RetrogeneDB ID:

retro_hsap_373

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:44620613..44620974(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000238037
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:OOSP1
Ensembl ID:ENSG00000214788
Aliases:None
Description:Oocyte-secreted protein 1 homolog [Source:UniProtKB/Swiss-Prot;Acc:A8MZH6]


Retrocopy-Parental alignment summary:






>retro_hsap_373
ATGAAGACTTTCCTGGGGTTAAAAGGACTCTTTCTGGTTCACTCCTTGATATCGACCTGTGCTGGGGATTGAGCAGCTGT
TCAAGTCCAACCCACCCAGTTTTGGTTCTATGCCAGGCTTAAATCCACGATATTTCACAATTCGTGTATGCCACCTGATG
AAGTGTTTTTAGGTGATGACTGCCTTGTAACCTAACATTTTGCCAAATGTTTATTGTAAATTTTTCTACCATCATCATTA
CTGTGGTATTGTAACTAAAACTCTCCAGGAAGTTATTCAGCTTAAAACTAAAATCGAGTATATCTCAAGTAACTCTACTG
TTTGATTTGAAATGCCTCTGTTATATGCTGTCTGCAATCAG

ORF - retro_hsap_373 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.12 %
Parental protein coverage: 97.56 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMKTILGFKGLFYLHSLIWTCAGDWSAIQVHCTQFWFFARIKPTIFYNLYVNPDEVFLGDGCHVT-HVLPN
MKT.LG.KGLF..HSLI.TCAGD..A.QV..TQFWF.AR.K.TIF.N....PDEVFLGD.C.VT...LPN
RetrocopyMKTFLGLKGLFLVHSLISTCAGD*AAVQVQPTQFWFYARLKSTIFHNSCMPPDEVFLGDDCLVT>NILPN
ParentalVYYEFFYHPHDCGIVTQPLQEVLLLKTKIRYISRDSTVRSEMPLSCVVHKQ
VY..FFYH.H.CGIVT..LQEV..LKTKI.YIS..STV..EMPL...V..Q
RetrocopyVYCKFFYHHHYCGIVTKTLQEVIQLKTKIEYISSNSTV*FEMPLLYAVCNQ

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 0 .00 RPM
bodymap2_adrenal 0 .00 RPM 0 .00 RPM
bodymap2_brain 0 .00 RPM 0 .05 RPM
bodymap2_breast 0 .00 RPM 0 .00 RPM
bodymap2_colon 0 .00 RPM 0 .00 RPM
bodymap2_heart 0 .00 RPM 0 .04 RPM
bodymap2_kidney 0 .00 RPM 0 .00 RPM
bodymap2_liver 0 .00 RPM 0 .00 RPM
bodymap2_lung 0 .00 RPM 0 .00 RPM
bodymap2_lymph_node 0 .00 RPM 0 .00 RPM
bodymap2_ovary 0 .00 RPM 0 .00 RPM
bodymap2_prostate 0 .00 RPM 0 .00 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .00 RPM
bodymap2_testis 0 .04 RPM 0 .02 RPM
bodymap2_thyroid 0 .00 RPM 0 .00 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_373 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_373 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_373 retrocopy 5' end.

Lab - click to see more details

retro_hsap_373 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_373 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_292
Gorilla gorilla retro_ggor_383
Pongo abelii retro_pabe_331
Parental genes homology:
Parental genes homology involve 6 parental genes, and 50 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000273481 retrocopy
retro_btau_1647,
Homo sapiens ENSG00000214788 2 retrocopies
retro_hsap_373 , retro_hsap_4328,
Gorilla gorilla ENSGGOG000000167926 retrocopies
retro_ggor_1709, retro_ggor_2172, retro_ggor_3079, retro_ggor_3085, retro_ggor_3086, retro_ggor_383,
Nomascus leucogenys ENSNLEG000000131943 retrocopies
retro_nleu_2825, retro_nleu_2997, retro_nleu_3033,
Pongo abelii ENSPPYG0000000322320 retrocopies
retro_pabe_1419, retro_pabe_1525, retro_pabe_1707, retro_pabe_1713, retro_pabe_1716, retro_pabe_1720, retro_pabe_1745, retro_pabe_1749, retro_pabe_1761, retro_pabe_2101, retro_pabe_3226, retro_pabe_3227, retro_pabe_3229, retro_pabe_331, retro_pabe_3530, retro_pabe_3539, retro_pabe_3546, retro_pabe_3561, retro_pabe_3580, retro_pabe_3585,
Pan troglodytes ENSPTRG0000003450618 retrocopies
retro_ptro_1635, retro_ptro_2588, retro_ptro_2591, retro_ptro_2593, retro_ptro_292, retro_ptro_3066, retro_ptro_3081, retro_ptro_3082, retro_ptro_3084, retro_ptro_3085, retro_ptro_3087, retro_ptro_3088, retro_ptro_3284, retro_ptro_3289, retro_ptro_3293, retro_ptro_3300, retro_ptro_3305, retro_ptro_3309,

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 ) 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 .00 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 .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 .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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