RetrogeneDB ID:

retro_hsap_1525

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:15:92824712..92825316(+)
Located in intron of:ENSG00000260661
Retrocopy
information
Ensembl ID:ENSG00000258726
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DUXA
Ensembl ID:ENSG00000258873
Aliases:None
Description:double homeobox A [Source:HGNC Symbol;Acc:32179]


Retrocopy-Parental alignment summary:






>retro_hsap_1525
ATGGCTGAAGACACCTCTTCACATAAGATGGTGACAACAAATCACAGGCGCAGTCTCACCAAAATCACAGATCAGTTGAA
AATCCTCATCAATACCTTCAATCAAAAACCTTACCCAGGTTATGCTACCAAACAAAAACTTGCTTTAGAAATCAATACGG
AAGAGTCCAGAATCCAGATTTGGTTTCAGAATTGAAGAGCTGGATTCCAGAAAAGACCAGAACCTGGGACTTTAGAATCA
AGCCAGAGCCATGGGCAAGATCGACCTGATGCAGAGTTTCAAAGTAGAGAAGCCAGATGGTGTTGTACCACCTACAGCGC
CTCTCAATTAAGCACTCTCATCAAGGCATCTATGAAAAGCCCATACCCTGGGATTGATTCCAGAGAACAAGTTGCTGAAG
AAATTGGTGTTCCAGAGTTAAGAGTCCAAATCTGGTTCCAAAACTGAAGATCTAGATTTCATCTCCAGAGAAACAGGGAA
CCTGTTGTGTCCTTAGAACAAGAAGACCAGGGGCAAGATTTCTGAGGGACATCAAGGTACAGAAGATACACAAAATGGCA
CCAACCTCACTAGCAATTCTCATTTCTATAGAGCCAGAAGGTGG

ORF - retro_hsap_1525 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.49 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAEDTYSHKMVKTNHRRCRTKFTEEQLKILINTFNQKPYPGYATKQKLALEINTEESRIQIWFQNRRARH
MAEDT.SHKMV.TNHRR..TK.T..QLKILINTFNQKPYPGYATKQKLALEINTEESRIQIWFQN.RA..
RetrocopyMAEDTSSHKMVTTNHRRSLTKITD-QLKILINTFNQKPYPGYATKQKLALEINTEESRIQIWFQN*RA--
ParentalGFQKRPEAETLESSQSQGQDQPGVEFQSREARRCRTTYSASQLHTLIKAFMKNPYPGIDSREELAKEIGV
GFQKRPE..TLESSQS.GQD.P..EFQSREAR.C.TTYSASQL.TLIKA.MK.PYPGIDSRE..A.EIGV
RetrocopyGFQKRPEPGTLESSQSHGQDRPDAEFQSREARWCCTTYSASQLSTLIKASMKSPYPGIDSREQVAEEIGV
ParentalPESRVQIWFQNRRSRLLLQRKREPVASLEQEEQ-GKIPEGLQGAEDTQNGTNFTSDSHFSGARTW
PE.RVQIWFQN.RSR..LQR.REPV.SLEQE.Q.GKI.EG.QG.EDTQNGTN.TS.SHF..AR.W
RetrocopyPELRVQIWFQN*RSRFHLQRNREPVVSLEQEDQ>GKISEGHQGTEDTQNGTNLTSNSHFYRARRW

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 0 .04 RPM
bodymap2_adrenal 0 .00 RPM 0 .00 RPM
bodymap2_brain 0 .00 RPM 0 .00 RPM
bodymap2_breast 0 .00 RPM 0 .00 RPM
bodymap2_colon 0 .00 RPM 0 .00 RPM
bodymap2_heart 0 .00 RPM 0 .04 RPM
bodymap2_kidney 0 .00 RPM 0 .00 RPM
bodymap2_liver 0 .00 RPM 0 .00 RPM
bodymap2_lung 0 .00 RPM 0 .00 RPM
bodymap2_lymph_node 0 .00 RPM 0 .15 RPM
bodymap2_ovary 0 .00 RPM 0 .00 RPM
bodymap2_prostate 0 .00 RPM 0 .00 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .00 RPM
bodymap2_testis 0 .00 RPM 0 .02 RPM
bodymap2_thyroid 0 .00 RPM 0 .00 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1525 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1525 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1525 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1525 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1525 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1034
Gorilla gorilla retro_ggor_1167
Macaca mulatta retro_mmul_2157
Parental genes homology:
Parental genes homology involve 14 parental genes, and 42 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000255051 retrocopy
retro_dnov_701,
Felis catus ENSFCAG000000075451 retrocopy
retro_fcat_1027,
Homo sapiens ENSG00000258873 5 retrocopies
retro_hsap_1525 , retro_hsap_2454, retro_hsap_4100, retro_hsap_566, retro_hsap_663,
Gorilla gorilla ENSGGOG000000056507 retrocopies
retro_ggor_1017, retro_ggor_1076, retro_ggor_1167, retro_ggor_1528, retro_ggor_2133, retro_ggor_2752, retro_ggor_510,
Loxodonta africana ENSLAFG000000301671 retrocopy
retro_lafr_996,
Macaca mulatta ENSMMUG000000077885 retrocopies
retro_mmul_2157, retro_mmul_2363, retro_mmul_2396, retro_mmul_2441, retro_mmul_636,
Nomascus leucogenys ENSNLEG000000108863 retrocopies
retro_nleu_1935, retro_nleu_2214, retro_nleu_568,
Oryctolagus cuniculus ENSOCUG000000113311 retrocopy
retro_ocun_981,
Pongo abelii ENSPPYG000000104578 retrocopies
retro_pabe_1192, retro_pabe_1328, retro_pabe_1805, retro_pabe_3357, retro_pabe_3376, retro_pabe_518, retro_pabe_660, retro_pabe_802,
Pan troglodytes ENSPTRG000000288715 retrocopies
retro_ptro_1034, retro_ptro_1418, retro_ptro_2781, retro_ptro_424, retro_ptro_482,
Pteropus vampyrus ENSPVAG000000030201 retrocopy
retro_pvam_870,
Tupaia belangeri ENSTBEG000000053211 retrocopy
retro_tbel_3384,
Tarsius syrichta ENSTSYG000000142231 retrocopy
retro_tsyr_1577,
Tursiops truncatus ENSTTRG000000142002 retrocopies
retro_ttru_1277, retro_ttru_1768,

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 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 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 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .03 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 .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 .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).





Copyright © RetrogeneDB 2014-2017