RetrogeneDB ID:

retro_hsap_4006

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:125932732..125933439(+)
Located in intron of:ENSG00000249816
Retrocopy
information
Ensembl ID:ENSG00000250428
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MRS2
Ensembl ID:ENSG00000124532
Aliases:MRS2, HPT, MRS2L
Description:MRS2 magnesium transporter [Source:HGNC Symbol;Acc:13785]


Retrocopy-Parental alignment summary:






>retro_hsap_4006
TCTGACCTGTGTGGGCCCGCCGGCTCTGCGTAGCAGGTGCAATGCATGGGTTTAGAACTTCTGATGTCTCTCAAGCCACT
GTAGGCAGTGTAGCCCCAGTATTTACCGCAACAAAATTTGACAAACAGGGAAATGTTACTCCTTTTGAAAGGAAGAAAAC
TGACTTATACCAAGAGTTAGGTCTTCAAGCCAGAGACTTGAGATTTCAGCATGTAGTGAGCATCACAACCAGAAACGGCA
GGTTTATCATGACAATGGAGTATTTGAAAGCTGTGATAACTCCAGAGTGTCTCCTGATATTAGATGATGGTAATTTAAAT
TTAGAGCAATGGCTGTTCTGGGAACTCCCTTCACAGTTGTCTGGAGAGGGTCAACCTGTTACATACTCTTTACCTTTTGA
GTTTAGTGCTATGGAAGCACCCCTGAAATACTGGATCAACCCCCTTTAGAGGAAACGTAGCGTTTTGCAGACACTGACCT
TTGAGACCTTAGAAGCTTTCAAACATTCTTCTGTGGACAAAAGCTAACCGCATATTTTACTACGGAATGACAAAAGTCTA
TCAGAGTTAGAAACAGATATTAAAATTTTCCAAGAGTCAATTTTGGAGATCTTGGGTGAGGAAAAGTTACTAGAAGAGCT
CTGTCTATCAAAATGGAGTGACCCACCAGTCTTTGAAAAGAGCAGTACTGGGATTCGCCATGCAGAA

ORF - retro_hsap_4006 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.33 %
Parental protein coverage: 58.58 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalAQLCGPD-RLRVAGEVHRFRTSDVSQATLASVAPVFTVTKFDKQGNVTSFERKKTELYQELGLQARDLRF
..LCGP..RL.VAG..H.FRTSDVSQAT..SVAPVFT.TKFDKQGNVT.FERKKT.LYQELGLQARDLRF
RetrocopySDLCGPA<RLCVAGAMHGFRTSDVSQATVGSVAPVFTATKFDKQGNVTPFERKKTDLYQELGLQARDLRF
ParentalQHVMSITVRNNRIIMRMEYLKAVITPECLLILDYRNLNLEQWLFRELPSQLSGEGQLVTYPLPFEFRAIE
QHV.SIT.RN.R.IM.MEYLKAVITPECLLILD..NLNLEQWLF.ELPSQLSGEGQ.VTY.LPFEF.A.E
RetrocopyQHVVSITTRNGRFIMTMEYLKAVITPECLLILDDGNLNLEQWLFWELPSQLSGEGQPVTYSLPFEFSAME
ParentalALLQYWINTLQGKLSILQPLILETLDALVDPKHSSVDRSKLHILLQNGKSLSELETDIKIFKESILEILD
A.L.YWIN.L..K.S.LQ.L..ETL.A....KHSSVD.S..HILL.N.KSLSELETDIKIF.ESILEIL.
RetrocopyAPLKYWINPL*RKRSVLQTLTFETLEAF---KHSSVDKS*PHILLRNDKSLSELETDIKIFQESILEILG
ParentalEEELLEELCVSKWSDPQVFEKSSAGIDHAE
EE.LLEELC.SKWSDP.VFEKSS.GI.HAE
RetrocopyEEKLLEELCLSKWSDPPVFEKSSTGIRHAE

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
bodymap2_adipose 0 .00 RPM 12 .70 RPM
bodymap2_adrenal 0 .00 RPM 24 .15 RPM
bodymap2_brain 0 .00 RPM 23 .11 RPM
bodymap2_breast 0 .00 RPM 37 .12 RPM
bodymap2_colon 0 .00 RPM 17 .11 RPM
bodymap2_heart 0 .00 RPM 52 .13 RPM
bodymap2_kidney 0 .00 RPM 34 .00 RPM
bodymap2_liver 0 .00 RPM 16 .33 RPM
bodymap2_lung 0 .00 RPM 10 .72 RPM
bodymap2_lymph_node 0 .00 RPM 21 .22 RPM
bodymap2_ovary 0 .00 RPM 19 .70 RPM
bodymap2_prostate 0 .00 RPM 28 .47 RPM
bodymap2_skeletal_muscle 0 .00 RPM 26 .55 RPM
bodymap2_testis 0 .08 RPM 20 .66 RPM
bodymap2_thyroid 0 .00 RPM 36 .65 RPM
bodymap2_white_blood_cells 0 .00 RPM 22 .54 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_4006 in 1 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002DBP POLR2A 8:125932567..125932897

EST - click to see more details

No EST(s) were mapped for retro_hsap_4006 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4006 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4006 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4006 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2720
Gorilla gorilla retro_ggor_2689
Macaca mulatta retro_mmul_2312
Parental genes homology:
Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000064241 retrocopy
retro_dnov_1486,
Equus caballus ENSECAG000000131051 retrocopy
retro_ecab_1032,
Homo sapiens ENSG00000124532 1 retrocopy
retro_hsap_4006 ,
Gorilla gorilla ENSGGOG000000090981 retrocopy
retro_ggor_2689,
Macaca mulatta ENSMMUG000000010182 retrocopies
retro_mmul_2312, retro_mmul_878,
Pongo abelii ENSPPYG000000162781 retrocopy
retro_pabe_939,
Pan troglodytes ENSPTRG000000177741 retrocopy
retro_ptro_2720,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).



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