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






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 .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

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2647 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2647 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2647 retrocopy 5' end.

Lab - click to see more details

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
retro_amel_1674,
Canis familiaris ENSCAFG000000010901 retrocopy
retro_cfam_369,
Callithrix jacchus ENSCJAG000000049993 retrocopies
retro_cjac_1194, retro_cjac_1527, retro_cjac_906,
Echinops telfairi ENSETEG000000107411 retrocopy
retro_etel_102,
Homo sapiens ENSG00000100410 3 retrocopies
retro_hsap_2033, retro_hsap_2647 , retro_hsap_2829,
Gorilla gorilla ENSGGOG000000011042 retrocopies
retro_ggor_1848, retro_ggor_1965,
Latimeria chalumnae ENSLACG000000120941 retrocopy
retro_lcha_25,
Microcebus murinus ENSMICG000000135201 retrocopy
retro_mmur_758,
Macaca mulatta ENSMMUG000000113543 retrocopies
retro_mmul_1390, retro_mmul_1471, retro_mmul_1503,
Mustela putorius furoENSMPUG000000163982 retrocopies
retro_mputfur_359, retro_mputfur_439,
Mus musculus ENSMUSG000000613603 retrocopies
retro_mmus_1070, retro_mmus_1071, retro_mmus_1155,
Oryctolagus cuniculus ENSOCUG000000127051 retrocopy
retro_ocun_640,
Otolemur garnettii ENSOGAG000000028391 retrocopy
retro_ogar_55,
Pongo abelii ENSPPYG000000118702 retrocopies
retro_pabe_1661, retro_pabe_2324,
Pan troglodytes ENSPTRG000000144273 retrocopies
retro_ptro_1352, retro_ptro_1917, retro_ptro_2479,
Pteropus vampyrus ENSPVAG000000011621 retrocopy
retro_pvam_66,
Rattus norvegicus ENSRNOG000000241703 retrocopies
retro_rnor_2660, retro_rnor_2704, retro_rnor_2712,
Tarsius syrichta ENSTSYG000000010821 retrocopy
retro_tsyr_259,
Tursiops truncatus ENSTTRG000000033691 retrocopy
retro_ttru_1483,

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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