RetrogeneDB ID:

retro_hsap_3062

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:84298686..84299150(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000251647
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:C18orf21
Ensembl ID:ENSG00000141428
Aliases:C18orf21, HsT3108, PNAS-131, XTP13
Description:chromosome 18 open reading frame 21 [Source:HGNC Symbol;Acc:28802]


Retrocopy-Parental alignment summary:






>retro_hsap_3062
GATAAGAGTACTTTTGAAGAAATGTGTCCACACTGTTTGCAGTTGCTGATTCTGGATAACTCTTGAGTGTGTCTCAAACC
CAAAGCCACATTGACACCCAAAATACAGAAACTGATTAATCAAGAAGCATGAAATTATACACTCAGTTTTAAAGAAGCAA
AAATTGTGAAAAAATTCAAAGACGACAAAAGTGTATTGTTGATTACTTGTAAAACATGCCGCAGAACAGTGAAACATCAT
GGTAAGAGTAGAAGCTTTCTATCAGCATTGAAGAGCAATCCTACTACTCCTCAAGTAAACTCAGCCTGAAGACACCAAAG
AGAAGGACTGCAAACCCAAATCATGAGATGTCTGGTTCCAAAGGCAAAAGCCCAGTATTGATTTCCAGAACACCTACATC
TGGAGAGTCAGTATTTTCTTGCTCCCCAAAGAATGTGAGCAAAACAAAGAAACATTTCCCTCAA

ORF - retro_hsap_3062 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.77 %
Parental protein coverage: 70.45 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalDKSTFEETCPYCFQLLVLDNSRVRLKPKARLTPKIQKLLNREARNYTLSFKEAKMVKKFKDSKSVLLITC
DKSTFEE.CP.C.QLL.LDNS.V.LKPKA.LTPKIQKL.N.EA.NYTLSFKEAK.VKKFKD.KSVLLITC
RetrocopyDKSTFEEMCPHCLQLLILDNS*VCLKPKATLTPKIQKLINQEA*NYTLSFKEAKIVKKFKDDKSVLLITC
ParentalKTCNRTVKHHGKSRSFVSTLKSNPATP-TSKLSLKTPERRTANPNHDMSGSKGKSPASVFRTPTSGQSVS
KTC.RTVKHHGKSRSF.S.LKSNP.TP..SKLSLKTP.RRTANPNH.MSGSKGKSP....RTPTSG.SV.
RetrocopyKTCRRTVKHHGKSRSFLSALKSNPTTP<SSKLSLKTPKRRTANPNHEMSGSKGKSPVLISRTPTSGESVF
ParentalTCSSKNTSKTKKHFSQ
.CS.KN.SKTKKHF.Q
RetrocopySCSPKNVSKTKKHFPQ

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 5 .55 RPM
bodymap2_adrenal 0 .00 RPM 10 .13 RPM
bodymap2_brain 0 .00 RPM 7 .31 RPM
bodymap2_breast 0 .00 RPM 7 .37 RPM
bodymap2_colon 0 .00 RPM 7 .89 RPM
bodymap2_heart 0 .00 RPM 6 .42 RPM
bodymap2_kidney 0 .00 RPM 8 .15 RPM
bodymap2_liver 0 .00 RPM 6 .06 RPM
bodymap2_lung 0 .00 RPM 4 .83 RPM
bodymap2_lymph_node 0 .00 RPM 8 .10 RPM
bodymap2_ovary 0 .00 RPM 8 .40 RPM
bodymap2_prostate 0 .00 RPM 8 .71 RPM
bodymap2_skeletal_muscle 0 .00 RPM 13 .79 RPM
bodymap2_testis 0 .00 RPM 25 .51 RPM
bodymap2_thyroid 0 .00 RPM 10 .70 RPM
bodymap2_white_blood_cells 0 .00 RPM 10 .59 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3062 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3062 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3062 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3062 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3062 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1981
Gorilla gorilla retro_ggor_2102
Pongo abelii retro_pabe_2536
Macaca mulatta retro_mmul_1876
Callithrix jacchus retro_cjac_2169
Parental genes homology:
Parental genes homology involve 17 parental genes, and 25 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000295481 retrocopy
retro_cfam_1636,
Callithrix jacchus ENSCJAG000000210412 retrocopies
retro_cjac_1030, retro_cjac_2169,
Cavia porcellus ENSCPOG000000254491 retrocopy
retro_cpor_1461,
Felis catus ENSFCAG000000006261 retrocopy
retro_fcat_1717,
Homo sapiens ENSG00000141428 1 retrocopy
retro_hsap_3062 ,
Gorilla gorilla ENSGGOG000000263341 retrocopy
retro_ggor_2102,
Macaca mulatta ENSMMUG000000187821 retrocopy
retro_mmul_1876,
Monodelphis domestica ENSMODG000000256051 retrocopy
retro_mdom_260,
Mus musculus ENSMUSG000000242732 retrocopies
retro_mmus_1676, retro_mmus_610,
Nomascus leucogenys ENSNLEG000000062371 retrocopy
retro_nleu_1655,
Oryctolagus cuniculus ENSOCUG000000280462 retrocopies
retro_ocun_1910, retro_ocun_435,
Ochotona princeps ENSOPRG000000111632 retrocopies
retro_opri_1222, retro_opri_283,
Pongo abelii ENSPPYG000000091101 retrocopy
retro_pabe_2536,
Pan troglodytes ENSPTRG000000099732 retrocopies
retro_ptro_1981, retro_ptro_2935,
Pteropus vampyrus ENSPVAG000000091743 retrocopies
retro_pvam_1086, retro_pvam_1488, retro_pvam_629,
Tupaia belangeri ENSTBEG000000166701 retrocopy
retro_tbel_4056,
Tarsius syrichta ENSTSYG000000108172 retrocopies
retro_tsyr_1675, retro_tsyr_1787,

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 ) > 0 RPM = 0.03 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 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 .02 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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