RetrogeneDB ID:

retro_mmul_1031

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:13:63933699..63934403(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.4980
Ensembl ID:ENSMMUG00000012989
Aliases:HNRNPA1, HNRPA1, hnRNP A1
Description:None


Retrocopy-Parental alignment summary:






>retro_mmul_1031
CAGTCTCCTAAAGAGCCTGAGCAGCTCTTCACTGGAGTGTTGAGCTTTCATATGACTGATGAGAGGCTGAGGAGCCCTTC
TGAGCAATGGGGAACGCTCACAGGCTGTGTGGTCATGAGAGATCCCAACACCAAGAGCTCCAGGGACTTTGGGTTTGTCA
CCTATGCCACTGTGGAGGAGGTGGATGCAGCCATGAATACAAGGCCACACAAGGTGGATGGGAGAGCTGTGGAACCAAAG
AGGGCTGTCTCAAGAGAAGGTTCTCAAAGACCAGGTGCCCACCTAACTGTGAAAAAGGTATTTGTTGCTGGCATTGAAGA
ATACATTGAAGAACATCACCTGAGAGATTATTTTGAACAGTATGGAAAAATTGAAGTGATTGAAGTTGTGACTGATTGAG
GCAGTGGCAAAAAAAGGAGCTTTGCCTTTATAACCTTTGATGACCATGACTCTGTGGATAAAATTGTCATTCAGAAATAC
CACTGTGTGAATGGCCACAACTGTGAAGTTAGGAAAGCCCTGCTAAAACAAGAGGTGGATAGTGCTTCACCCAACCAAAG
AGGTTGACGTGGTTCTGGAAACTTTGGTGGTGGTTGTGGAGGTGGCTTCAGTGGAAATGACAACTTTGATTGTGGAGGAA
ACTTCAATGCTGTGGTCATGGTGGATATGGTGGCAGTGGGGATGGCTATAATGGATTTGGTGAT

ORF - retro_mmul_1031 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.66 %
Parental protein coverage: 83.22 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalQSPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA
QSPKEPEQ...LF.G.LSF..TDE.LRS..EQWGTLT.CVVMRDPNTK.SR.FGFVTYATVEEVDAAMN.
RetrocopyQSPKEPEQ---LFTGVLSFHMTDERLRSPSEQWGTLTGCVVMRDPNTKSSRDFGFVTYATVEEVDAAMNT
ParentalRPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGK
RPHKVDGR.VEPKRAVSRE.SQRPGAHLTVKK.FV.GI.E..EEHHLRDYFEQYGKIEVIE..TD.GSGK
RetrocopyRPHKVDGRAVEPKRAVSREGSQRPGAHLTVKKVFVAGIEEYIEEHHLRDYFEQYGKIEVIEVVTD*GSGK
ParentalKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGFGGND
KR.FAF.TFDDHDSVDKIVIQKYH.VNGHNCEVRKAL.KQE..SAS..QRG..GSGNFGGG.GGGF.GND
RetrocopyKRSFAFITFDDHDSVDKIVIQKYHCVNGHNCEVRKALLKQEVDSASPNQRG*RGSGNFGGGCGGGFSGND
ParentalNFGRGGNFSG-RGGFGGSRGGGGYGGSGD
NF..GGNF....G..G....G.GY.G.GD
RetrocopyNFDCGGNFNA<CGHGGYGGSGDGYNGFGD

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






(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 72 .61 RPM
SRP007412_brain_prefrontal_cortex 0 .00 RPM 144 .14 RPM
SRP007412_cerebellum 0 .06 RPM 88 .27 RPM
SRP007412_heart 0 .00 RPM 141 .68 RPM
SRP007412_kidney 0 .12 RPM 70 .66 RPM
SRP007412_liver 0 .16 RPM 68 .12 RPM
SRP007412_testis 0 .00 RPM 87 .83 RPM
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_1031 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_1031 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_1031 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 9 parental genes, and 40 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG0000000658016 retrocopies
Dasypus novemcinctus ENSDNOG000000092287 retrocopies
Macaca mulatta ENSMMUG000000018584 retrocopies
Macaca mulatta ENSMMUG00000012989 5 retrocopies
Mustela putorius furoENSMPUG000000046201 retrocopy
Mustela putorius furoENSMPUG000000057352 retrocopies
Oryctolagus cuniculus ENSOCUG000000133501 retrocopy
Otolemur garnettii ENSOGAG000000297073 retrocopies
Oreochromis niloticus ENSONIG000000122481 retrocopy



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