RetrogeneDB ID:

retro_hsap_4740

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:112765732..112766262(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000220541
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PPIH
Ensembl ID:ENSG00000171960
Aliases:PPIH, CYP-20, CYPH, SnuCyp-20, USA-CYP
Description:peptidylprolyl isomerase H (cyclophilin H) [Source:HGNC Symbol;Acc:14651]


Retrocopy-Parental alignment summary:






>retro_hsap_4740
ATGGTGGTGGCAAATTCAAGCCCTGAGCCCCCGTGGTGTTCTTTGATGTCAGCATTGTCAGTCAGGAAGTTGGCCACATG
AAGATCCAGCTCTTTGTAGACATTGTGCCTAACACAGCTGAGAACTTTGGGCAGTTCTGCACTGGAGAATTCAGAGAAGA
TCGGGTTCCAATAGGATACAAAGGGAGCACCTTTCACAGGGTCATAAAGGATTTCATGATTCAGGGTGGAGATTTTGTTA
ATGGAGATGTTACTGGAGTCACCAGCATTTACCAGGGACCATTTGCAGATGAAAATTTTAAAATCAGATACCCAGCTCCG
GTCCTGCTTTCCATGGTGAACAGCAGTCCCAGTACAAATGGCTGTCAGTTCTTTATCACCCGCTCTAAGTGCAATGGCCT
GGATGGGAAGCATGTAGTGTTTGGAAAAATCACTGATGGACTTCTACTGATAAGAAAGATTGAAAATGTTCCCACAGGCA
CCAATAATAAGGCCAAGGTACATATGGTGATCTCACGGTGTGGGGAGATG

ORF - retro_hsap_4740 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.34 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMAVANSSPVNP-VVFFDVSIGGQEVGRMKIELFADVVPKTAENFRQFCTGEFRKDGVPIGYKGSTFHRVI
M.VANSSP..P.VVFFDVSI..QEVG.MKI.LF.D.VP.TAENF.QFCTGEFR.D.VPIGYKGSTFHRVI
RetrocopyMVVANSSPEPP<VVFFDVSIVSQEVGHMKIQLFVDIVPNTAENFGQFCTGEFREDRVPIGYKGSTFHRVI
ParentalKDFMIQGGDFVNGDGTGVASIYRGPFADENFKLRHSAPGLLSMANSGPSTNGCQFFITCSKCDWLDGKHV
KDFMIQGGDFVNGD.TGV.SIY.GPFADENFK.R..AP.LLSM.NS.PSTNGCQFFIT.SKC..LDGKHV
RetrocopyKDFMIQGGDFVNGDVTGVTSIYQGPFADENFKIRYPAPVLLSMVNSSPSTNGCQFFITRSKCNGLDGKHV
ParentalVFGKIIDGLLVMRKIENVPTGPNNKPKLPVVISQCGEM
VFGKI.DGLL..RKIENVPTG.NNK.K...VIS.CGEM
RetrocopyVFGKITDGLLLIRKIENVPTGTNNKAKVHMVISRCGEM

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 10 .79 RPM
bodymap2_adrenal 0 .00 RPM 22 .91 RPM
bodymap2_brain 0 .05 RPM 10 .95 RPM
bodymap2_breast 0 .00 RPM 11 .56 RPM
bodymap2_colon 0 .00 RPM 10 .98 RPM
bodymap2_heart 0 .00 RPM 6 .09 RPM
bodymap2_kidney 0 .00 RPM 7 .65 RPM
bodymap2_liver 0 .00 RPM 4 .10 RPM
bodymap2_lung 0 .00 RPM 10 .72 RPM
bodymap2_lymph_node 0 .00 RPM 15 .11 RPM
bodymap2_ovary 0 .00 RPM 15 .61 RPM
bodymap2_prostate 0 .00 RPM 13 .28 RPM
bodymap2_skeletal_muscle 0 .00 RPM 3 .53 RPM
bodymap2_testis 0 .00 RPM 21 .29 RPM
bodymap2_thyroid 0 .00 RPM 15 .52 RPM
bodymap2_white_blood_cells 0 .00 RPM 15 .71 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_4740 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4740 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4740 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4740 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4740 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3155
Gorilla gorilla retro_ggor_2945
Pongo abelii retro_pabe_3686
Callithrix jacchus retro_cjac_4110
Parental genes homology:
Parental genes homology involve 20 parental genes, and 42 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000005261 retrocopy
retro_amel_1481,
Bos taurus ENSBTAG000000045901 retrocopy
retro_btau_1530,
Callithrix jacchus ENSCJAG000000031455 retrocopies
retro_cjac_129, retro_cjac_1886, retro_cjac_2205, retro_cjac_3120, retro_cjac_4110,
Cavia porcellus ENSCPOG000000082148 retrocopies
retro_cpor_1511, retro_cpor_785, retro_cpor_786, retro_cpor_794, retro_cpor_795, retro_cpor_796, retro_cpor_797, retro_cpor_798,
Dipodomys ordii ENSDORG000000161523 retrocopies
retro_dord_151, retro_dord_173, retro_dord_447,
Homo sapiens ENSG000001371681 retrocopy
retro_hsap_2086,
Homo sapiens ENSG00000171960 2 retrocopies
retro_hsap_4740 , retro_hsap_928,
Gorilla gorilla ENSGGOG000000225072 retrocopies
retro_ggor_2945, retro_ggor_748,
Macropus eugenii ENSMEUG000000016911 retrocopy
retro_meug_1699,
Myotis lucifugus ENSMLUG000000254002 retrocopies
retro_mluc_1922, retro_mluc_2243,
Macaca mulatta ENSMMUG000000131291 retrocopy
retro_mmul_1124,
Mustela putorius furoENSMPUG000000139662 retrocopies
retro_mputfur_285, retro_mputfur_542,
Nomascus leucogenys ENSNLEG000000123132 retrocopies
retro_nleu_1242, retro_nleu_289,
Oryctolagus cuniculus ENSOCUG000000114531 retrocopy
retro_ocun_1195,
Procavia capensis ENSPCAG000000111391 retrocopy
retro_pcap_81,
Pongo abelii ENSPPYG000000014672 retrocopies
retro_pabe_3686, retro_pabe_797,
Pan troglodytes ENSPTRG000000006142 retrocopies
retro_ptro_3155, retro_ptro_644,
Pteropus vampyrus ENSPVAG000000055001 retrocopy
retro_pvam_107,
Ictidomys tridecemlineatus ENSSTOG000000001152 retrocopies
retro_itri_1248, retro_itri_412,
Tarsius syrichta ENSTSYG000000031822 retrocopies
retro_tsyr_224, retro_tsyr_647,

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 = 0.07 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 .07 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 .02 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:

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



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