RetrogeneDB ID:

retro_hsap_4812

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:41182183..41182588(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000226641
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SHISA5
Ensembl ID:ENSG00000164054
Aliases:SHISA5, SCOTIN
Description:shisa homolog 5 (Xenopus laevis) [Source:HGNC Symbol;Acc:30376]


Retrocopy-Parental alignment summary:






>retro_hsap_4812
ATGGGGTTCAGAGCGACCGTGGCCGTCGGCCTGACCATCTTTGTGCTGTCTGTCGTCACTATCATCATCTGCTTCACCTG
CTCCTGCTGCTCCCTCTACAAGATGTGCCGCTGACCATGTCCAGTTGTGAGCACCACCACGCCCACCACTGTGGTGCATG
CCCCTTACCCTCAGCCTCCAAGTGTGCCACCTAGCTACCCTGGACTACCAGGGCTACCACCCCATGCCCCCCCCAAGCCA
GGAATGCCAGCAGCATCCTACCCAGTGCAGTACCCATCACCTTACCCGGCCCAGCCCATGGGCCCGCCGGCCTACTTCGA
GACCCTGGCTGGAGGAGCAGCCACGCCCTACCCCACCAGCCAGCCTCCTTCCAACCCAGACTACATGGATGCCCCGAAGG
CGGCC

ORF - retro_hsap_4812 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.56 %
Parental protein coverage: 99.27 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGFGATLAVGLTIFVLSVVTIIICFTCSCCCLYKTCRRPRPVVTTTTSTTVVHAPYPQPPSVPPSYPG-P
MGF.AT.AVGLTIFVLSVVTIIICFTCSCC.LYK.CR.P.PVV.TTT.TTVVHAPYPQPPSVPPSYPG.P
RetrocopyMGFRATVAVGLTIFVLSVVTIIICFTCSCCSLYKMCR*PCPVVSTTTPTTVVHAPYPQPPSVPPSYPGLP
ParentalSYQGYHTMPPQPGMPAAPYPMQYPPPYPAQPMGPPAYHETLAGGAAAPYPASQPPYNPAYMDAPKAA
.........P..GMPAA.YP.QYP.PYPAQPMGPPAY.ETLAGGAA.PYP.SQPP.NP.YMDAPKAA
RetrocopyGLPPHXXXKP--GMPAASYPVQYPSPYPAQPMGPPAYFETLAGGAATPYPTSQPPSNPDYMDAPKAA

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 102 .03 RPM
bodymap2_adrenal 0 .02 RPM 106 .83 RPM
bodymap2_brain 0 .00 RPM 35 .11 RPM
bodymap2_breast 0 .02 RPM 67 .51 RPM
bodymap2_colon 0 .00 RPM 77 .65 RPM
bodymap2_heart 0 .02 RPM 23 .85 RPM
bodymap2_kidney 0 .00 RPM 74 .47 RPM
bodymap2_liver 0 .00 RPM 49 .70 RPM
bodymap2_lung 0 .00 RPM 174 .09 RPM
bodymap2_lymph_node 0 .00 RPM 118 .18 RPM
bodymap2_ovary 0 .00 RPM 105 .16 RPM
bodymap2_prostate 0 .00 RPM 120 .53 RPM
bodymap2_skeletal_muscle 0 .00 RPM 20 .53 RPM
bodymap2_testis 0 .00 RPM 65 .82 RPM
bodymap2_thyroid 0 .02 RPM 60 .24 RPM
bodymap2_white_blood_cells 0 .00 RPM 253 .76 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4812 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4812 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4812 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4812 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4812 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2996
Macaca mulatta retro_mmul_2565
Callithrix jacchus retro_cjac_4152
Parental genes homology:
Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000029152 retrocopies
retro_cjac_4077, retro_cjac_4152,
Homo sapiens ENSG00000164054 2 retrocopies
retro_hsap_4706, retro_hsap_4812 ,
Gorilla gorilla ENSGGOG000000282072 retrocopies
retro_ggor_2996, retro_ggor_86,
Macaca mulatta ENSMMUG000000100621 retrocopy
retro_mmul_2565,
Nomascus leucogenys ENSNLEG000000064851 retrocopy
retro_nleu_1984,
Pongo abelii ENSPPYG000000139023 retrocopies
retro_pabe_2120, retro_pabe_3653, retro_pabe_3739,
Pan troglodytes ENSPTRG000000148881 retrocopy
retro_ptro_3128,

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 = 0.02 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 .02 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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