RetrogeneDB ID:

retro_hsap_3703

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:16928244..16928435(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000227965
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:LSM5
Ensembl ID:ENSG00000106355
Aliases:LSM5, YER146W
Description:LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:HGNC Symbol;Acc:17162]


Retrocopy-Parental alignment summary:






>retro_hsap_3703
ATGGCGGCTAACACTAGTACCAGCTCCTTACAGCTGCTACTGCTAGAGCTTGTAGACAAATGTAAGAATCAAAAATTCTC
ATTGTGATGAAAACTGATAAGGAAATTGTTGATACTCTTCTAGGATTTGATAACTTTGTCAATATGGTACTGCAAGATAT
CACTGAGTTTGAAATCCCACCAGAAGAAAGA

ORF - retro_hsap_3703 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.31 %
Parental protein coverage: 70.33 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAANATTNPSQLLPLELVDKCIG-SRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITPEGR
MAAN..T...QLL.LELVDKC...S.I.IVMK.DKEIV.TLLGFD.FVNMVL.D.TEFEI.PE.R
RetrocopyMAANTSTSSLQLLLLELVDKCKN<SKILIVMKTDKEIVDTLLGFDNFVNMVLQDITEFEIPPEER

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 14 .07 RPM
bodymap2_adrenal 0 .00 RPM 30 .58 RPM
bodymap2_brain 0 .00 RPM 21 .21 RPM
bodymap2_breast 0 .00 RPM 22 .96 RPM
bodymap2_colon 0 .00 RPM 25 .00 RPM
bodymap2_heart 0 .00 RPM 19 .24 RPM
bodymap2_kidney 0 .00 RPM 24 .63 RPM
bodymap2_liver 0 .00 RPM 18 .17 RPM
bodymap2_lung 0 .00 RPM 14 .28 RPM
bodymap2_lymph_node 0 .00 RPM 24 .56 RPM
bodymap2_ovary 0 .00 RPM 24 .79 RPM
bodymap2_prostate 0 .00 RPM 25 .32 RPM
bodymap2_skeletal_muscle 0 .00 RPM 10 .77 RPM
bodymap2_testis 0 .02 RPM 25 .77 RPM
bodymap2_thyroid 0 .00 RPM 32 .88 RPM
bodymap2_white_blood_cells 0 .00 RPM 22 .44 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3703 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3703 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3703 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3703 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3703 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2504
Parental genes homology:
Parental genes homology involve 11 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000091853 retrocopies
retro_cjac_1883, retro_cjac_2760, retro_cjac_3068,
Echinops telfairi ENSETEG000000180688 retrocopies
retro_etel_1305, retro_etel_1502, retro_etel_1907, retro_etel_198, retro_etel_2054, retro_etel_2193, retro_etel_454, retro_etel_964,
Homo sapiens ENSG00000106355 2 retrocopies
retro_hsap_3703 , retro_hsap_4216,
Gorilla gorilla ENSGGOG000000103252 retrocopies
retro_ggor_2504, retro_ggor_2824,
Microcebus murinus ENSMICG000000053533 retrocopies
retro_mmur_1345, retro_mmur_69, retro_mmur_950,
Myotis lucifugus ENSMLUG000000170281 retrocopy
retro_mluc_2439,
Oryctolagus cuniculus ENSOCUG000000290435 retrocopies
retro_ocun_1284, retro_ocun_1452, retro_ocun_1513, retro_ocun_1556, retro_ocun_903,
Ochotona princeps ENSOPRG000000024433 retrocopies
retro_opri_26, retro_opri_562, retro_opri_701,
Pongo abelii ENSPPYG000000176611 retrocopy
retro_pabe_3449,
Rattus norvegicus ENSRNOG000000421263 retrocopies
retro_rnor_1171, retro_rnor_567, retro_rnor_694,
Sus scrofa ENSSSCG000000260641 retrocopy
retro_sscr_385,

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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