RetrogeneDB ID:

retro_hsap_3327

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:60187759..60188838(-)
Located in intron of:ENSG00000049167
Retrocopy
information
Ensembl ID:ENSG00000215032
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GNL3L
Ensembl ID:ENSG00000130119
Aliases:None
Description:guanine nucleotide binding protein-like 3 (nucleolar)-like [Source:HGNC Symbol;Acc:25553]


Retrocopy-Parental alignment summary:






>retro_hsap_3327
GCTTTCAAGGCCAGGACCCAGCATCAGGTCAGCTTTGGAGCTGAAAACCTCATGAGGGTTCTGGGGAACTATTGCTGCCT
TGGTGAAATGCGCACCCACATCCATATGGACATTGTAGGCCTTCCCAATATTGGGAAAAGCAGCCTGATTAAAAGCCTGA
AGCACAGCCATGCATGCAGTGTGGGAGCCATTCCTGGGGTCACGAAATTCATGCAGGAGGTCTACCTGGACAAGTTCATC
CGGCTGCTGGATGCTCCAGCCATTGTTCCAGGGCCCAGCTCAGAGGTGGGCACCATCCTGCATAACTGCATCCACATCTA
GAGACTGGCAGACCCCATGACCCCAGTGGAGACCATCTTGCAGTGCTGCAACCTGGAGGAGATTTCCAACTATTACCTTC
TCTCTGGGTACCAGACTACTGAGCACTTTCTGACAGCAGTGGCCCACCATTTGGGGAAGAAGAGAGACTTACACAGTCAG
GAGCAGGCAGCCAAAACTGTCCTAGCTGACTGGGTGAGCGGGAAGATCAGCTTCTATAGACCACCACCACCCACTCACAC
TCTGCCTGCCCATCTCAGTGCTGAGAATTAAGGAAATGACCAAGTTCTTTGACATCGAGGATACCGAGCAAGTCAATGAA
GACACCATGGAATGCTTGGCCACTGGAGAATCTGATGAGCTATTGGGTGACACAGACCCACTCAAAATGGAGATCAAGTT
GCTCCATTCTCCGATGATGGAAATAGCAGATGCCATTGAAGATAAAGCTACTGTATATAAGATTGGAGATCTCACTGGTT
ATTGCACCAATCCGAATCGTCATCAGATGGGGTGGGCTAAACTCAATGTAGACCACCACCCTAAAAAAAAACAGTAAGGT
GGATGTGTGCCCAGTGGACTGCTGCCCAGTACTGCAGAGGATCATGGAGATGGACCCCCTACAACAGGGCCAGGCTCTAG
CATCCTCCCTGAAGAGTAAGAATTTACAGAAATGTGCAGATAAAATCCCCAGGGAGCTGTCTGATTCCATGATGTCTGCC
CTCCACCTCTCTGGCAATGCTGATGGCAGTGTTGGTAAC

ORF - retro_hsap_3327 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.23 %
Parental protein coverage: 62.37 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalASESLLKSKACFGAENLMRVLGNYCRLGEVRTHIRVGVVGLPNVGKSSLINSLKRSRACSVGAVPGITKF
A..........FGAENLMRVLGNYC.LGE.RTHI....VGLPN.GKSSLI.SLK.S.ACSVGA.PG.TKF
RetrocopyAFKARTQHQVSFGAENLMRVLGNYCCLGEMRTHIHMDIVGLPNIGKSSLIKSLKHSHACSVGAIPGVTKF
ParentalMQEVYLDKFIRLLDAPGIVPGPNSEVGTILRNCVHVQKLADPVTPVETILQRCNLEEISNYYGVSGFQTT
MQEVYLDKFIRLLDAP.IVPGP.SEVGTIL.NC.H...LADP.TPVETILQ.CNLEEISNYY..SG.QTT
RetrocopyMQEVYLDKFIRLLDAPAIVPGPSSEVGTILHNCIHI*RLADPMTPVETILQCCNLEEISNYYLLSGYQTT
ParentalEHFLTAVAHRLGKKKKGGLYSQEQAAKAVLADWVSGKISFYI-PP-PATHTLPTHLSAEIVKEMTEVFDI
EHFLTAVAH.LGKK....L.SQEQAAK.VLADWVSGKISFY..PP.P.T..LP...S....KEMT..FDI
RetrocopyEHFLTAVAHHLGKKRD--LHSQEQAAKTVLADWVSGKISFYRPPP>PLTLCLP--ISVLRIKEMTKFFDI
ParentalEDTEQANEDTMECLATGESDELLGDTDPLEMEIKLLHSPMTKIADAIENKTTVYKIGDLTGYCTNPNRHQ
EDTEQ.NEDTMECLATGESDELLGDTDPL.MEIKLLHSPM..IADAIE.K.TVYKIGDLTGYCTNPNRHQ
RetrocopyEDTEQVNEDTMECLATGESDELLGDTDPLKMEIKLLHSPMMEIADAIEDKATVYKIGDLTGYCTNPNRHQ
ParentalMGWAKRNVDHRP-KSNSMVDVCSVDRRSVLQRIMETDPLQQGQALASALKNKKKMQKRADKIASKLSDSM
MGWAK.NVDH.P....S.VDVC.VD...VLQRIME.DPLQQGQALAS.LK..K..QK.ADKI...LSDSM
RetrocopyMGWAKLNVDHHP>XXXSKVDVCPVDCCPVLQRIMEMDPLQQGQALASSLKS-KNLQKCADKIPRELSDSM
ParentalMSALDLSGNADDGVGD
MSAL.LSGNAD..VG.
RetrocopyMSALHLSGNADGSVGN

