RetrogeneDB ID:

retro_hsap_25

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:37012635..37012965(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000226976
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:COX6A1
Ensembl ID:ENSG00000111775
Aliases:COX6A1, COX6A, COX6AL
Description:cytochrome c oxidase subunit VIa polypeptide 1 [Source:HGNC Symbol;Acc:2277]


Retrocopy-Parental alignment summary:






>retro_hsap_25
ATGGCGGCAGTTGGTGTGTTCTCGGTTTCTCGGCTGCTGGGTCGGTCCCGCCCACAGCTGGGGCGGCCTATGTCGAGTGG
CGCCCATGGAGAAGAGGGCTCAGCTCGCATGTGGAAGACCCTCACCTTCTTCGTCGCGCTCCCCGGGGTGGCAGTCAGCA
TGCTGAATGTGTACCTGAAGTCGCACCACGGAGAGCACGAGAGACCCGAGTTCATCGCCTACCCCCATCTCCGCATCAGG
ACCAAGCCGTTTCCCTGGGGAGATGGTAACCATACTCTATTCCATAACCCTCATGTGAATCCACTTCCAACTGGCTACGA
AGATGAATAA

ORF - retro_hsap_25 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.17 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAVVGVSSVSRLLGRSRPQLGRPMSSGAHGEEGSARMWKTLTFFVALPGVAVSMLNVYLKSHHGEHERPE
MA.VGV.SVSRLLGRSRPQLGRPMSSGAHGEEGSARMWKTLTFFVALPGVAVSMLNVYLKSHHGEHERPE
RetrocopyMAAVGVFSVSRLLGRSRPQLGRPMSSGAHGEEGSARMWKTLTFFVALPGVAVSMLNVYLKSHHGEHERPE
ParentalFIAYPHLRIRTKPFPWGDGNHTLFHNPHVNPLPTGYEDE
FIAYPHLRIRTKPFPWGDGNHTLFHNPHVNPLPTGYEDE
RetrocopyFIAYPHLRIRTKPFPWGDGNHTLFHNPHVNPLPTGYEDE

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 .46 RPM 23 .89 RPM
bodymap2_adrenal 0 .57 RPM 30 .32 RPM
bodymap2_brain 0 .56 RPM 53 .79 RPM
bodymap2_breast 0 .14 RPM 26 .38 RPM
bodymap2_colon 0 .23 RPM 37 .69 RPM
bodymap2_heart 0 .02 RPM 7 .75 RPM
bodymap2_kidney 0 .27 RPM 69 .05 RPM
bodymap2_liver 0 .25 RPM 38 .40 RPM
bodymap2_lung 0 .05 RPM 26 .55 RPM
bodymap2_lymph_node 0 .31 RPM 31 .01 RPM
bodymap2_ovary 0 .12 RPM 17 .62 RPM
bodymap2_prostate 0 .09 RPM 29 .29 RPM
bodymap2_skeletal_muscle 0 .00 RPM 3 .53 RPM
bodymap2_testis 0 .25 RPM 31 .73 RPM
bodymap2_thyroid 0 .19 RPM 28 .68 RPM
bodymap2_white_blood_cells 0 .08 RPM 23 .21 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_25 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_25 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_25 retrocopy 5' end.

