RetrogeneDB ID:

retro_hsap_3516

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:121974957..121975717(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000218180
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC25A5
Ensembl ID:ENSG00000005022
Aliases:SLC25A5, 2F1, AAC2, ANT2, T2, T3
Description:solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 5 [Source:HGNC Symbol;Acc:10991]


Retrocopy-Parental alignment summary:






>retro_hsap_3516
AAGGACTTCCTGGCAGGTAGAGTGGCCACGGCCATCTCCAAGACGGAGGTTGCTCCCATCAAGCGGATCGAGCTGCTGCT
GCAGGTACAGTGTGCCAGCAAGCAGATCACCGCAGATAAGCAATACAAGGGCATTATAGACCATATAGGTCCGTATTCTC
AAGGAGCAGGGAGTCCTGTCCTTCTGGCGCAGTAACCTGGCCAATGTCATCAGATACTTCCCCACCCAGGCTCTTAACTT
TGCTTTCAAAGATAAATAAAAGCAGATCTTCCTGGGTGGTGTGGACAAGAGGACCCAGTTTTGGCGCTACTTTGAAGGGA
ATCTGGCATCAGGCAGTGTTTCTGGGGCCACATCCTTGTGTTATGTGTACCCTCTTGATTTTGCCCATCTAGCAGCCGAT
GTGGGTAAAGCTGGAGCTGAAAGGGAATTCCGAGGCCTCAGTGACTGCCTGGTTAAGATCTACAAATGTGATGGGATTAA
GGGCCTGTACCAAGGCTTTCACGTGTCTGTGCAGGGTATTATCATCTACCGAGCTGCCTACTTCAGTATCTATGACACTG
CAAAGGGAATGCTTCCAGATCCCAAGAACACTTACATCATCATCAACCGGATGATCGCAAAGACTATCACTGCCATTGCT
GGGTTGACTTCCTATCCATTTGACACCATTGGCTGCCACATGATGATGCAGTCAGGGTGCAAAGGAACTGACATCATGTA
CACAGGCATGCTTGACTACTGATGGAAGAGTGCTAGAGAA

ORF - retro_hsap_3516 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.81 %
Parental protein coverage: 85.57 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalKDFLAGGVAAAISKTAVAPIERVKLLLQVQHASKQITADKQYKGIIDCV-VRIPKEQGVLSFWRGNLANV
KDFLAG.VA.AISKT.VAPI.R..LLLQVQ.ASKQITADKQYKGIID...VRI.KEQGVLSFWR.NLANV
RetrocopyKDFLAGRVATAISKTEVAPIKRIELLLQVQCASKQITADKQYKGIIDHI>VRILKEQGVLSFWRSNLANV
ParentalIRYFPTQALNFAFKDKYKQIFLGGVDKRTQFWLYFAGNLASGGAAGATSLCFVYPLDFARTRLAADVGKA
IRYFPTQALNFAFKDK.KQIFLGGVDKRTQFW.YF.GNLASG...GATSLC.VYPLDFA...LAADVGKA
RetrocopyIRYFPTQALNFAFKDK*KQIFLGGVDKRTQFWRYFEGNLASGSVSGATSLCYVYPLDFAH--LAADVGKA
ParentalGAEREFRGLGDCLVKIYKSDGIKGLYQGFNVSVQGIIIYRAAYFGIYDTAKGMLPDPKNTHIVISWMIAQ
GAEREFRGL.DCLVKIYK.DGIKGLYQGF.VSVQGIIIYRAAYF.IYDTAKGMLPDPKNT.I.I..MIA.
RetrocopyGAEREFRGLSDCLVKIYKCDGIKGLYQGFHVSVQGIIIYRAAYFSIYDTAKGMLPDPKNTYIIINRMIAK
ParentalTVTAVAGLTSYPFDTVRRRMMMQSGRKGTDIMYTGTLDCWRKIARD
T.TA.AGLTSYPFDT....MMMQSG.KGTDIMYTG.LD...K.AR.
RetrocopyTITAIAGLTSYPFDTIGCHMMMQSGCKGTDIMYTGMLDY*WKSARE