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 .18 RPM 20 .81 RPM
bodymap2_adrenal 0 .37 RPM 22 .21 RPM
bodymap2_brain 0 .21 RPM 7 .95 RPM
bodymap2_breast 0 .25 RPM 11 .63 RPM
bodymap2_colon 0 .02 RPM 7 .73 RPM
bodymap2_heart 0 .11 RPM 15 .51 RPM
bodymap2_kidney 0 .35 RPM 8 .67 RPM
bodymap2_liver 0 .00 RPM 5 .49 RPM
bodymap2_lung 0 .35 RPM 7 .05 RPM
bodymap2_lymph_node 0 .29 RPM 10 .91 RPM
bodymap2_ovary 0 .23 RPM 16 .46 RPM
bodymap2_prostate 0 .19 RPM 6 .75 RPM
bodymap2_skeletal_muscle 0 .00 RPM 20 .01 RPM
bodymap2_testis 0 .25 RPM 7 .64 RPM
bodymap2_thyroid 0 .32 RPM 22 .45 RPM
bodymap2_white_blood_cells 0 .30 RPM 30 .16 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3327 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3327 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3327 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3327 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3327 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1296
Pongo abelii retro_pabe_2742
Macaca mulatta retro_mmul_2084
Callithrix jacchus retro_cjac_1853
Parental genes homology:
Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000002522 retrocopies
retro_cjac_1591, retro_cjac_1853,
Homo sapiens ENSG00000130119 1 retrocopy
retro_hsap_3327 ,
Gorilla gorilla ENSGGOG000000075501 retrocopy
retro_ggor_1296,
Microcebus murinus ENSMICG000000101441 retrocopy
retro_mmur_662,
Macaca mulatta ENSMMUG000000082311 retrocopy
retro_mmul_2084,
Nomascus leucogenys ENSNLEG000000162331 retrocopy
retro_nleu_1672,
Oryzias latipes ENSORLG000000141171 retrocopy
retro_olat_29,
Pongo abelii ENSPPYG000000203831 retrocopy
retro_pabe_2742,

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 = 1.31 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .66 RPM
CEU_NA11843 0 .54 RPM
CEU_NA11930 1 .08 RPM
CEU_NA12004 0 .61 RPM
CEU_NA12400 0 .53 RPM
CEU_NA12751 1 .17 RPM
CEU_NA12760 0 .54 RPM
CEU_NA12827 0 .94 RPM
CEU_NA12872 1 .03 RPM
CEU_NA12873 1 .05 RPM
FIN_HG00183 1 .18 RPM
FIN_HG00277 1 .11 RPM
FIN_HG00315 0 .61 RPM
FIN_HG00321 1 .27 RPM
FIN_HG00328 0 .99 RPM
FIN_HG00338 0 .77 RPM
FIN_HG00349 0 .60 RPM
FIN_HG00375 0 .56 RPM
FIN_HG00377 0 .55 RPM
FIN_HG00378 0 .66 RPM
GBR_HG00099 1 .31 RPM
GBR_HG00111 0 .62 RPM
GBR_HG00114 1 .26 RPM
GBR_HG00119 1 .10 RPM
GBR_HG00131 0 .95 RPM
GBR_HG00133 0 .68 RPM
GBR_HG00134 0 .79 RPM
GBR_HG00137 0 .44 RPM
GBR_HG00142 1 .03 RPM
GBR_HG00143 0 .77 RPM
TSI_NA20512 0 .34 RPM
TSI_NA20513 0 .68 RPM
TSI_NA20518 0 .78 RPM
TSI_NA20532 1 .16 RPM
TSI_NA20538 0 .92 RPM
TSI_NA20756 0 .96 RPM
TSI_NA20765 0 .97 RPM
TSI_NA20771 0 .60 RPM
TSI_NA20786 0 .63 RPM
TSI_NA20798 0 .72 RPM
YRI_NA18870 0 .64 RPM
YRI_NA18907 0 .31 RPM
YRI_NA18916 0 .78 RPM
YRI_NA19093 0 .44 RPM
YRI_NA19099 0 .61 RPM
YRI_NA19114 0 .92 RPM
YRI_NA19118 0 .50 RPM
YRI_NA19213 0 .65 RPM
YRI_NA19214 0 .96 RPM
YRI_NA19223 0 .52 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).



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