RetrogeneDB ID:

retro_hsap_163

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:62654851..62655141(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000234204
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PIGP
Ensembl ID:ENSG00000185808
Aliases:PIGP, DCRC, DCRC-S, DSCR5, DSRC
Description:phosphatidylinositol glycan anchor biosynthesis, class P [Source:HGNC Symbol;Acc:3046]


Retrocopy-Parental alignment summary:






>retro_hsap_163
AGACTGTCTAAAGCCGTAGGATAGTCATGGAGAATTCACCATTACATCTGCCAGAAAGAGCAATGTATGGCTCTGTTCTT
TTCTTAAACTCCCAATTTGGCTTCATGCCTTGTCTACTATGGACTTTGGCTCCTGAATCTTGGCAAAATTCTTCATGCTT
AAATTATTGGCTTCAAAAATACTGGGCAGTTGCATTACCTGTCTACCTCCTTAGTACTATAGTAACCAGTTATGTACTCT
TTTTTGGCACTAAAGTAATGAGTATCTCTCTCTCCACTCAACTCCATTCG

ORF - retro_hsap_163 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.24 %
Parental protein coverage: 61.39 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalRLSKAPG-KMVENSPSPLPERAIYGFVLFLSSQFGFILYLVWAFIPESWLNSLGLTYWPQKYWAVALPVY
RLSKA.G....ENSP..LPERA.YG.VLFL.SQFGF...L.W...PESW.NS..L.YW.QKYWAVALPVY
RetrocopyRLSKAVG<IVMENSPLHLPERAMYGSVLFLNSQFGFMPCLLWTLAPESWQNSSCLNYWLQKYWAVALPVY
ParentalLLIAIVIGYVLLFGINMMSTSPLDSIHT
LL..IV..YVL.FG...MS.S.....H.
RetrocopyLLSTIVTSYVLFFGTKVMSISLSTQLHS

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 .81 RPM
bodymap2_adrenal 0 .00 RPM 9 .15 RPM
bodymap2_brain 0 .00 RPM 9 .00 RPM
bodymap2_breast 0 .00 RPM 16 .56 RPM
bodymap2_colon 0 .00 RPM 23 .38 RPM
bodymap2_heart 0 .00 RPM 17 .06 RPM
bodymap2_kidney 0 .00 RPM 10 .48 RPM
bodymap2_liver 0 .00 RPM 12 .51 RPM
bodymap2_lung 0 .00 RPM 9 .34 RPM
bodymap2_lymph_node 0 .00 RPM 9 .67 RPM
bodymap2_ovary 0 .00 RPM 10 .18 RPM
bodymap2_prostate 0 .00 RPM 35 .51 RPM
bodymap2_skeletal_muscle 0 .00 RPM 25 .04 RPM
bodymap2_testis 0 .00 RPM 24 .13 RPM
bodymap2_thyroid 0 .00 RPM 16 .85 RPM
bodymap2_white_blood_cells 0 .00 RPM 11 .89 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_163 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_163 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_163 retrocopy 5' end.

Lab - click to see more details

retro_hsap_163 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_163 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_156
Pongo abelii retro_pabe_464
Macaca mulatta retro_mmul_377
Parental genes homology:
Parental genes homology involve 22 parental genes, and 61 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000097024 retrocopies
retro_cfam_1022, retro_cfam_1559, retro_cfam_1976, retro_cfam_238,
Callithrix jacchus ENSCJAG000000026832 retrocopies
retro_cjac_1276, retro_cjac_2587,
Cavia porcellus ENSCPOG000000071562 retrocopies
retro_cpor_426, retro_cpor_680,
Equus caballus ENSECAG000000193491 retrocopy
retro_ecab_348,
Felis catus ENSFCAG000000284008 retrocopies
retro_fcat_1269, retro_fcat_1286, retro_fcat_1408, retro_fcat_1495, retro_fcat_1671, retro_fcat_181, retro_fcat_1859, retro_fcat_729,
Homo sapiens ENSG00000185808 4 retrocopies
retro_hsap_163 , retro_hsap_1909, retro_hsap_2110, retro_hsap_2423,
Gorilla gorilla ENSGGOG000000102753 retrocopies
retro_ggor_1397, retro_ggor_1508, retro_ggor_1639,
Macaca mulatta ENSMMUG000000162112 retrocopies
retro_mmul_377, retro_mmul_624,
Monodelphis domestica ENSMODG000000209881 retrocopy
retro_mdom_1807,
Mustela putorius furoENSMPUG000000083125 retrocopies
retro_mputfur_1069, retro_mputfur_1388, retro_mputfur_421, retro_mputfur_642, retro_mputfur_826,
Mus musculus ENSMUSG000000229401 retrocopy
retro_mmus_2841,
Nomascus leucogenys ENSNLEG000000045234 retrocopies
retro_nleu_1235, retro_nleu_1276, retro_nleu_1558, retro_nleu_2444,
Oryctolagus cuniculus ENSOCUG000000224513 retrocopies
retro_ocun_586, retro_ocun_664, retro_ocun_881,
Otolemur garnettii ENSOGAG000000110971 retrocopy
retro_ogar_2382,
Pongo abelii ENSPPYG000000114093 retrocopies
retro_pabe_1787, retro_pabe_1993, retro_pabe_464,
Pan troglodytes ENSPTRG000000138973 retrocopies
retro_ptro_1397, retro_ptro_1547, retro_ptro_156,
Pteropus vampyrus ENSPVAG000000008573 retrocopies
retro_pvam_1100, retro_pvam_1182, retro_pvam_682,
Sarcophilus harrisii ENSSHAG000000142841 retrocopy
retro_shar_548,
Sus scrofa ENSSSCG000000120611 retrocopy
retro_sscr_1085,