RetrogeneDB ID:

retro_mmul_1837

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:4:69400256..69400784(-)
Located in intron of:ENSMMUG00000015320
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RBPMS2
Ensembl ID:ENSMMUG00000013270
Aliases:None
Description:RNA binding protein with multiple splicing 2 [Source:HGNC Symbol;Acc:19098]


Retrocopy-Parental alignment summary:






>retro_mmul_1837
ATCAGCGGCCTCCCCATGGACATTAAACCCAGAGAACTCTACTTGTTCTTCTGGCCTTTCAAGGGGGTATGAAGAGTCCG
TGATCAAGCTCACCGCGAGACAGCTTGTTTGTTTTGTGATCTTTGACAGCTGGGCAGGAGCAGAAGCGGCCAATAATGCA
CTGAACCGTATTCGCTTAGATCCCGAGAACCCACAGGCCCTGAGACTAGAGTTTGCCAAAGCCAACACCAAGATGGCCAA
GAGCAAGCTAACGGCAACTCCAAATCCCACCAAAGTGCACCCCGCCCTAGGAGCACACTTACTTCATCTCTCGGGACCCC
TATGAGCTGAAGGGGGCTGCTCTGATCCCTGCATCCCCAGAGGCCTGGGCTCCTACCCTTTGTACACTACAGAGCTGACC
CCACCCATCACCCATGCTTCATTCACCTACCCAGCTGCCACTGCAGCTGCCGCCGCCCTCCATGCCAGGTGCGCTGGTAC
CCATCCTCTGACACCACTCAGCAAGGATGGAAGTATCATCATTTCTGT

ORF - retro_mmul_1837 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.11 %
Parental protein coverage: 96.69 %
Number of stop codons detected: 1
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalVSGLPVDIKPRELYLLFRPFKG-YEGSLIKLTARQPVGFVIFDSRAGAEAAKNALNGIRFDPENPQTLRL
.SGLP.DIKPRELYL.F.PFKG.YE.S.IKLTARQ.V.FVIFDS.AGAEAA.NALN.IR.DPENPQ.LRL
RetrocopyISGLPMDIKPRELYLFFWPFKG>YEESVIKLTARQLVCFVIFDSWAGAEAANNALNRIRLDPENPQALRL
ParentalEFAKANTKMAKSKLMATPNPSNVHPTLGAHFV-ARDPYDLMGAALIPASP-EAWAP-YPLYTTELAPAIS
EFAKANTKMAKSKL.ATPNP..VHP.LGAH......P....G....P..P.EAWAP.YPLYTTEL.P.I.
RetrocopyEFAKANTKMAKSKLTATPNPTKVHPALGAHLLHLSGPL*AEGGCSDPCIP>EAWAP<YPLYTTELTPPIT
ParentalHAAFTYPAATAAAAALHA-QVRWYPSSDTTQQGWKYRQFC
HA.FTYPAATAAAAALHA.QVRWYPSSDTTQQGWKY..FC
RetrocopyHASFTYPAATAAAAALHA<QVRWYPSSDTTQQGWKYHHFC

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 .11 RPM 0 .45 RPM
SRP007412_brain_prefrontal_cortex 0 .16 RPM 0 .87 RPM
SRP007412_cerebellum 0 .06 RPM 0 .06 RPM
SRP007412_heart 0 .06 RPM 37 .86 RPM
SRP007412_kidney 0 .00 RPM 16 .78 RPM
SRP007412_liver 0 .04 RPM 8 .11 RPM
SRP007412_testis 2 .19 RPM 0 .98 RPM

ChIP-Seq - click to see more details

Macaca mulatta was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mmul_1837 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_1837 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_1837 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3613
Pan troglodytes retro_ptro_2441
Gorilla gorilla retro_ggor_2438
Pongo abelii retro_pabe_2963
Parental genes homology:
Parental genes homology involve 17 parental genes, and 38 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000110371 retrocopy
retro_btau_1674,
Callithrix jacchus ENSCJAG000000052002 retrocopies
retro_cjac_1775, retro_cjac_298,
Dipodomys ordii ENSDORG000000040251 retrocopy
retro_dord_438,
Homo sapiens ENSG000001668312 retrocopies
retro_hsap_2513, retro_hsap_3613,
Gorilla gorilla ENSGGOG000000089841 retrocopy
retro_ggor_2438,
Loxodonta africana ENSLAFG000000187256 retrocopies
retro_lafr_344, retro_lafr_393, retro_lafr_445, retro_lafr_481, retro_lafr_550, retro_lafr_859,
Macaca mulatta ENSMMUG00000013270 1 retrocopy
retro_mmul_1837 ,
Monodelphis domestica ENSMODG000000104871 retrocopy
retro_mdom_571,
Mus musculus ENSMUSG000000323879 retrocopies
retro_mmus_2671, retro_mmus_3408, retro_mmus_3410, retro_mmus_3429, retro_mmus_3431, retro_mmus_3437, retro_mmus_3562, retro_mmus_3588, retro_mmus_3596,
Nomascus leucogenys ENSNLEG000000125051 retrocopy
retro_nleu_2209,
Otolemur garnettii ENSOGAG000000260171 retrocopy
retro_ogar_3254,
Pongo abelii ENSPPYG000000065531 retrocopy
retro_pabe_2963,
Pan troglodytes ENSPTRG000000071652 retrocopies
retro_ptro_1458, retro_ptro_2441,
Sus scrofa ENSSSCG000000045491 retrocopy
retro_sscr_851,
Ictidomys tridecemlineatus ENSSTOG000000100552 retrocopies
retro_itri_1512, retro_itri_556,
Tarsius syrichta ENSTSYG000000089963 retrocopies
retro_tsyr_1433, retro_tsyr_171, retro_tsyr_445,
Tursiops truncatus ENSTTRG000000118403 retrocopies
retro_ttru_1046, retro_ttru_1212, retro_ttru_1790,


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