RetrogeneDB ID:

retro_hsap_1264

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:13:48902217..48902636(-)
Located in intron of:ENSG00000139687
Retrocopy
information
Ensembl ID:ENSG00000177197
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PCNP
Ensembl ID:ENSG00000081154
Aliases:None
Description:PEST proteolytic signal containing nuclear protein [Source:HGNC Symbol;Acc:30023]


Retrocopy-Parental alignment summary:






>retro_hsap_1264
AGTAATGGAGAGGAAAGTTCCAGCCGCAGCGCTGAGAAGCGATCAGCTGAAGAAGAAGCTGCAGACCTCCAACAAAGCCT
GCAAAGATCTCCAACTTTGGATTTGCCATAGGTAGTCAGACGACAAAGAAAGCATCACCCATATCCATCAAACTTGGATC
AAGTAAGCCTAAAGAAACTGTTCCAACTCTTGCTCCAAAAACTCTTTCAGTAGCAGCAGCTTTTAATGAAGATGAAGATA
GTGAATCAGAGGAAAGGCCTCCAGAAGCAAAGATGAGGATGAAGAATATTGCAAGGGATACACCAACATCAGCTGGACCA
AACTCCTTCAATAAAGGAAAGCATGGGTTTTCTGATAACCAGAAGCTATGGGAGTGGAATATAAAATCTCATCTTCGAAA
TGTCTATGACCAAGACAAT

ORF - retro_hsap_1264 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.2 %
Parental protein coverage: 78.65 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSNGGESSSRSAEKRSAEEEAADL-PTKPTKISKFGFAIGSQTTKKASAISIKLGSSKPKETVPTLAPKTL
SNG.ESSSRSAEKRSAEEEAADL.PTKP.KIS.FGFAIGSQTTKKAS.ISIKLGSSKPKETVPTLAPKTL
RetrocopySNGEESSSRSAEKRSAEEEAADL<PTKPAKISNFGFAIGSQTTKKASPISIKLGSSKPKETVPTLAPKTL
ParentalSVAAAFNEDEDSEPEEMPPEAKMRMKNIGRDTPTSAGPNSFNKGKHGFSDNQKLWERNIKSHLGNVHDQD
SVAAAFNEDEDSE.EE.PPEAKMRMKNI.RDTPTSAGPNSFNKGKHGFSDNQKLWE.NIKSHL.NV.DQD
RetrocopySVAAAFNEDEDSESEERPPEAKMRMKNIARDTPTSAGPNSFNKGKHGFSDNQKLWEWNIKSHLRNVYDQD
ParentalN
N
RetrocopyN

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 140 .40 RPM
bodymap2_adrenal 0 .23 RPM 162 .77 RPM
bodymap2_brain 0 .00 RPM 255 .29 RPM
bodymap2_breast 0 .25 RPM 142 .14 RPM
bodymap2_colon 0 .00 RPM 259 .06 RPM
bodymap2_heart 0 .04 RPM 124 .85 RPM
bodymap2_kidney 0 .00 RPM 176 .71 RPM
bodymap2_liver 0 .00 RPM 51 .50 RPM
bodymap2_lung 0 .00 RPM 266 .40 RPM
bodymap2_lymph_node 0 .00 RPM 179 .19 RPM
bodymap2_ovary 0 .00 RPM 248 .32 RPM
bodymap2_prostate 0 .02 RPM 274 .14 RPM
bodymap2_skeletal_muscle 0 .00 RPM 131 .83 RPM
bodymap2_testis 0 .02 RPM 160 .16 RPM
bodymap2_thyroid 0 .00 RPM 224 .13 RPM
bodymap2_white_blood_cells 0 .00 RPM 161 .07 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1264 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1264 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1264 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1264 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1264 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_864
Gorilla gorilla retro_ggor_994
Pongo abelii retro_pabe_1051
Macaca mulatta retro_mmul_1312
Callithrix jacchus retro_cjac_401
Parental genes homology:
Parental genes homology involve 16 parental genes, and 70 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG0000000797211 retrocopies
retro_chof_1170, retro_chof_1215, retro_chof_2070, retro_chof_2280, retro_chof_2290, retro_chof_2553, retro_chof_2575, retro_chof_594, retro_chof_651, retro_chof_806, retro_chof_819,
Callithrix jacchus ENSCJAG000000005086 retrocopies
retro_cjac_101, retro_cjac_1569, retro_cjac_1722, retro_cjac_3205, retro_cjac_3332, retro_cjac_401,
Dasypus novemcinctus ENSDNOG000000088735 retrocopies
retro_dnov_1606, retro_dnov_259, retro_dnov_370, retro_dnov_910, retro_dnov_98,
Homo sapiens ENSG00000081154 3 retrocopies
retro_hsap_1130, retro_hsap_1155, retro_hsap_1264 ,
Gorilla gorilla ENSGGOG000000254234 retrocopies
retro_ggor_882, retro_ggor_901, retro_ggor_902, retro_ggor_994,
Loxodonta africana ENSLAFG000000055182 retrocopies
retro_lafr_1189, retro_lafr_458,
Microcebus murinus ENSMICG0000000807210 retrocopies
retro_mmur_1010, retro_mmur_1138, retro_mmur_1286, retro_mmur_148, retro_mmur_1535, retro_mmur_1547, retro_mmur_1625, retro_mmur_167, retro_mmur_458, retro_mmur_887,
Macaca mulatta ENSMMUG000000177823 retrocopies
retro_mmul_1312, retro_mmul_1377, retro_mmul_2598,
Mustela putorius furoENSMPUG000000116961 retrocopy
retro_mputfur_850,
Mus musculus ENSMUSG000000715334 retrocopies
retro_mmus_2331, retro_mmus_2339, retro_mmus_2822, retro_mmus_3034,
Nomascus leucogenys ENSNLEG000000032242 retrocopies
retro_nleu_2100, retro_nleu_2971,
Oryctolagus cuniculus ENSOCUG000000111107 retrocopies
retro_ocun_1072, retro_ocun_1144, retro_ocun_1496, retro_ocun_1537, retro_ocun_573, retro_ocun_687, retro_ocun_868,
Procavia capensis ENSPCAG000000070073 retrocopies
retro_pcap_161, retro_pcap_194, retro_pcap_273,
Pongo abelii ENSPPYG000000135915 retrocopies
retro_pabe_1051, retro_pabe_1598, retro_pabe_3778, retro_pabe_935, retro_pabe_961,
Pan troglodytes ENSPTRG000000151723 retrocopies
retro_ptro_676, retro_ptro_790, retro_ptro_864,
Rattus norvegicus ENSRNOG000000284111 retrocopy
retro_rnor_2138,

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 = 0.17 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .13 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .11 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .08 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .05 RPM
GBR_HG00119 0 .10 RPM
GBR_HG00131 0 .11 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .17 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .08 RPM
TSI_NA20513 0 .12 RPM
TSI_NA20518 0 .17 RPM
TSI_NA20532 0 .10 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .08 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .05 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .06 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .06 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .05 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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