RetrogeneDB ID:

retro_hsap_546

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:19026271..19027229(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000225509
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:AIFM1
Ensembl ID:ENSG00000156709
Aliases:AIFM1, AIF, CMT2D, CMTX4, COWCK, COXPD6, NADMR, NAMSD, PDCD8
Description:apoptosis-inducing factor, mitochondrion-associated, 1 [Source:HGNC Symbol;Acc:8768]


Retrocopy-Parental alignment summary:






>retro_hsap_546
GAACTGTGGTTTTCAGATGACTCAGATGTCACAAAGACAGTGTGATTCAGACAGTGGAATGGAAAAAGAGAGAAGCATGT
ATTTCCAGCCACCTCTTTCTGTGTCTCTGCCCAGGACTTGCCTCACATTGAGAATGGTGTTGTGGCCATCCTCACGAGGT
AGAAGATGGTATAGCTGAAAGTGAGAGGCAACACAGTGAAACTTAATGATGGCTCCCAAATAGCCTATGAAAACTGCTTG
ATTGCAACAAGAGGTCCTCCAAGAAGTCTGTCTGAAATTGATGAAGCTGGATCAGAGGTGAAGAGCAGAGCAACACTCTC
TAGAAAGATTGGAGACTCTAGGACTCTGGAGAAGATTTCATGGAAGTCAAGTCAATTATGGTTATCGGTGGGGGCTTGCT
TGGTGGTGAACTGGCCTGTGCTCTTGGCAGAAAGGGTTGGAGCCTTGGGCACAGAAGTGATTCACCTGTTTTCTGAGAAG
GGAAATATGGGAAAGGTCTTCTGCAAATCCCTCTGCAACTGAACCGTGGAAAAAGTCAGACGAGAGGGGGTTAAGATGAT
ACCCATTGCTGTTGTGCAACCGGTTGGAGTCAGCAGTGGCAAGTTACTCATCACGTTGAAAGATGGTGGGAAGGTAGAAA
CTGACCACATAGCAGCAGCCGTGAGCCTGAAGCCCAGTGCTGAGTTGGCCGAGAACTGGTGGGCTGGAAATAGGCCCAGA
TTTTGGTGGCTTCTGGGTAAATGTAGAGCTATACTCATGCCTAAACATCTGGGTGGCAGGAGATGCTGCATGCTTCTATG
ATATAAATCTGGGGAGGAGGCGGTTAGAGCACCATGATCAAGCTTTTGTGAGCAGAAGATTGGCTGGAGAAAATATGACT
GGAGCTGCTAAGCCGTATTGGCATCAGTCAGTGTGCTGGAATGATTTGAGCCCTGATGCTGGCTATGAAGCTATTGGC

ORF - retro_hsap_546 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.31 %
Parental protein coverage: 52.38 %
Number of stop codons detected: 4
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalELWFSDDPNVTKTLRFKQWNGK-ERSIYFQPP-SFYVSAQDLPHIENGGVAVLTGKKVVQLDVRDNMVKL
ELWFSDD..VTKT..F.QWNGK.ERS.YFQPP.SF.VSAQDLPHIENG.VA.LT..K.V.L.VR.N.VKL
RetrocopyELWFSDDSDVTKTV*FRQWNGK>ERSMYFQPP<SFCVSAQDLPHIENGVVAILTR*KMV*LKVRGNTVKL
ParentalNDGSQITYEKCLIATGGTPRSLSAIDRAGAEVKSRTTLFRKIGDFRSLEKIS-REVKSITIIGGGFLGSE
NDGSQI.YE.CLIAT.G.PRSLS.ID.AG.EVKSR.TL.RKIGD.R.LEKIS..EVKSI..IGGG.LG.E
RetrocopyNDGSQIAYENCLIATRGPPRSLSEIDEAGSEVKSRATLSRKIGDSRTLEKIS<MEVKSIMVIGGGLLGGE
ParentalLACALGRK-ARALGTEVIQLFPEKGNMGKILPEYLSNWTMEKVRREGVKVMPNAIVQSVGVSSGKLLIKL
LACALGRK...ALGTEVI.LF.EKGNMGK.....L.N.T.EKVRREGVK..P.A.VQ.VGVSSGKLLI.L
RetrocopyLACALGRK>VGALGTEVIHLFSEKGNMGKVFCKSLCN*TVEKVRREGVKMIPIAVVQPVGVSSGKLLITL
ParentalKDGRKVETDHIVAAVGLEPNVELA-KTGGLEIDSDFGGFRVNAELQARSNIWVAGDAACFYDIKLGRRRV
KDG.KVETDHI.AAV.L.P..ELA..TGGLEI..DFGGF.VN.EL....NIWVAGDAACFYDI.LGRRR.
RetrocopyKDGGKVETDHIAAAVSLKPSAELA>RTGGLEIGPDFGGFWVNVELYSCLNIWVAGDAACFYDINLGRRRL
ParentalEHHDHAVVSGRLAGENMTGAAKPYWHQSMFWSDLGPDVGYEAIG
EHHD.A.VS.RLAGENMTGAAKPYWHQS..W.DL.PD.GYEAIG
RetrocopyEHHDQAFVSRRLAGENMTGAAKPYWHQSVCWNDLSPDAGYEAIG

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 24 .07 RPM
bodymap2_adrenal 0 .00 RPM 28 .80 RPM
bodymap2_brain 0 .00 RPM 17 .37 RPM
bodymap2_breast 0 .00 RPM 35 .88 RPM
bodymap2_colon 0 .00 RPM 24 .98 RPM
bodymap2_heart 0 .00 RPM 78 .79 RPM
bodymap2_kidney 0 .00 RPM 140 .59 RPM
bodymap2_liver 0 .00 RPM 79 .55 RPM
bodymap2_lung 0 .00 RPM 12 .85 RPM
bodymap2_lymph_node 0 .00 RPM 20 .50 RPM
bodymap2_ovary 0 .00 RPM 36 .09 RPM
bodymap2_prostate 0 .00 RPM 22 .67 RPM
bodymap2_skeletal_muscle 0 .00 RPM 30 .56 RPM
bodymap2_testis 0 .02 RPM 46 .49 RPM
bodymap2_thyroid 0 .00 RPM 37 .76 RPM
bodymap2_white_blood_cells 0 .00 RPM 24 .39 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_546 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_546 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_546 retrocopy 5' end.

Lab - click to see more details

retro_hsap_546 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_546 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000187181 retrocopy
retro_dnov_767,
Homo sapiens ENSG00000156709 1 retrocopy
retro_hsap_546 ,
Gorilla gorilla ENSGGOG000000076351 retrocopy
retro_ggor_497,
Microcebus murinus ENSMICG000000160061 retrocopy
retro_mmur_492,
Tarsius syrichta ENSTSYG000000000601 retrocopy
retro_tsyr_615,

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 ) 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 .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_546 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_546 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. 10:19001659..19061500 100 100 100 100 100 100 100 100 100 100 99.49 100 100 100

Indel #1, located at the genomic coordinates 10:19001659..19061500.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 100 % Puerto Ricansfrom Puerto Rico PUR 100 % Colombians fromMedellin, Colombia CLM 100 % Americans of AfricanAncestry in SW USA ASW 100 % Yoruba in Ibadan,Nigeria YRI 100 % Luhya in Webuye,Kenya LWK 100 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 100 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 100 % Finnish in Finland FIN 100 % Toscani in Italia TSI 99.49 % Han Chinese in Bejing,China CHB 100 % Japanese in Tokyo,Japan 100 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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