RetrogeneDB ID:

retro_hsap_4258

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:43007107..43008037(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000269225
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GXYLT1
Ensembl ID:ENSG00000151233
Aliases:GXYLT1, GLT8D3
Description:glucoside xylosyltransferase 1 [Source:HGNC Symbol;Acc:27482]


Retrocopy-Parental alignment summary:






>retro_hsap_4258
GGTGAAAGACTGGAAGAAACTATGACCATGTTGAAGTCAGCTATTATTTTCAGGATCAAACCTCTTCAATTCCAGATTTT
TGCTGAAGATCAACTACATCATAGCTTTAAAGGAAGGCTTGACAGGGGTCATTTCTACAAATATTTAATTATACAATATA
CTCCATAACCTTTCCAAGTGAGAATGCAGCAGAGTGGAAAAACTCTTTAAACCATGTGGTTTGCAGAGATTGTCCTTGCC
GTTATTCCTGAAAGAAGTTGACTCTCACACTGATAGCCTTTTTAAAAGACCAGCTGATAATATTTGGTCTTTACTAAAGA
AATTTAATTCCACACAAATTCTGCAATGGCCCCAGAACACAAGGAATGTCAAATAGGATGGTATAGTCGCTGTGCTAGGC
ATCCATAGTGTGGAAAAGCTGGAGTAAACTCTGGAGTTATGTTGACAAACATGACTTGAATGAGAAGGAAGTATTTCAAG
AATAATATGACAACTGTGTGACTACAATGAGGAGATATACTTATGACATGGCTTAAAATATACAAGTTAAACATTACATG
GGCGATCAAGATCTGTTGGATATCCTGTTTTTTCATAATCCAGAAAGCCTTTTTGTCTTTCCGTGTCAATGGAAGTGTCG
TCCAGATCACTGTCTATATGGAAGCAGTTGCCAAGAAGCAGAAGAAGGAATCTTTATTTTTCACGGGAACAGAGGTGTTT
ACCATGATGATAAGCAACCAGCATTTAGAGCTGTTTATGAAGCACTGAGAAATTGTTCTTTTAAGATGACAATGTTCATT
CATTAATAAAACCTTTAGAATTGGAACTACAAAAAATAGTGCATACATATCGTGGAAAAATTTACTAAATATTTATCAAA
CAATTAGCAAAAACATAAGAGATCGCTATGTCAGATCACCAAAGGAAAGG

ORF - retro_hsap_4258 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.8 %
Parental protein coverage: 72.05 %
Number of stop codons detected: 5
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalGERLEETMTMLKSAIIFSIKPLQFHIFAEDQLHHSFKGRLDNW-SFLQTFNYTLYPITFPSENAAEWK-K
GERLEETMTMLKSAIIF.IKPLQF.IFAEDQLHHSFKGRLD...SFLQ.FNYT.Y.ITFPSENAAEWK.K
RetrocopyGERLEETMTMLKSAIIFRIKPLQFQIFAEDQLHHSFKGRLDRG<SFLQIFNYTIYSITFPSENAAEWK<K
ParentalLFKPCASQRLFLPLILKEVDSLLYVDTDILFLRPVDDIWSLLKKFNSTQI-AAMAPEHEEPRIGWYNRFA
LFKPC..QRL.LPL.LKEVDS.....TD.LF.RP.D.IWSLLKKFNSTQI..AMAPEH.E..IGWY.R.A
RetrocopyLFKPCGLQRLSLPLFLKEVDS----HTDSLFKRPADNIWSLLKKFNSTQI<SAMAPEHKECQIGWYSRCA
ParentalRHPYYGKTGVNSGVMLMNMTRMRRKYFKNDMTTVRLQWGDILMPLLKKYKLNITW-GDQDLLNIVFFHNP
RHP..GK.GVNSGVML.NMT.MRRKYFKN.MTTV.LQ.GDILM..LK.YKLNITW.GDQDLL.I.FFHNP
RetrocopyRHP*CGKAGVNSGVMLTNMT*MRRKYFKNNMTTV*LQ*GDILMTWLKIYKLNITW<GDQDLLDILFFHNP
ParentalESLFVFPCQWNYRPDHCIYGSNCQEAEEGGIFILHGNRGVYHDDKQPAFRAVYEALRNCSFE-DDNIRSL
ESLFVFPCQW..RPDHC.YGS.CQEAEE.GIFI.HGNRGVYHDDKQPAFRAVYEALRNCSF..DDN..SL
RetrocopyESLFVFPCQWKCRPDHCLYGSSCQEAEE-GIFIFHGNRGVYHDDKQPAFRAVYEALRNCSFK<DDNVHSL
ParentalLKPLELELQKTVHTYCGKIYKIFIKQLA-KSVRDRYARSPKEK
.KPLELELQK.VHTY.GKIY.IFIKQLA.K..RDRY.RSPKE.
RetrocopyIKPLELELQKIVHTYRGKIY*IFIKQLA<KNIRDRYVRSPKER

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 32 .48 RPM
bodymap2_adrenal 0 .00 RPM 18 .16 RPM
bodymap2_brain 0 .00 RPM 14 .81 RPM
bodymap2_breast 0 .00 RPM 24 .01 RPM
bodymap2_colon 0 .00 RPM 31 .52 RPM
bodymap2_heart 0 .00 RPM 16 .39 RPM
bodymap2_kidney 0 .00 RPM 39 .52 RPM
bodymap2_liver 0 .00 RPM 20 .38 RPM
bodymap2_lung 0 .00 RPM 22 .94 RPM
bodymap2_lymph_node 0 .00 RPM 28 .32 RPM
bodymap2_ovary 0 .00 RPM 38 .32 RPM
bodymap2_prostate 0 .00 RPM 19 .59 RPM
bodymap2_skeletal_muscle 0 .00 RPM 8 .33 RPM
bodymap2_testis 0 .00 RPM 38 .01 RPM
bodymap2_thyroid 0 .00 RPM 37 .79 RPM
bodymap2_white_blood_cells 0 .00 RPM 35 .08 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4258 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4258 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4258 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4258 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4258 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 8 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000151233 5 retrocopies
retro_hsap_2295, retro_hsap_4167, retro_hsap_4177, retro_hsap_4258 , retro_hsap_4267,
Gorilla gorilla ENSGGOG000000279283 retrocopies
retro_ggor_1702, retro_ggor_1950, retro_ggor_2798,
Monodelphis domestica ENSMODG000000089131 retrocopy
retro_mdom_512,
Mus musculus ENSMUSG000000361971 retrocopy
retro_mmus_2325,
Nomascus leucogenys ENSNLEG000000179471 retrocopy
retro_nleu_2700,
Pongo abelii ENSPPYG000000044192 retrocopies
retro_pabe_1849, retro_pabe_1976,
Pan troglodytes ENSPTRG000000048365 retrocopies
retro_ptro_1623, retro_ptro_2832, retro_ptro_2960, retro_ptro_3006, retro_ptro_848,
Rattus norvegicus ENSRNOG000000052341 retrocopy
retro_rnor_2754,

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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