKQELG.VIHLS
RetrocopyNKINEAFIEMATTEDAQAAVDYYTTTPALVFSKPVRVHLSQKYKRIKKPKGKPDQKFDQKQELGHVIHLS
ParentalNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALW-FQG-RCVKVDLS
NLPHSGYSDSA.LKLAE.YGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKAL..F.G.RC.KVDLS
RetrocopyNLPHSGYSDSAILKLAELYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALC>FRG>RCIKVDLS
ParentalEKYKKLVLRIPNRGIDLLKKDKSRKRSYSPDGKESPSDKKSKTDGS-QKTESTTEGKEQEEKSGEDGEKD
EKYKKLVLRIPN.GIDLLKKDKSRKRSYSPDGKES.SDKKSKTDGS.QKT.STTEGKEQEEKSGEDG.KD
RetrocopyEKYKKLVLRIPNTGIDLLKKDKSRKRSYSPDGKESLSDKKSKTDGS<QKT*STTEGKEQEEKSGEDGDKD
ParentalTKDDQTEQEPNMLLESEDELLVDEEEAAALLESGSSVGDETDLANLGDVASDGKK-EPSDKAVKKDASAS
TKDDQTEQEP.MLLESEDEL.VDEEEAAALLESGSSVGDETDLANLGDVASDGKK.E.SDKAVKKDA.AS
RetrocopyTKDDQTEQEPSMLLESEDELVVDEEEAAALLESGSSVGDETDLANLGDVASDGKK>EASDKAVKKDATAS
ParentalAAAKKKLKKVDKIEELDQENEAALENGIKNEENTEPGAESAENADDPNKDTSENADGQSDENKEDYTIPD
AAAKKKLKKVDKI.ELDQENEAALENGIKNEENTEPGAESAENAD.PNKDTSENADGQSDENKEDYTIPD
RetrocopyAAAKKKLKKVDKIKELDQENEAALENGIKNEENTEPGAESAENADNPNKDTSENADGQSDENKEDYTIPD
ParentalEYRIGPYQPNVPVGIDYVIPKTGFYCKLCSLFYTNEEVAKNTHCSSLPHYQKLKKFLNKLAEERRQKKET
EYR.GP.QPNV.VGIDYVIPKTGFY.KLCSL.YTNEEVAK.THCSSLPHYQKLKKFLNKLAEE.RQKKET
RetrocopyEYRLGPHQPNVLVGIDYVIPKTGFYYKLCSLCYTNEEVAKKTHCSSLPHYQKLKKFLNKLAEECRQKKET

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Otolemur garnettii was not studied using ChIP-Seq data.

EST - click to see more details

Otolemur garnettii was not studied using EST data.

TSS - click to see more details

Otolemur garnettii was not studied using FANTOM5 data.

Lab - click to see more details

retro_ogar_3417 was not experimentally validated.

Retrocopy orthology:
Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000068881 retrocopy
retro_cjac_3950,
Homo sapiens ENSG000000154791 retrocopy
retro_hsap_199,
Gorilla gorilla ENSGGOG000000073082 retrocopies
retro_ggor_276, retro_ggor_421,
Nomascus leucogenys ENSNLEG000000090931 retrocopy
retro_nleu_1849,
Oryctolagus cuniculus ENSOCUG000000263111 retrocopy
retro_ocun_652,
Otolemur garnettii ENSOGAG00000010607 1 retrocopy
retro_ogar_3417 ,
Pongo abelii ENSPPYG000000158352 retrocopies
retro_pabe_1722, retro_pabe_438,
Pan troglodytes ENSPTRG000000172941 retrocopy
retro_ptro_181,
Rattus norvegicus ENSRNOG000000198752 retrocopies
retro_rnor_1124, retro_rnor_475,


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