RetrogeneDB ID:

retro_hsap_2305

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:109311205..109311441(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000233648
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:COX7B
Ensembl ID:ENSG00000131174
Aliases:None
Description:cytochrome c oxidase subunit VIIb [Source:HGNC Symbol;Acc:2291]


Retrocopy-Parental alignment summary:






>retro_hsap_2305
TTCGCTTGCTCAAAAAATGCAGTAAGTCATCTCCAAGATCAAAGCATTCAGCAAACAATGGCAAGGCAGAGCCACCAGAA
AAGTACACCTGATTTTCATGACAATACGATAATGCTGTATTAGCTAGTGGAGCCACTTTCTGTATTGCTATATGGACATA
TGTAGCAACACAAATCAGAATAGAATGGAACCTGTGCCCTGGTGGCAGAGTCACCCCAAAGGAATGGAGAGATCAG

ORF - retro_hsap_2305 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75. %
Parental protein coverage: 98.75 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalFPLVKSALNRLQVRSIQQTMARQSHQKRTPDFHD-KYGNAVLASGATFCIVTWTYVATQVGIEWNLSPVG
F...K.A...LQ..SIQQTMARQSHQK.TPDFHD..Y.NAVLASGATFCI..WTYVATQ..IEWNL.P.G
RetrocopyFACSKNAVSHLQDQSIQQTMARQSHQKSTPDFHD<QYDNAVLASGATFCIAIWTYVATQIRIEWNLCPGG
ParentalRVTPKEWRNQ
RVTPKEWR.Q
RetrocopyRVTPKEWRDQ

