RetrogeneDB ID:

retro_hsap_402

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:66041955..66043252(-)
Located in intron of:ENSG00000116678
Retrocopy
information
Ensembl ID:ENSG00000224570
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GALNT11
Ensembl ID:ENSG00000178234
Aliases:GALNT11, GALNACT11
Description:UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11 (GalNAc-T11) [Source:HGNC Symbol;Acc:19875]


Retrocopy-Parental alignment summary:






>retro_hsap_402
TTATCAGTAACTGCAGGCTACCACAGAGATGTGCCAGGGACAAAGAATACAGCATGTAAAGTCCTACCTCCTGACCTGCC
AGTTGCTTACATAATTGTTATCTGTTTCCACAATGAAGCTTTTTCTGCCCTGTCTCCAGATGCTGCACATTGTCACAAAT
TGCATGCCAGCAAACCTGCTTCATGAAATCATCTTTATGGATGTTGTTAGCGACCTTGATGACTTGAAAGGAGGACGAGA
TGAATATGTCCAAAAATACCTCCTTGGAAAAATTAAGGTATAAGAAACATAAAGTGTGAGGGATTGATTCAAGGAAGAAT
GAGTGTAGCAGTCCACACAACAGAAGTCCTTGTGTTCCTAGACAGCCAATTGAAGTGAATGTGATGTGGCAGCAGCCCTT
GCTGGCTGTCATCTGTGTGGACTAGCAGACCATGATGTTCTCAGTGATTGATATCATTAGTGCCAACACGCTAGCCTACA
GCTCATCCTCTGTTGTCCGTGGAGGATTCAACTGAGGGCTGCACTTCAAATAGGAGCTTGTTCCCCTTTCTGAGCTAGGA
TGAGCAGAAAAAGCCACAGCACCAACAAAGTCACCGATAATGGCTGGAGGATTGTTTGCCAGGAACAGACAGTATTTCCA
GGAACTTGGACAGTATGATACTGGCATGGATATCTGGAGAGGAGAAAACTTGGAAATAACATTTCAGATCTGGGTGTGTG
GAGGTAAGTTCTTCATCATGCCTTGCTCTACAGTAGGACACATTTTCCAAAAAAAGGGGACCATATGGATCTCCTGAAGG
CCGGGATGCCATGAACACAACTTTTTGCAGCTGGCACATGTCTGGCTGGATGAATAAAGGCGCAGTATTTTTCCTTAAGA
CTTAATCTGGAGAGGAAAAGCTTTGGAACCATCAGTGAGCATGTTGAATTGAGAAAGAAGTTAGGATGCAAATCATTTGA
ATGGTATTTGGGTAATATTTACCCAAAGATGCAGATATCTGGGACCCATGACAAATCCCAGCAACCCACTTTTATCAGTA
GAGGGCCAAAATGCCCCAAAGTCCTTCAACTTGGAAGGCTCTATCACCTCCAGACCAACAAATGTCTGGTGGCTCAGGGC
TGCCCAAGTTGGAAAGGAGGCCTACTAGTGCTTAAGACTTGTGAGCATGGGGACCCAAATCAGATCTGGATTTATAATGA
AGAGCATGAATTGGTTTTAAACCATCTTCTTTGTCTAGGTATGACAGAAACTAGCTCATCAGACCCACCACAACTCGTGG
AGTGCCATGGGTCAGGC

