RetrogeneDB ID:

retro_hsap_150

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:52174754..52175611(+)
Located in intron of:ENSG00000117859
Retrocopy
information
Ensembl ID:ENSG00000232846
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC25A6
Ensembl ID:ENSG00000169100
Aliases:None
Description:solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 6 [Source:HGNC Symbol;Acc:10992]


Retrocopy-Parental alignment summary:






>retro_hsap_150
TCCTTTGTCAAGGACTTACTGGCCGGAGGCATTGCCCTCGCTATTTCCAAGAGGGCAGCGACCCGAGTTGAGCCAGTCAA
GGCACTGCTGCAGGTGCAACATGCCAGTAAGCAGATTGTGGCGACACCGTACAAAGGCGTGGTGTGGTGGGCTGCAAGGT
CCACATCCCCAAGGAGCAGGGCACTTGTCCTTCTGGAGGGGCACCTGGCCAGCACCATCCACTGCTTCCCCATGCAAGCC
CTCAACTTTGCCTTTAGGGATAAGTACAAGCAGGTCCTTCTGGGAGGCGTGCATAAGCATGCACAGTTCTGGAGATATTT
TGCAGGCAACCTGGCTTCCTGAGGGGCGGCTGGGGCCATCTCCCTGTGCTTCTTCTATCCCCTGGAATTTGCCAGAACCT
GCCTGGCAGCCAACGTTGGGAAATTGGGCATATAGTGGGAGCTCAAAGGCCTGGCAGACTGCCTGGAGAAGATCAAGGCT
GATGGGATCCGAGGCCTGTCCCAGGGCTTCAGCATCTCGGTGCAGGGCATCCATATGTACTGGGCAACCTACCTCAGCGT
GTATGATACAGCCAAGGGCATGCTCCCTGACCCCAAGAACACCCACCACATGGTGAGCTGGATGATTGCCAGGCCATGAC
AGTGGCCCATGTGGCCTCCTACCTACTCCTCACAGTGCGGGCGGATGGTGATGCAGTCCAGGTGCAAAGGAGGTGATATT
ACGAACACGGGTGCCCTTGATTGTTGGCAGAAGCTCTCCTAAAATGAAGGGGCGAAGCCTCCTTCAAGGATGCATGGTCC
AACATCCTCACAGGCATGGGGCCAAGTCTGGGCCTGTATTATGAGCTGAAGAAAGTC

ORF - retro_hsap_150 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.41 %
Parental protein coverage: 97.65 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalSFAKDFLAGGIAAAISKTAVAPIERVKLLLQVQHASKQIAADKQYKGIVDCIVRIPKEQG-VLSFWRGNL
SF.KD.LAGGIA.AISK.A....E.VK.LLQVQHASKQI.A...YKG.V....R........L....G.L
RetrocopySFVKDLLAGGIALAISKRAATRVEPVKALLQVQHASKQIVA-TPYKGVVWWAARSTSPRSRALVLLEGHL
ParentalANVIRYFPTQALNFAFKDKYKQIFLGGVDKHTQFWRYFAGNLASGGAAGATSLCFVYPLDFARTRLAADV
A..I..FP.QALNFAF.DKYKQ..LGGV.KH.QFWRYFAGNLAS.GAAGA.SLCF.YPL.FART.LAA.V
RetrocopyASTIHCFPMQALNFAFRDKYKQVLLGGVHKHAQFWRYFAGNLAS*GAAGAISLCFFYPLEFARTCLAANV
ParentalGKSGTEREFRGLGDCLVKITKSDGIRGLYQGFSVSVQGIIIYRAAYFGVYDTAKGMLPDPKNTHIVVSWM
GK.G...E..GL.DCL.KI.K.DGIRGL.QGFS.SVQGI..Y.A.Y..VYDTAKGMLPDPKNTH..VSWM
RetrocopyGKLGI*WELKGLADCLEKI-KADGIRGLSQGFSISVQGIHMYWATYLSVYDTAKGMLPDPKNTHHMVSWM
ParentalIA-QTVTAVAGVVSYPFDTVR-RRMMMQSGRKGADIMYTGTVDCWRKIFRDEG-GKAFFKGAWSNVLRGM
IA.Q..T.VA.V.SY...TVR.R..M.QS..KG.DI..TG..DCW.K....EG.G.A.FK.AWSN.L.GM
RetrocopyIA<QAMT-VAHVASYLLLTVR>RMVM-QSRCKGGDITNTGALDCWQKLS*NEG<GEASFKDAWSNILTGM
ParentalGGAFVLVLYDELKKV
G....L.LY.ELKKV
RetrocopyGPS--LGLYYELKKV

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 314 .07 RPM
bodymap2_adrenal 0 .00 RPM 338 .52 RPM
bodymap2_brain 0 .00 RPM 77 .31 RPM
bodymap2_breast 0 .00 RPM 243 .60 RPM
bodymap2_colon 0 .00 RPM 328 .05 RPM
bodymap2_heart 0 .04 RPM 54 .59 RPM
bodymap2_kidney 0 .00 RPM 175 .14 RPM
bodymap2_liver 0 .00 RPM 42 .12 RPM
bodymap2_lung 0 .00 RPM 179 .15 RPM
bodymap2_lymph_node 0 .00 RPM 193 .70 RPM
bodymap2_ovary 0 .00 RPM 334 .67 RPM
bodymap2_prostate 0 .00 RPM 261 .14 RPM
bodymap2_skeletal_muscle 0 .00 RPM 72 .51 RPM
bodymap2_testis 0 .00 RPM 138 .91 RPM
bodymap2_thyroid 0 .02 RPM 240 .40 RPM
bodymap2_white_blood_cells 0 .00 RPM 294 .37 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_150 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_150 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_150 retrocopy 5' end.

Lab - click to see more details

retro_hsap_150 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_150 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_146
Gorilla gorilla retro_ggor_239
Parental genes homology:
Parental genes homology involve 9 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000056091 retrocopy
retro_amel_255,
Homo sapiens ENSG000000050227 retrocopies
retro_hsap_2243, retro_hsap_3132, retro_hsap_3336, retro_hsap_3516, retro_hsap_3715, retro_hsap_3730, retro_hsap_4239,
Homo sapiens ENSG00000169100 5 retrocopies
retro_hsap_1207, retro_hsap_150 , retro_hsap_2460, retro_hsap_4147, retro_hsap_4207,
Gorilla gorilla ENSGGOG000000230042 retrocopies
retro_ggor_239, retro_ggor_2785,
Loxodonta africana ENSLAFG000000015841 retrocopy
retro_lafr_713,
Microcebus murinus ENSMICG000000061362 retrocopies
retro_mmur_1021, retro_mmur_922,
Macaca mulatta ENSMMUG000000068991 retrocopy
retro_mmul_1182,
Nomascus leucogenys ENSNLEG000000003891 retrocopy
retro_nleu_895,
Otolemur garnettii ENSOGAG000000009632 retrocopies
retro_ogar_2492, retro_ogar_2499,

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 ) > 0 RPM = 0.04 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 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 .03 RPM
GBR_HG00111 0 .02 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 .02 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .02 RPM

Indel association:

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



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