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 27 .65 RPM
bodymap2_adrenal 0 .00 RPM 69 .64 RPM
bodymap2_brain 0 .00 RPM 92 .35 RPM
bodymap2_breast 0 .08 RPM 85 .90 RPM
bodymap2_colon 0 .00 RPM 74 .64 RPM
bodymap2_heart 0 .00 RPM 308 .47 RPM
bodymap2_kidney 0 .00 RPM 160 .15 RPM
bodymap2_liver 0 .00 RPM 95 .48 RPM
bodymap2_lung 0 .00 RPM 74 .54 RPM
bodymap2_lymph_node 0 .00 RPM 59 .10 RPM
bodymap2_ovary 0 .00 RPM 49 .54 RPM
bodymap2_prostate 0 .00 RPM 78 .17 RPM
bodymap2_skeletal_muscle 0 .00 RPM 53 .51 RPM
bodymap2_testis 0 .00 RPM 42 .34 RPM
bodymap2_thyroid 0 .00 RPM 87 .55 RPM
bodymap2_white_blood_cells 0 .00 RPM 50 .58 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2305 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2305 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2305 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2305 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2305 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1629
Parental genes homology:
Parental genes homology involve 20 parental genes, and 101 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000061536 retrocopies
retro_amel_25, retro_amel_313, retro_amel_459, retro_amel_484, retro_amel_669, retro_amel_807,
Bos taurus ENSBTAG000000477683 retrocopies
retro_btau_214, retro_btau_22, retro_btau_59,
Callithrix jacchus ENSCJAG000000040455 retrocopies
retro_cjac_2496, retro_cjac_2716, retro_cjac_345, retro_cjac_844, retro_cjac_973,
Cavia porcellus ENSCPOG000000147812 retrocopies
retro_cpor_117, retro_cpor_252,
Echinops telfairi ENSETEG000000166959 retrocopies
retro_etel_1049, retro_etel_1180, retro_etel_1651, retro_etel_1736, retro_etel_1805, retro_etel_2057, retro_etel_59, retro_etel_860, retro_etel_910,
Felis catus ENSFCAG000000230912 retrocopies
retro_fcat_534, retro_fcat_590,
Homo sapiens ENSG00000131174 4 retrocopies
retro_hsap_157, retro_hsap_16, retro_hsap_2305 , retro_hsap_920,
Gorilla gorilla ENSGGOG000000233479 retrocopies
retro_ggor_1539, retro_ggor_1617, retro_ggor_1634, retro_ggor_1707, retro_ggor_1779, retro_ggor_245, retro_ggor_443, retro_ggor_52, retro_ggor_579,
Loxodonta africana ENSLAFG000000229964 retrocopies
retro_lafr_27, retro_lafr_555, retro_lafr_716, retro_lafr_927,
Microcebus murinus ENSMICG000000145213 retrocopies
retro_mmur_256, retro_mmur_379, retro_mmur_56,
Myotis lucifugus ENSMLUG000000224433 retrocopies
retro_mluc_1491, retro_mluc_2521, retro_mluc_277,
Macaca mulatta ENSMMUG000000158615 retrocopies
retro_mmul_1120, retro_mmul_1941, retro_mmul_2400, retro_mmul_571, retro_mmul_800,
Mus musculus ENSMUSG000000312315 retrocopies
retro_mmus_195, retro_mmus_2062, retro_mmus_2157, retro_mmus_2731, retro_mmus_502,
Pongo abelii ENSPPYG0000002049418 retrocopies
retro_pabe_1824, retro_pabe_1904, retro_pabe_2016, retro_pabe_2017, retro_pabe_2025, retro_pabe_2026, retro_pabe_2028, retro_pabe_2029, retro_pabe_2030, retro_pabe_2034, retro_pabe_2038, retro_pabe_2121, retro_pabe_22, retro_pabe_270, retro_pabe_465, retro_pabe_587, retro_pabe_793, retro_pabe_836,
Pan troglodytes ENSPTRG000000220499 retrocopies
retro_ptro_12, retro_ptro_1431, retro_ptro_1510, retro_ptro_153, retro_ptro_1629, retro_ptro_1714, retro_ptro_3014, retro_ptro_349, retro_ptro_760,
Pteropus vampyrus ENSPVAG000000032372 retrocopies
retro_pvam_1, retro_pvam_1234,
Rattus norvegicus ENSRNOG000000284515 retrocopies
retro_rnor_2351, retro_rnor_2387, retro_rnor_2959, retro_rnor_763, retro_rnor_999,
Sus scrofa ENSSSCG000000309702 retrocopies
retro_sscr_938, retro_sscr_991,
Tursiops truncatus ENSTTRG000000043873 retrocopies
retro_ttru_1097, retro_ttru_556, retro_ttru_7,
Vicugna pacos ENSVPAG000000013242 retrocopies
retro_vpac_7, retro_vpac_87,

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 = 0.06 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 .06 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 .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:

The presence of retro_hsap_2305 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_2305 presence in various populations. Based on Kabza et al. 2015 (PubMed).


# Indel coordinates AFR, African AMR, Ad Mixed American EUR, European EAS, East Asian
ASW YRI LWK MXL PUR CLM CEU IBS GBR FIN TSI JPT CHB CHS
1. 2:109310323..109312000 76.23 81.82 86.6 79.55 63.64 71.67 60.59 57.14 65.73 70.97 53.57 93.82 98.45 98.5

Indel #1, located at the genomic coordinates 2:109310323..109312000.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 79.55 % Puerto Ricansfrom Puerto Rico PUR 63.64 % Colombians fromMedellin, Colombia CLM 71.67 % Americans of AfricanAncestry in SW USA ASW 76.23 % Yoruba in Ibadan,Nigeria YRI 81.82 % Luhya in Webuye,Kenya LWK 86.6 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 60.59 % Iberian Populationin Spain IBS 57.14 % British in Englandand Scotland GBR 65.73 % Finnish in Finland FIN 70.97 % Toscani in Italia TSI 53.57 % Han Chinese in Bejing,China CHB 98.45 % Japanese in Tokyo,Japan 93.82 % Southern Han Chinese CHS 98.5 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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