RetrogeneDB ID:

retro_hsap_2647

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:49812717..49813044(+)
Located in intron of:ENSG00000176095
Retrocopy
information
Ensembl ID:ENSG00000244730
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PHF5A
Ensembl ID:ENSG00000100410
Aliases:PHF5A, INI, Rds3, SAP14b, SF3B7, SF3b14b, bK223H9.2
Description:PHD finger protein 5A [Source:HGNC Symbol;Acc:18000]


Retrocopy-Parental alignment summary:






>retro_hsap_2647
ATGGCTAAACATCATCCTAATTTGATCTTTTGCTGCAAGCCAGCTGGTGTTGTCATTGGAAGATTGTGTGAAAAATGTGA
CAGCAAGTGTGTGATTTGTGACTTTGTGCGTCCCTGCACTCTGGTGTGCTATGTGATGAGTGTAACTACGTATCTTAGCA
GGGGTGCCGTGTGATCTGTGGAGGCCCTGGGGTCTCTGGTGCCTATTACTGTAAGGAGTGCACCATCTAGGAGAAGGATA
GAGATGGCTGCCCAAAGATTGTCAATTTGGGGAGCTCTAAGACAGACCTCTTCTACGAACACAAAAAAATGCAGCTTCAA
GAAGAGG

ORF - retro_hsap_2647 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.14 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAKHHPDLIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVR-ICDECNYGSYQGRCVICGGPGVSDA
MAKHHP.LIFC.K.AGV.IGRLCEKCD.KCVICD..VRPCTLV...CDECNY.S.QG..VICGGPGVS.A
RetrocopyMAKHHPNLIFCCKPAGVVIGRLCEKCDSKCVICD-FVRPCTLVC<LCDECNYVS*QGCRVICGGPGVSGA
ParentalYYCKECTIQEKDRDGCPKIVNLGSSKTDLFYERKKY-GFKKR
YYCKECTI.EKDRDGCPKIVNLGSSKTDLFYE.KK...FKKR
RetrocopyYYCKECTI*EKDRDGCPKIVNLGSSKTDLFYEHKKM>SFKKR

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 .04 RPM 9 .92 RPM
bodymap2_adrenal 0 .16 RPM 15 .07 RPM
bodymap2_brain 0 .02 RPM 8 .46 RPM
bodymap2_breast 0 .00 RPM 7 .72 RPM
bodymap2_colon 0 .00 RPM 14 .93 RPM
bodymap2_heart 0 .04 RPM 6 .70 RPM
bodymap2_kidney 0 .00 RPM 13 .26 RPM
bodymap2_liver 0 .00 RPM 10 .03 RPM
bodymap2_lung 0 .00 RPM 14 .87 RPM
bodymap2_lymph_node 0 .00 RPM 16 .83 RPM
bodymap2_ovary 0 .10 RPM 11 .62 RPM
bodymap2_prostate 0 .00 RPM 18 .46 RPM
bodymap2_skeletal_muscle 0 .00 RPM 12 .60 RPM
bodymap2_testis 0 .00 RPM 15 .67 RPM
bodymap2_thyroid 0 .00 RPM 13 .48 RPM
bodymap2_white_blood_cells 0 .00 RPM 26 .11 RPM
RNA Polymerase II actvity near the 5' end of retro_hsap_2647 was not detected
No EST(s) were mapped for retro_hsap_2647 retrocopy.
No TSS is located nearby retro_hsap_2647 retrocopy 5' end.
retro_hsap_2647 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2647 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1848

Parental genes homology:
Parental genes homology involve 19 parental genes, and 34 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000156871 retrocopy
Canis familiaris ENSCAFG000000010901 retrocopy
Callithrix jacchus ENSCJAG000000049993 retrocopies
Echinops telfairi ENSETEG000000107411 retrocopy
Homo sapiens ENSG00000100410 3 retrocopies
retro_hsap_2033, retro_hsap_2647 , retro_hsap_2829,
Gorilla gorilla ENSGGOG000000011042 retrocopies
Latimeria chalumnae ENSLACG000000120941 retrocopy
Microcebus murinus ENSMICG000000135201 retrocopy
Macaca mulatta ENSMMUG000000113543 retrocopies
Mustela putorius furoENSMPUG000000163982 retrocopies
Mus musculus ENSMUSG000000613603 retrocopies
Oryctolagus cuniculus ENSOCUG000000127051 retrocopy
Otolemur garnettii ENSOGAG000000028391 retrocopy
Pongo abelii ENSPPYG000000118702 retrocopies
Pan troglodytes ENSPTRG000000144273 retrocopies
Pteropus vampyrus ENSPVAG000000011621 retrocopy
Rattus norvegicus ENSRNOG000000241703 retrocopies
Tarsius syrichta ENSTSYG000000010821 retrocopy
Tursiops truncatus ENSTTRG000000033691 retrocopy

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 = 0.08 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 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 .06 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .08 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 .07 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .02 RPM


Indel association:

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




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