RetrogeneDB ID:

retro_hsap_2798

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:63188896..63189052(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000240359
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:UBL5
Ensembl ID:ENSG00000198258
Aliases:UBL5, HUB1
Description:ubiquitin-like 5 [Source:HGNC Symbol;Acc:13736]


Retrocopy-Parental alignment summary:






>retro_hsap_2798
GAGACCTTAAGAGACCGTAAGAAGCTGATTGCAGCCCAAGCTGTCACCCATTGTAAAAAGATTATCCTGAAGAAATGGTA
CATGATTTTTAGGGACCACACGATACTGGGGGACCATGAAATCCATGATGGGATGGACCTGGAGCTTTATTTTCAA

ORF - retro_hsap_2798 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.31 %
Parental protein coverage: 71.23 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLELYYQ
.T..D.KKLIAAQ..T...KI.LKKWY.IF.DH..LGD.EIHDGM.LELY.Q
RetrocopyETLRDRKKLIAAQAVTHCKKIILKKWYMIFRDHTILGDHEIHDGMDLELYFQ

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 54 .49 RPM
bodymap2_adrenal 0 .00 RPM 75 .20 RPM
bodymap2_brain 0 .00 RPM 74 .42 RPM
bodymap2_breast 0 .00 RPM 74 .94 RPM
bodymap2_colon 0 .00 RPM 85 .12 RPM
bodymap2_heart 0 .00 RPM 72 .66 RPM
bodymap2_kidney 0 .00 RPM 83 .38 RPM
bodymap2_liver 0 .00 RPM 54 .23 RPM
bodymap2_lung 0 .00 RPM 78 .53 RPM
bodymap2_lymph_node 0 .00 RPM 69 .46 RPM
bodymap2_ovary 0 .00 RPM 80 .69 RPM
bodymap2_prostate 0 .00 RPM 86 .20 RPM
bodymap2_skeletal_muscle 0 .00 RPM 45 .00 RPM
bodymap2_testis 0 .00 RPM 125 .79 RPM
bodymap2_thyroid 0 .00 RPM 109 .15 RPM
bodymap2_white_blood_cells 0 .00 RPM 89 .17 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2798 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2798 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2798 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2798 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2798 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1895
Pongo abelii retro_pabe_2226
Macaca mulatta retro_mmul_1437
Parental genes homology:
Parental genes homology involve 15 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000060971 retrocopy
retro_cjac_1394,
Dasypus novemcinctus ENSDNOG000000063845 retrocopies
retro_dnov_1858, retro_dnov_196, retro_dnov_2470, retro_dnov_2590, retro_dnov_860,
Homo sapiens ENSG00000198258 3 retrocopies
retro_hsap_1821, retro_hsap_2798 , retro_hsap_3154,
Gorilla gorilla ENSGGOG000000059991 retrocopy
retro_ggor_173,
Loxodonta africana ENSLAFG000000128922 retrocopies
retro_lafr_1245, retro_lafr_699,
Macropus eugenii ENSMEUG000000155062 retrocopies
retro_meug_300, retro_meug_304,
Myotis lucifugus ENSMLUG000000273692 retrocopies
retro_mluc_1516, retro_mluc_1766,
Macaca mulatta ENSMMUG000000078772 retrocopies
retro_mmul_1437, retro_mmul_1996,
Mus musculus ENSMUSG000000847861 retrocopy
retro_mmus_98,
Pongo abelii ENSPPYG000000095363 retrocopies
retro_pabe_1489, retro_pabe_2226, retro_pabe_2814,
Pan troglodytes ENSPTRG000000104513 retrocopies
retro_ptro_1170, retro_ptro_1895, retro_ptro_2280,
Pteropus vampyrus ENSPVAG000000086281 retrocopy
retro_pvam_1461,
Sarcophilus harrisii ENSSHAG000000109741 retrocopy
retro_shar_753,
Sus scrofa ENSSSCG000000233312 retrocopies
retro_sscr_544, retro_sscr_608,
Tursiops truncatus ENSTTRG000000085351 retrocopy
retro_ttru_166,

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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