RetrogeneDB ID:

retro_hsap_782

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:56277172..56277672(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000254660
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:UCHL1
Ensembl ID:ENSG00000154277
Aliases:UCHL1, HEL-117, NDGOA, PARK5, PGP 9.5, PGP9.5, PGP95, Uch-L1
Description:ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase) [Source:HGNC Symbol;Acc:12513]


Retrocopy-Parental alignment summary:






>retro_hsap_782
TGCCAGCACCTGCCTACTCTTTGTATCAGAGCCTCACACAAGAACTTCAGGAAAAATTGATTGAAGAACTGAAGAGACAA
GGAGATAGTCCTAAAGGGTACTTCATGAAGCAGAGTATCGGAAACTTCTGTCACACAATTAGACTTATACATGCAATGGC
CAATAACCAAGACAAACTAAAATTTGAGGCAGGTCAATCCTGAAATATTTTATTTCTGACATGGAGAAAAATATCACTTG
AAGACAGCACAAAATCCTTTGAAAAGAATAAGGCCTTTCAGGCAGTTTATGAGGCTATCTTATAGCAAGGCCAATGTCAG
GCAGATGACAAAGTGAATTTTTGTTTTATTCTGTTTAGCAATGCGGATGGCCACCTCTCTGAACTTGGTGGATGAGTGCC
TTTCCTAGTGAACTATGGTGCCAGTTCAGAGGACTCACTGATGCAGGATTGTAGTGATTAGGCTGCCAAGGTCTGCATGA
AATTTACTAAGGAAGAAGAA

ORF - retro_hsap_782 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60.59 %
Parental protein coverage: 73.09 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalCALLLLFPLTAQHENFRK-KQIEELKGQEVSPKVYFMKQTIGNSCGTIGLIHAVANNQDKLGFEDG-SVL
C..L......A.H.NFRK.K.IEELK.Q..SPK.YFMKQ.IGN.C.TI.LIHA.ANNQDKL.FE.G.S.L
RetrocopyCQHLPTLCIRASHKNFRK<KLIEELKRQGDSPKGYFMKQSIGNFCHTIRLIHAMANNQDKLKFEAG<SIL
ParentalKQFLSETE-KMSPEDRAKCFEKNEAIQAAHDAVAQEGQCRVDDKVNFHFILFNNVDGHLYELDGRMPFPV
K.F.S..E.K.S.ED..K.FEKN.A.QA...A....GQC..DDKVNF.FILF.N.DGHL.EL.G..PF.V
RetrocopyKYFISDME>KISLEDSTKSFEKNKAFQAVYEAIL*QGQCQADDKVNFCFILFSNADGHLSELGG*VPFLV
ParentalNHGASSEDTLLKD----AAKVCREFTEREQ
N.GASSED.L..D....AAKVC..FT..E.
RetrocopyNYGASSEDSLMQDCSD*AAKVCMKFTKEEE

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 10 .85 RPM
bodymap2_adrenal 0 .00 RPM 5 .06 RPM
bodymap2_brain 0 .00 RPM 469 .22 RPM
bodymap2_breast 0 .00 RPM 83 .23 RPM
bodymap2_colon 0 .00 RPM 43 .35 RPM
bodymap2_heart 0 .00 RPM 5 .02 RPM
bodymap2_kidney 0 .00 RPM 67 .00 RPM
bodymap2_liver 0 .00 RPM 0 .34 RPM
bodymap2_lung 0 .00 RPM 7 .40 RPM
bodymap2_lymph_node 0 .00 RPM 15 .22 RPM
bodymap2_ovary 0 .00 RPM 31 .21 RPM
bodymap2_prostate 0 .00 RPM 40 .60 RPM
bodymap2_skeletal_muscle 0 .00 RPM 3 .89 RPM
bodymap2_testis 0 .00 RPM 23 .11 RPM
bodymap2_thyroid 0 .00 RPM 17 .70 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_782 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_782 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_782 retrocopy 5' end.

Lab - click to see more details

retro_hsap_782 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_782 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3029
Parental genes homology:
Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000193461 retrocopy
retro_cjac_365,
Erinaceus europaeus ENSEEUG000000021853 retrocopies
retro_eeur_150, retro_eeur_573, retro_eeur_598,
Echinops telfairi ENSETEG000000123471 retrocopy
retro_etel_44,
Homo sapiens ENSG00000154277 2 retrocopies
retro_hsap_781, retro_hsap_782 ,
Gorilla gorilla ENSGGOG000000088091 retrocopy
retro_ggor_648,
Macropus eugenii ENSMEUG000000137741 retrocopy
retro_meug_8,
Myotis lucifugus ENSMLUG000000101382 retrocopies
retro_mluc_1216, retro_mluc_2113,
Nomascus leucogenys ENSNLEG000000171762 retrocopies
retro_nleu_2582, retro_nleu_2583,
Oryctolagus cuniculus ENSOCUG000000013531 retrocopy
retro_ocun_309,
Pan troglodytes ENSPTRG000000160092 retrocopies
retro_ptro_3028, retro_ptro_3029,
Tarsius syrichta ENSTSYG000000083051 retrocopy
retro_tsyr_1191,

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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