RetrogeneDB ID:

retro_hsap_3123

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:172090518..172090963(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000248755
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:USE1
Ensembl ID:ENSG00000053501
Aliases:USE1, P31, SLT1
Description:unconventional SNARE in the ER 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:30882]


Retrocopy-Parental alignment summary:






>retro_hsap_3123
AAAAGAGTCTCCGAGGTGATTCATTAATATCTCTGTATGGTGGATTTTCCAGAGGAGATGCTGCAGGCAAAGAAACCGAC
CTCCTTCTCCATGAAGGCACCAGCCAACAAGTGTCTGGTCCCTGCCACATGCAGCCCACATCACAGAGAGAGTGCCTGCT
GCAATGACAGTGCATGTGTGGTCACCGTGGGGTACACCAGTGAGATGTGGAGTGAACTGCCGGCACTGGCTCTGCAGCAA
AGCCTGTGCAGAAAGTGAGAAAGAGGGCTGGAGTGGCAGGACAGAAGCCAGCGGAGGAGAAGCACTTGGGGGTGAACTAG
ACCTTCTCCTGCTGTGACATCAGAATCCCCAGGAAAAACTGGTGCAGGAGATTCTAGGCTTGGCCTAGAGTCTCAAGACA
CTGGCTACACAGAGCATCATCAAGAAGGACAATCAGACCGTCACA

ORF - retro_hsap_3123 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.32 %
Parental protein coverage: 58.3 %
Number of stop codons detected: 3
Number of frameshifts detected: 5


Retrocopy - Parental Gene Alignment:

ParentalKPASEVINEYSWKVDFLKGMLQAEKLTSSSEKALANQFLA-PGRVPTTAR-ERVPATKTVHLQS-RARYT
K..SEVI..Y...VDF...MLQA.K.TS.S.KA.AN..L..P.....T...ERVPA..TVH..S....YT
RetrocopyKRVSEVIH*YLCMVDFPEEMLQAKKPTSFSMKAPANKCLV<PCHMQPTSQ<ERVPAAMTVHVWS<TVGYT
ParentalSEMRSEL-LGTDSA-EPEMDVRKRTGVAGSQPVSEKQLAA-ELDLVLQRHQNLQEKLAEEMLGLARSLKT
SEM.SEL..GT.SA..P...VRKR.GVAG..P..EK.L...ELDL.L..HQN.QEKL..E.LGLA.SLKT
RetrocopySEMWSEL<AGTGSAAKPVQKVRKRAGVAGQKPAEEKHLGV<ELDLLLL*HQNPQEKLVQEILGLA*SLKT
ParentalNTLAAQSVIKKDNQTLS
..LA.QS.IKKDNQT..
Retrocopy--LATQSIIKKDNQTVT

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 7 .51 RPM
bodymap2_adrenal 0 .00 RPM 14 .37 RPM
bodymap2_brain 0 .00 RPM 11 .51 RPM
bodymap2_breast 0 .00 RPM 13 .93 RPM
bodymap2_colon 0 .00 RPM 10 .60 RPM
bodymap2_heart 0 .00 RPM 7 .05 RPM
bodymap2_kidney 0 .00 RPM 7 .84 RPM
bodymap2_liver 0 .00 RPM 10 .88 RPM
bodymap2_lung 0 .00 RPM 6 .10 RPM
bodymap2_lymph_node 0 .00 RPM 12 .19 RPM
bodymap2_ovary 0 .00 RPM 10 .66 RPM
bodymap2_prostate 0 .00 RPM 13 .60 RPM
bodymap2_skeletal_muscle 0 .00 RPM 15 .42 RPM
bodymap2_testis 0 .00 RPM 9 .99 RPM
bodymap2_thyroid 0 .00 RPM 11 .20 RPM
bodymap2_white_blood_cells 0 .00 RPM 8 .17 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_3123 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3123 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3123 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3123 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3123 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000053501 1 retrocopy
retro_hsap_3123 ,

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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