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 150 .50 RPM
bodymap2_adrenal 0 .00 RPM 158 .47 RPM
bodymap2_brain 0 .00 RPM 170 .34 RPM
bodymap2_breast 0 .00 RPM 130 .43 RPM
bodymap2_colon 0 .00 RPM 216 .39 RPM
bodymap2_heart 0 .00 RPM 60 .88 RPM
bodymap2_kidney 0 .00 RPM 364 .18 RPM
bodymap2_liver 0 .00 RPM 184 .77 RPM
bodymap2_lung 0 .00 RPM 195 .71 RPM
bodymap2_lymph_node 0 .00 RPM 157 .52 RPM
bodymap2_ovary 0 .00 RPM 116 .39 RPM
bodymap2_prostate 0 .00 RPM 124 .64 RPM
bodymap2_skeletal_muscle 0 .00 RPM 35 .70 RPM
bodymap2_testis 0 .00 RPM 101 .84 RPM
bodymap2_thyroid 0 .00 RPM 132 .35 RPM
bodymap2_white_blood_cells 0 .00 RPM 186 .84 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3516 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3516 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3516 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3516 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3516 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2377
Pan troglodytes retro_ptro_2388
Parental genes homology:
Parental genes homology involve 20 parental genes, and 92 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000001431 retrocopy
retro_amel_1291,
Canis familiaris ENSCAFG000000183842 retrocopies
retro_cfam_1473, retro_cfam_1641,
Dasypus novemcinctus ENSDNOG000000083841 retrocopy
retro_dnov_1894,
Echinops telfairi ENSETEG000000049002 retrocopies
retro_etel_23, retro_etel_48,
Felis catus ENSFCAG000000070572 retrocopies
retro_fcat_1035, retro_fcat_127,
Homo sapiens ENSG00000005022 7 retrocopies
retro_hsap_2243, retro_hsap_3132, retro_hsap_3336, retro_hsap_3516 , retro_hsap_3715, retro_hsap_3730, retro_hsap_4239,
Homo sapiens ENSG000001691005 retrocopies
retro_hsap_1207, retro_hsap_150, retro_hsap_2460, retro_hsap_4147, retro_hsap_4207,
Gorilla gorilla ENSGGOG000000142798 retrocopies
retro_ggor_1673, retro_ggor_1674, retro_ggor_2146, retro_ggor_2377, retro_ggor_2512, retro_ggor_2517, retro_ggor_2840, retro_ggor_941,
Loxodonta africana ENSLAFG000000293981 retrocopy
retro_lafr_844,
Microcebus murinus ENSMICG000000027573 retrocopies
retro_mmur_322, retro_mmur_411, retro_mmur_974,
Myotis lucifugus ENSMLUG000000157424 retrocopies
retro_mluc_139, retro_mluc_1580, retro_mluc_2564, retro_mluc_86,
Macaca mulatta ENSMMUG000000226636 retrocopies
retro_mmul_1022, retro_mmul_1287, retro_mmul_1699, retro_mmul_1775, retro_mmul_1800, retro_mmul_2090,
Nomascus leucogenys ENSNLEG000000148527 retrocopies
retro_nleu_131, retro_nleu_1314, retro_nleu_1383, retro_nleu_1679, retro_nleu_2253, retro_nleu_2560, retro_nleu_3105,
Oryctolagus cuniculus ENSOCUG0000001326811 retrocopies
retro_ocun_1002, retro_ocun_1233, retro_ocun_1457, retro_ocun_1694, retro_ocun_1705, retro_ocun_1862, retro_ocun_1877, retro_ocun_1890, retro_ocun_1932, retro_ocun_610, retro_ocun_708,
Otolemur garnettii ENSOGAG000000100087 retrocopies
retro_ogar_1131, retro_ogar_1275, retro_ogar_1669, retro_ogar_2161, retro_ogar_2408, retro_ogar_2450, retro_ogar_2474,
Pongo abelii ENSPPYG000000206695 retrocopies
retro_pabe_1006, retro_pabe_2587, retro_pabe_3130, retro_pabe_3141, retro_pabe_3398,
Pteropus vampyrus ENSPVAG000000149242 retrocopies
retro_pvam_1118, retro_pvam_911,
Rattus norvegicus ENSRNOG0000003998011 retrocopies
retro_rnor_1242, retro_rnor_1364, retro_rnor_1475, retro_rnor_1612, retro_rnor_1904, retro_rnor_1922, retro_rnor_2533, retro_rnor_2758, retro_rnor_721, retro_rnor_722, retro_rnor_723,
Ictidomys tridecemlineatus ENSSTOG000000204383 retrocopies
retro_itri_314, retro_itri_532, retro_itri_868,
Tupaia belangeri ENSTBEG000000060084 retrocopies
retro_tbel_1558, retro_tbel_1860, retro_tbel_4654, retro_tbel_4661,

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 = 0.02 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 .02 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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