RetrogeneDB ID:

retro_hsap_4748

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:119407006..119407384(+)
Located in intron of:ENSG00000125355
Retrocopy
information
Ensembl ID:ENSG00000232042
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PFDN4
Ensembl ID:ENSG00000101132
Aliases:PFDN4, C1, PFD4
Description:prefoldin subunit 4 [Source:HGNC Symbol;Acc:8868]


Retrocopy-Parental alignment summary:






>retro_hsap_4748
GCTGCAGAAAATTTCAACGCTACTTTTGAAGATCAACATTAGGTAAACAAATTTGCAAGGAATATGAGTAGAATCACAGA
GCTGAAGGAAGAAACAGAAGTTAAAAGGAAACAACTCCACAATTTAGAAGTTGTTTGCAATGACATCATGCTTGCAGATG
ATGACTGCTTAATGATACCTTATCAAATTGGTGATGTTTTCATTAGCCATTCTCAAGATGAAACACAAGAAATGTTAGAA
GAAGCAAAGAAAAATTGGTAAGAAGAAACTGATGCCTTAGAATCCAGAGTGGTATCAATTCAGTGAGTGTTAGTAGATTT
GAAACTTCAGTTATATACAAAATTTGGGGGTAACATAAACCTTAAAGCTAATGAAAAT

ORF - retro_hsap_4748 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.37 %
Parental protein coverage: 94.03 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAAEDVNVTFEDQQKINKFARNTSRITELKEEIEVKKKQLQNLEDACDDIMLADDDCLMIPYQIGDVFISH
AAE..N.TFEDQ...NKFARN.SRITELKEE.EVK.KQL.NLE..C.DIMLADDDCLMIPYQIGDVFISH
RetrocopyAAENFNATFEDQH*VNKFARNMSRITELKEETEVKRKQLHNLEVVCNDIMLADDDCLMIPYQIGDVFISH
ParentalSQEETQEMLEEAKKNLQEEIDALESRVESIQRVLADLKVQLYAKFGSNINLEADES
SQ.ETQEMLEEAKKN..EE.DALESRV.SIQ.VL.DLK.QLY.KFG.NINL.A.E.
RetrocopySQDETQEMLEEAKKNW*EETDALESRVVSIQ*VLVDLKLQLYTKFGGNINLKANEN

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 14 .03 RPM
bodymap2_adrenal 0 .00 RPM 19 .43 RPM
bodymap2_brain 0 .00 RPM 28 .76 RPM
bodymap2_breast 0 .00 RPM 19 .65 RPM
bodymap2_colon 0 .00 RPM 25 .47 RPM
bodymap2_heart 0 .00 RPM 12 .35 RPM
bodymap2_kidney 0 .00 RPM 12 .18 RPM
bodymap2_liver 0 .00 RPM 7 .18 RPM
bodymap2_lung 0 .00 RPM 9 .39 RPM
bodymap2_lymph_node 0 .00 RPM 11 .82 RPM
bodymap2_ovary 0 .00 RPM 18 .33 RPM
bodymap2_prostate 0 .00 RPM 21 .41 RPM
bodymap2_skeletal_muscle 0 .00 RPM 5 .98 RPM
bodymap2_testis 0 .00 RPM 34 .41 RPM
bodymap2_thyroid 0 .00 RPM 16 .55 RPM
bodymap2_white_blood_cells 0 .00 RPM 14 .51 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4748 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4748 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4748 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4748 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4748 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2950
Macaca mulatta retro_mmul_2530
Parental genes homology:
Parental genes homology involve 23 parental genes, and 50 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000131642 retrocopies
retro_amel_1313, retro_amel_1469,
Bos taurus ENSBTAG000000088121 retrocopy
retro_btau_585,
Canis familiaris ENSCAFG000000118561 retrocopy
retro_cfam_60,
Callithrix jacchus ENSCJAG000000026153 retrocopies
retro_cjac_1996, retro_cjac_2869, retro_cjac_4114,
Cavia porcellus ENSCPOG000000124783 retrocopies
retro_cpor_1417, retro_cpor_1428, retro_cpor_598,
Erinaceus europaeus ENSEEUG000000027331 retrocopy
retro_eeur_597,
Felis catus ENSFCAG000000133552 retrocopies
retro_fcat_1031, retro_fcat_219,
Homo sapiens ENSG00000101132 2 retrocopies
retro_hsap_3693, retro_hsap_4748 ,
Gorilla gorilla ENSGGOG000000273372 retrocopies
retro_ggor_2497, retro_ggor_2950,
Myotis lucifugus ENSMLUG000000085823 retrocopies
retro_mluc_1343, retro_mluc_510, retro_mluc_940,
Mustela putorius furoENSMPUG000000061732 retrocopies
retro_mputfur_664, retro_mputfur_791,
Mus musculus ENSMUSG000000520331 retrocopy
retro_mmus_2763,
Nomascus leucogenys ENSNLEG000000070232 retrocopies
retro_nleu_1247, retro_nleu_2548,
Oryctolagus cuniculus ENSOCUG000000049405 retrocopies
retro_ocun_1210, retro_ocun_1432, retro_ocun_1525, retro_ocun_287, retro_ocun_344,
Otolemur garnettii ENSOGAG000000163751 retrocopy
retro_ogar_2411,
Ochotona princeps ENSOPRG000000053855 retrocopies
retro_opri_1006, retro_opri_211, retro_opri_396, retro_opri_425, retro_opri_866,
Oryzias latipes ENSORLG000000191791 retrocopy
retro_olat_25,
Pongo abelii ENSPPYG000000258401 retrocopy
retro_pabe_187,
Pan troglodytes ENSPTRG000000136412 retrocopies
retro_ptro_2504, retro_ptro_3161,
Sus scrofa ENSSSCG000000074872 retrocopies
retro_sscr_1009, retro_sscr_787,
Ictidomys tridecemlineatus ENSSTOG000000282531 retrocopy
retro_itri_1565,
Tarsius syrichta ENSTSYG000000089744 retrocopies
retro_tsyr_1040, retro_tsyr_1667, retro_tsyr_281, retro_tsyr_702,
Tursiops truncatus ENSTTRG000000038503 retrocopies
retro_ttru_103, retro_ttru_861, retro_ttru_898,

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 = 0.03 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 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 .03 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 .03 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:

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





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