RetrogeneDB ID:

retro_hsap_1705

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:16:75742956..75743713(-)
Located in intron of:ENSG00000166848
Retrocopy
information
Ensembl ID:ENSG00000261424
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ATP5F1
Ensembl ID:ENSG00000116459
Aliases:None
Description:ATP synthase, H+ transporting, mitochondrial Fo complex, subunit B1 [Source:HGNC Symbol;Acc:840]


Retrocopy-Parental alignment summary:






>retro_hsap_1705
ATGCTGTCCTGGGTGGTACTTTTTGCTGCCACCACAGTGGCCCTCTCTCTGAAGAATGCAGCCTTCCTAGGTCCAGGGGT
ATTGCAGGCAACAAGGACATTTCACACAGTGCAGCCACACCTTGCCCTTCTACCACCTCTTCCTGAATACGGAGGAAAAG
TTCATCCTGGACTGATCCCTGAGGAATTCTTCCTGTTTCTTTATCCTAAAGCTGGTGTAACAGGACTCTATGTGCTCGGA
ATTGGGCTTATTTTGTATGCTTTATCCAAAGAAATATATGTGATTACCACAGAGACCTTCTCTACCATATCAGTAGTAGG
GTTACTTGTCTATGCAATTAAAAAATATGGTGCCTCTCTTGCAGAATTTGCTGATAAACTCAATGAGCAAAAACTTGTCC
AACTAGAAGAGGCGAAGCAGGCTTCCATCAAACAAATCCAGGATGCAACTGATTTGGAGAAGTCACAGCAGGTACTGCCA
TTACTTTTTGATGTGCAGAGGAAAAACATTCCTATGGCTTCAGAGTTTACTTACCAGGAACAGCTGTATAGAGTACATAA
GGAAGTAAAGAATTGCCTAGACTATCATATATCCGTGCAGAACATGATGCATCAAAAGGAACAAGAGCACATTATAAATT
GGGTGGAGAAGCATGTGGTTCAGAGCATCTCTGCACAGTAGGAAAAAGGAGACAATTCCCAAGTGCATTACAGACCTAAA
GCTGCTGGCAAAGAAGGCTCAAGCACAGCCAGTTATG

ORF - retro_hsap_1705 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.09 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMLSRVVLSAAATAAPSLKNAAFLGPGVLQATRTFHTGQPHLVPVPPLPEYGGKVRYGLIPEEFFQFLYPK
MLS.VVL.AA.T.A.SLKNAAFLGPGVLQATRTFHT.QPHL...PPLPEYGGKV..GLIPEEFF.FLYPK
RetrocopyMLSWVVLFAATTVALSLKNAAFLGPGVLQATRTFHTVQPHLALLPPLPEYGGKVHPGLIPEEFFLFLYPK
ParentalTGVTGPYVLGTGLILYALSKEIYVISAETFTALSVLGVMVYGIKKYGPFVADFADKLNEQKLAQLEEAKQ
.GVTG.YVLG.GLILYALSKEIYVI..ETF...SV.G..VY.IKKYG...A..A..........L.....
RetrocopyAGVTGLYVLGIGLILYALSKEIYVITTETFSTISVVGLLVYAIKKYG---ASLAEFADKLNEQKLVQLEE
ParentalASIQHIQNAIDTEKSQQALVQKRHYLFDVQRNNIAMALEVTYRERLYRVYKEVKNRLDYHISVQNMMRRK
A....I....D.........Q....LFDVQR.NI.MA.E.TY.E.LYRV.KEVKN.LDYHISVQNMM..K
RetrocopyAKQASIKQIQDATDLEKSQ-QVLPLLFDVQRKNIPMASEFTYQEQLYRVHKEVKNCLDYHISVQNMMHQK
ParentalEQEHMINWVEKHVVQSISTQ-QEKETIAKCIADLKLLAKKAQAQPVM
EQEH.INWVEKHVVQSIS.Q...KETI.KCI.DLKLLAKKAQAQPVM
RetrocopyEQEHIINWVEKHVVQSISAQ>RKKETIPKCITDLKLLAKKAQAQPVM