Lab - click to see more details

retro_hsap_25 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_25 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_54
Gorilla gorilla retro_ggor_176
Parental genes homology:
Parental genes homology involve 22 parental genes, and 74 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000127881 retrocopy
retro_btau_229,
Canis familiaris ENSCAFG000000314581 retrocopy
retro_cfam_506,
Choloepus hoffmanni ENSCHOG000000092222 retrocopies
retro_chof_2085, retro_chof_2579,
Cavia porcellus ENSCPOG000000064261 retrocopy
retro_cpor_1265,
Equus caballus ENSECAG000000125122 retrocopies
retro_ecab_578, retro_ecab_845,
Echinops telfairi ENSETEG000000168261 retrocopy
retro_etel_1482,
Felis catus ENSFCAG000000311889 retrocopies
retro_fcat_1049, retro_fcat_1399, retro_fcat_1505, retro_fcat_1518, retro_fcat_1653, retro_fcat_1891, retro_fcat_318, retro_fcat_753, retro_fcat_886,
Homo sapiens ENSG00000111775 1 retrocopy
retro_hsap_25 ,
Gorilla gorilla ENSGGOG000000141012 retrocopies
retro_ggor_176, retro_ggor_2527,
Myotis lucifugus ENSMLUG000000103304 retrocopies
retro_mluc_1127, retro_mluc_1405, retro_mluc_1879, retro_mluc_465,
Macaca mulatta ENSMMUG000000160002 retrocopies
retro_mmul_127, retro_mmul_2535,
Nomascus leucogenys ENSNLEG000000156444 retrocopies
retro_nleu_1116, retro_nleu_412, retro_nleu_484, retro_nleu_985,
Oryctolagus cuniculus ENSOCUG000000098736 retrocopies
retro_ocun_1320, retro_ocun_1668, retro_ocun_1700, retro_ocun_174, retro_ocun_1898, retro_ocun_1928,
Otolemur garnettii ENSOGAG0000000356118 retrocopies
retro_ogar_1068, retro_ogar_111, retro_ogar_1150, retro_ogar_1466, retro_ogar_188, retro_ogar_1904, retro_ogar_2063, retro_ogar_2312, retro_ogar_2933, retro_ogar_3021, retro_ogar_3106, retro_ogar_3190, retro_ogar_3227, retro_ogar_3240, retro_ogar_346, retro_ogar_852, retro_ogar_871, retro_ogar_872,
Pongo abelii ENSPPYG000000050284 retrocopies
retro_pabe_2905, retro_pabe_3087, retro_pabe_3206, retro_pabe_713,
Pan troglodytes ENSPTRG000000055323 retrocopies
retro_ptro_311, retro_ptro_54, retro_ptro_556,
Pteropus vampyrus ENSPVAG000000022263 retrocopies
retro_pvam_1060, retro_pvam_790, retro_pvam_910,
Rattus norvegicus ENSRNOG000000011702 retrocopies
retro_rnor_2581, retro_rnor_2680,
Tupaia belangeri ENSTBEG000000080184 retrocopies
retro_tbel_2490, retro_tbel_3010, retro_tbel_3167, retro_tbel_395,
Tarsius syrichta ENSTSYG000000115411 retrocopy
retro_tsyr_1025,
Tursiops truncatus ENSTTRG000000001422 retrocopies
retro_ttru_1873, retro_ttru_889,
Vicugna pacos ENSVPAG000000103591 retrocopy
retro_vpac_218,

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 = 0.81 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .81 RPM
CEU_NA11843 0 .40 RPM
CEU_NA11930 0 .55 RPM
CEU_NA12004 0 .46 RPM
CEU_NA12400 0 .67 RPM
CEU_NA12751 0 .29 RPM
CEU_NA12760 0 .67 RPM
CEU_NA12827 0 .38 RPM
CEU_NA12872 0 .49 RPM
CEU_NA12873 0 .48 RPM
FIN_HG00183 0 .66 RPM
FIN_HG00277 0 .26 RPM
FIN_HG00315 0 .72 RPM
FIN_HG00321 0 .30 RPM
FIN_HG00328 0 .57 RPM
FIN_HG00338 0 .40 RPM
FIN_HG00349 0 .65 RPM
FIN_HG00375 0 .51 RPM
FIN_HG00377 0 .55 RPM
FIN_HG00378 0 .45 RPM
GBR_HG00099 0 .38 RPM
GBR_HG00111 0 .43 RPM
GBR_HG00114 0 .53 RPM
GBR_HG00119 0 .48 RPM
GBR_HG00131 0 .29 RPM
GBR_HG00133 0 .55 RPM
GBR_HG00134 0 .26 RPM
GBR_HG00137 0 .33 RPM
GBR_HG00142 0 .28 RPM
GBR_HG00143 0 .45 RPM
TSI_NA20512 0 .45 RPM
TSI_NA20513 0 .41 RPM
TSI_NA20518 0 .80 RPM
TSI_NA20532 0 .31 RPM
TSI_NA20538 0 .32 RPM
TSI_NA20756 0 .55 RPM
TSI_NA20765 0 .27 RPM
TSI_NA20771 0 .26 RPM
TSI_NA20786 0 .34 RPM
TSI_NA20798 0 .22 RPM
YRI_NA18870 0 .68 RPM
YRI_NA18907 0 .55 RPM
YRI_NA18916 0 .21 RPM
YRI_NA19093 0 .57 RPM
YRI_NA19099 0 .51 RPM
YRI_NA19114 0 .26 RPM
YRI_NA19118 0 .79 RPM
YRI_NA19213 0 .33 RPM
YRI_NA19214 0 .20 RPM
YRI_NA19223 0 .48 RPM

Indel association:

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





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