ORF - retro_hsap_402 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.85 %
Parental protein coverage: 71.55 %
Number of stop codons detected: 4
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalISDRLGYHRDVPDTRNAACKEKFYPPDLPAASV-VICFYNEAFSAL-LRTVHSVIDRTPAHLLHEIILVD
.S...GYHRDVP.T.N.ACK....PPDLP.A...VICF.NEAFSAL.L...H.V....PA.LLHEII..D
RetrocopyLSVTAGYHRDVPGTKNTACK--VLPPDLPVAYIIVICFHNEAFSAL>LQMLHIVTNCMPANLLHEIIFMD
ParentalDDSDFDDLKGELDEYVQKYLPGKIKV-IRNTKREGLIRGRMIGAAHATGEVLVFLDSHC-EVNVMWLQPL
..SD.DDLKG..DEYVQKYL.GKIKV.IRN.K.EGLI.GRM..A.H.T.EVLVFLDS...EVNVMW.QPL
RetrocopyVVSDLDDLKGGRDEYVQKYLLGKIKV<IRNIKCEGLIQGRMSVAVHTT-EVLVFLDSQL<EVNVMWQQPL
ParentalLAAIREDRHTVVCPVIDIISADTLAYSSSPVVRGGFNWGLHFKWDLVPLSELGRAEGATAPIKSPTMAGG
LA.I..D..T....VIDIISA.TLAYSSS.VVRGGFN.GLHFK..LVPLSELG.AE.ATAP.KSP.MAGG
RetrocopyLAVICVD*QTMMFSVIDIISANTLAYSSSSVVRGGFN*GLHFK*ELVPLSELG*AEKATAPTKSPIMAGG
ParentalLFAMNRQYFHELGQYDSGMDIWGGENLEISFRIWMCGGKLFIIPCSRVGHIF-RKRRPYGSPEGQDTMT-
LFA.NRQYF.ELGQYD.GMDIW.GENLEI.F.IW.CGGK.FI.PCS.VGHIF..KR.PYGSPEG.D.M..
RetrocopyLFARNRQYFQELGQYDTGMDIWRGENLEITFQIWVCGGKFFIMPCSTVGHIF>KKRGPYGSPEGRDAMN<
ParentalHNSLRLAHVWLDE-YKEQYFSLRPDLKTKSYGNISERVELRKKLGCKSFKWYLDNVYPEMQISGSHAKPQ
HN.L.LAHVWLDE..K.QYFSLR..L..KS.G.ISE.VELRKKLGCKSF.WYL.N.YP.MQISG.H.K.Q
RetrocopyHNFLQLAHVWLDE<IKAQYFSLRLNLERKSFGTISEHVELRKKLGCKSFEWYLGNIYPKMQISGTHDKSQ
ParentalQPIFVNRGPKRPKVLQRGRLYHLQTNKCLVAQGRPSQKGGLVVLKACDYSDPNQIWIYNEEHELVLNSLL
QP.F..RGPK.PKVLQ.GRLYHLQTNKCLVAQG.PS.KGGL.VLK.C...DPNQIWIYNEEHELVLN.LL
RetrocopyQPTFISRGPKCPKVLQLGRLYHLQTNKCLVAQGCPSWKGGLLVLKTCEHGDPNQIWIYNEEHELVLNHLL
ParentalCLDMSETRSSDPPRLMKCHGSG
CL.M.ET.SSDPP.L..CHGSG
RetrocopyCLGMTETSSSDPPQLVECHGSG

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 29 .60 RPM
bodymap2_adrenal 0 .00 RPM 35 .21 RPM
bodymap2_brain 0 .02 RPM 46 .97 RPM
bodymap2_breast 0 .02 RPM 38 .07 RPM
bodymap2_colon 0 .00 RPM 30 .51 RPM
bodymap2_heart 0 .00 RPM 18 .74 RPM
bodymap2_kidney 0 .00 RPM 84 .85 RPM
bodymap2_liver 0 .19 RPM 13 .27 RPM
bodymap2_lung 0 .39 RPM 29 .34 RPM
bodymap2_lymph_node 0 .00 RPM 35 .21 RPM
bodymap2_ovary 0 .02 RPM 43 .10 RPM
bodymap2_prostate 0 .00 RPM 54 .45 RPM
bodymap2_skeletal_muscle 0 .00 RPM 9 .11 RPM
bodymap2_testis 0 .00 RPM 25 .72 RPM
bodymap2_thyroid 0 .00 RPM 51 .48 RPM
bodymap2_white_blood_cells 0 .00 RPM 27 .44 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_402 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_402 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_402 retrocopy 5' end.

Lab - click to see more details

retro_hsap_402 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_402 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_308
Gorilla gorilla retro_ggor_399
Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000011211 retrocopy
retro_chof_1535,
Homo sapiens ENSG00000178234 1 retrocopy
retro_hsap_402 ,
Gorilla gorilla ENSGGOG000000087841 retrocopy
retro_ggor_399,
Nomascus leucogenys ENSNLEG000000046131 retrocopy
retro_nleu_1573,
Pan troglodytes ENSPTRG000000198911 retrocopy
retro_ptro_308,

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 = 0.05 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 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .03 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 .02 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:

The presence of retro_hsap_402 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_402 presence in various populations. Based on Kabza et al. 2015 (PubMed).


# Indel coordinates AFR, African AMR, Ad Mixed American EUR, European EAS, East Asian
ASW YRI LWK MXL PUR CLM CEU IBS GBR FIN TSI JPT CHB CHS
1. 1:66040938..66043900 96.72 94.32 91.24 100 96.36 100 100 100 100 100 100 100 100 100

Indel #1, located at the genomic coordinates 1:66040938..66043900.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 100 % Puerto Ricansfrom Puerto Rico PUR 96.36 % Colombians fromMedellin, Colombia CLM 100 % Americans of AfricanAncestry in SW USA ASW 96.72 % Yoruba in Ibadan,Nigeria YRI 94.32 % Luhya in Webuye,Kenya LWK 91.24 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 100 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 100 % Finnish in Finland FIN 100 % Toscani in Italia TSI 100 % Han Chinese in Bejing,China CHB 100 % Japanese in Tokyo,Japan 100 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA




Copyright © RetrogeneDB 2014-2017