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 72 .67 RPM
bodymap2_adrenal 0 .00 RPM 98 .15 RPM
bodymap2_brain 0 .09 RPM 125 .71 RPM
bodymap2_breast 0 .00 RPM 96 .44 RPM
bodymap2_colon 0 .00 RPM 114 .82 RPM
bodymap2_heart 0 .02 RPM 320 .80 RPM
bodymap2_kidney 0 .00 RPM 217 .00 RPM
bodymap2_liver 0 .00 RPM 96 .64 RPM
bodymap2_lung 0 .00 RPM 71 .20 RPM
bodymap2_lymph_node 0 .00 RPM 80 .73 RPM
bodymap2_ovary 0 .00 RPM 100 .22 RPM
bodymap2_prostate 0 .00 RPM 128 .01 RPM
bodymap2_skeletal_muscle 0 .00 RPM 107 .09 RPM
bodymap2_testis 0 .06 RPM 129 .26 RPM
bodymap2_thyroid 0 .02 RPM 122 .69 RPM
bodymap2_white_blood_cells 0 .00 RPM 145 .06 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1705 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1705 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1705 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1705 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1705 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1154
Gorilla gorilla retro_ggor_1279
Parental genes homology:
Parental genes homology involve 26 parental genes, and 77 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000054331 retrocopy
retro_amel_1118,
Bos taurus ENSBTAG000000064411 retrocopy
retro_btau_745,
Callithrix jacchus ENSCJAG000000133539 retrocopies
retro_cjac_1943, retro_cjac_2270, retro_cjac_2482, retro_cjac_2747, retro_cjac_2815, retro_cjac_2854, retro_cjac_3067, retro_cjac_528, retro_cjac_833,
Cavia porcellus ENSCPOG000000140703 retrocopies
retro_cpor_1120, retro_cpor_448, retro_cpor_563,
Equus caballus ENSECAG000000185991 retrocopy
retro_ecab_494,
Echinops telfairi ENSETEG000000107133 retrocopies
retro_etel_105, retro_etel_1784, retro_etel_408,
Felis catus ENSFCAG000000283211 retrocopy
retro_fcat_1012,
Homo sapiens ENSG00000116459 6 retrocopies
retro_hsap_1705 , retro_hsap_1951, retro_hsap_3673, retro_hsap_3762, retro_hsap_3812, retro_hsap_828,
Gorilla gorilla ENSGGOG000000052156 retrocopies
retro_ggor_1279, retro_ggor_1721, retro_ggor_2482, retro_ggor_2530, retro_ggor_2564, retro_ggor_678,
Loxodonta africana ENSLAFG000000048091 retrocopy
retro_lafr_602,
Microcebus murinus ENSMICG000000119921 retrocopy
retro_mmur_846,
Myotis lucifugus ENSMLUG000000124171 retrocopy
retro_mluc_2184,
Macaca mulatta ENSMMUG000000033133 retrocopies
retro_mmul_1086, retro_mmul_1659, retro_mmul_1791,
Mus musculus ENSMUSG000000005632 retrocopies
retro_mmus_2215, retro_mmus_791,
Nomascus leucogenys ENSNLEG000000039718 retrocopies
retro_nleu_172, retro_nleu_2090, retro_nleu_2153, retro_nleu_2154, retro_nleu_2546, retro_nleu_260, retro_nleu_524, retro_nleu_975,
Oryctolagus cuniculus ENSOCUG000000078091 retrocopy
retro_ocun_25,
Otolemur garnettii ENSOGAG000000114863 retrocopies
retro_ogar_2102, retro_ogar_2295, retro_ogar_2887,
Pongo abelii ENSPPYG000000010323 retrocopies
retro_pabe_2056, retro_pabe_3012, retro_pabe_3111,
Pan troglodytes ENSPTRG000000010995 retrocopies
retro_ptro_1154, retro_ptro_1305, retro_ptro_2553, retro_ptro_2586, retro_ptro_578,
Pteropus vampyrus ENSPVAG000000106043 retrocopies
retro_pvam_1061, retro_pvam_1110, retro_pvam_283,
Sorex araneus ENSSARG000000021073 retrocopies
retro_sara_424, retro_sara_428, retro_sara_610,
Sarcophilus harrisii ENSSHAG000000131851 retrocopy
retro_shar_700,
Ictidomys tridecemlineatus ENSSTOG000000076303 retrocopies
retro_itri_1146, retro_itri_1219, retro_itri_503,
Tarsius syrichta ENSTSYG000000004205 retrocopies
retro_tsyr_1226, retro_tsyr_1553, retro_tsyr_1852, retro_tsyr_502, retro_tsyr_511,
Tursiops truncatus ENSTTRG000000015461 retrocopy
retro_ttru_1654,
Vicugna pacos ENSVPAG000000002062 retrocopies
retro_vpac_154, retro_vpac_319,

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 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .04 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 .03 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 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 .02 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .03 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 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .03 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 .00 RPM

Indel association:

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





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