RetrogeneDB ID:

retro_hsap_562

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:43050887..43051172(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000270762
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FXYD6
Ensembl ID:ENSG00000137726
Aliases:None
Description:FXYD domain containing ion transport regulator 6 [Source:HGNC Symbol;Acc:4030]


Retrocopy-Parental alignment summary:






>retro_hsap_562
ATGGAGGTGGTGCTGATCTTTCTATGCAGCCTGTTGGCCCACATTGTCCTGGCCGATGCAGTTGAGAGGGAGAAGCAAAT
TGACCCTTTTCATTATGACTACCAGACCCTGAGGATTAGGGGGTTGGTATGTGCTGTGGTCCTCTTCTCCATTGGGATCC
TCCTTATCCTAGGTTGCAGATGCAAGTGCAGTTTCAATCAGAAGCCCAGGACCCCAGGAGAGGAGGAAGCCCAGGTGGAG
AACCTCATCACTGCAAATGCAACAAAGCTCCAGAAAGCAGAGAGC

ORF - retro_hsap_562 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80. %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMELVLVFLCSLLAPMVLASAAEKEKEMDPFHYDYQTLRIGGLVFAVVLFSVGILLILSRRCKCSFNQKPR
ME.VL.FLCSLLA..VLA.A.E.EK..DPFHYDYQTLRI.GLV.AVVLFS.GILLIL..RCKCSFNQKPR
RetrocopyMEVVLIFLCSLLAHIVLADAVEREKQIDPFHYDYQTLRIRGLVCAVVLFSIGILLILGCRCKCSFNQKPR
ParentalAPGDEEAQVENLITANATEPQKAEN
.PG.EEAQVENLITANAT..QKAE.
RetrocopyTPGEEEAQVENLITANATKLQKAES

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 18 .69 RPM
bodymap2_adrenal 0 .00 RPM 38 .18 RPM
bodymap2_brain 0 .02 RPM 130 .37 RPM
bodymap2_breast 0 .00 RPM 18 .72 RPM
bodymap2_colon 0 .00 RPM 135 .00 RPM
bodymap2_heart 0 .00 RPM 15 .32 RPM
bodymap2_kidney 0 .00 RPM 29 .08 RPM
bodymap2_liver 0 .00 RPM 6 .76 RPM
bodymap2_lung 0 .00 RPM 45 .76 RPM
bodymap2_lymph_node 0 .00 RPM 32 .07 RPM
bodymap2_ovary 0 .00 RPM 132 .59 RPM
bodymap2_prostate 0 .00 RPM 139 .15 RPM
bodymap2_skeletal_muscle 0 .00 RPM 3 .33 RPM
bodymap2_testis 0 .00 RPM 86 .59 RPM
bodymap2_thyroid 0 .00 RPM 22 .45 RPM
bodymap2_white_blood_cells 0 .00 RPM 12 .13 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_562 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_562 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_562 retrocopy 5' end.

Lab - click to see more details

retro_hsap_562 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_562 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 9 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000130441 retrocopy
retro_cjac_2098,
Erinaceus europaeus ENSEEUG000000119891 retrocopy
retro_eeur_382,
Homo sapiens ENSG00000137726 2 retrocopies
retro_hsap_562 , retro_hsap_662,
Gorilla gorilla ENSGGOG000000064732 retrocopies
retro_ggor_507, retro_ggor_574,
Macaca mulatta ENSMMUG000000076172 retrocopies
retro_mmul_2439, retro_mmul_2440,
Nomascus leucogenys ENSNLEG000000073482 retrocopies
retro_nleu_1982, retro_nleu_2890,
Otolemur garnettii ENSOGAG000000153942 retrocopies
retro_ogar_2451, retro_ogar_3061,
Pongo abelii ENSPPYG000000039183 retrocopies
retro_pabe_583, retro_pabe_644, retro_pabe_648,
Pan troglodytes ENSPTRG000000043293 retrocopies
retro_ptro_3127, retro_ptro_421, retro_ptro_481,

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 = 0.03 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 .03 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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