RetrogeneDB ID:

retro_hsap_4147

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:31253898..31254771(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000232203
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_4147
ATGACGGAACAAGCCATCTCCTTCGCCAAGGACTTCCTAGCTGGAGGCATCACCGCCGCTATCTCCAAGACAGCCGTGGC
ATCGATCAAGCGGGTCCAGCTGCTGCTGCAGATGCAGCACGCCAGCATGCCGATGGCCGCCGCCAAGCAGTGCAAGGGCA
TCGTGGACTGCATCGTCCGCATCCCCAAAGATCAGGGCGTGCTGTCCTTCTGGAGGGGCAACCTGGCCAATGTCATCCGC
TACTCCCCCACGCAAGCCCTCAATTTCGCCTTCAAGGATAAGTACAAGCAGATCTTCCTGGCGGGCGTGGACAAGCACAC
GCAGTTCTGCAGGTACTTTGCGGGCAACCTGGCCTCTGGCGGCACGGCCGTCGTGTATCCCCTGGATTTCACCAGAACCC
GCCTGGCAGCCGACGTGGGAAAGTCAGGCACGGAGCGCGAGTTCCGAGGCCTGGGAGACTGCCTAGTGAAGATCAGCAAG
TCCGACGGCATCCGGGGCCTTTACCAGGGCTTCAGCGTCTCCGTGCAGGCCATCATCATCTACCAGGCAGCCTACTTCAG
GGTGTACGATACGGCCAATGGCATGTTCCCCGACCCCAAGAACACACACATCCTGGTGAGCTGGATGACCGCGCAGACCG
TGACGGCCGTGGCTGGCGTGCTCTCCTAACCCTTCGACACAGTGCGGCGGCGGACGATGATGCAGTCCCGGCGCAAAGGA
GCTGACATCATGTACACGGGCACCGTCGACTGTTGGAGGAAGATCTTCAGAGATGAGCGGGGCGAGGCCTTTTTCAAGGG
TGTGTGGTCCAACGCCCTCAAAGGCATGGGGGTGGGGGCGGGCTTCGTGCTGGTCCTGTACGACGAGCTGAAG

ORF - retro_hsap_4147 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.51 %
Parental protein coverage: 98.99 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMTEQAISFAKDFLAGGIAAAISKTAVAPIERVKLLLQVQHASKQIAADKQYKGIVDCIVRIPKEQGVLSF
MTEQAISFAKDFLAGGI.AAISKTAVA.I.RV.LLLQ.QHAS...AA.KQ.KGIVDCIVRIPK.QGVLSF
RetrocopyMTEQAISFAKDFLAGGITAAISKTAVASIKRVQLLLQMQHASMPMAAAKQCKGIVDCIVRIPKDQGVLSF
ParentalWRGNLANVIRYFPTQALNFAFKDKYKQIFLGGVDKHTQFWRYFAGNLASGGAAGATSLCFVYPLDFARTR
WRGNLANVIRY.PTQALNFAFKDKYKQIFL.GVDKHTQF.RYFAGNL....A.G.T....VYPLDF.RTR
RetrocopyWRGNLANVIRYSPTQALNFAFKDKYKQIFLAGVDKHTQFCRYFAGNL----ASGGTAV--VYPLDFTRTR
ParentalLAADVGKSGTEREFRGLGDCLVKITKSDGIRGLYQGFSVSVQGIIIYRAAYFGVYDTAKGMLPDPKNTHI
LAADVGKSGTEREFRGLGDCLVKI.KSDGIRGLYQGFSVSVQ.IIIY.AAYF.VYDTA.GM.PDPKNTHI
RetrocopyLAADVGKSGTEREFRGLGDCLVKISKSDGIRGLYQGFSVSVQAIIIYQAAYFRVYDTANGMFPDPKNTHI
ParentalVVSWMIAQTVTAVAGVVSYPFDTVRRRMMMQSGRKGADIMYTGTVDCWRKIFRDEGGKAFFKGAWSNVLR
.VSWM.AQTVTAVAGV.S.PFDTVRRR.MMQS.RKGADIMYTGTVDCWRKIFRDE.G.AFFKG.WSN.L.
RetrocopyLVSWMTAQTVTAVAGVLS*PFDTVRRRTMMQSRRKGADIMYTGTVDCWRKIFRDERGEAFFKGVWSNALK
ParentalGM--GGAFVLVLYDELK
GM..G..FVLVLYDELK
RetrocopyGMGVGAGFVLVLYDELK

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 .04 RPM 314 .07 RPM
bodymap2_adrenal 0 .00 RPM 338 .52 RPM
bodymap2_brain 0 .00 RPM 77 .31 RPM
bodymap2_breast 0 .02 RPM 243 .60 RPM
bodymap2_colon 0 .00 RPM 328 .05 RPM
bodymap2_heart 0 .00 RPM 54 .59 RPM
bodymap2_kidney 0 .00 RPM 175 .14 RPM
bodymap2_liver 0 .00 RPM 42 .12 RPM
bodymap2_lung 0 .02 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 .06 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_4147 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4147 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4147 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4147 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4147 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Macaca mulatta retro_mmul_1182
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 = 0.08 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .08 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .08 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 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 .03 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .06 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .03 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 .06 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .08 RPM
YRI_NA19114 0 .03 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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