RetrogeneDB ID:

retro_hsap_2932

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:57458823..57461884(+)
Located in intron of:ENSG00000249693
Retrocopy
information
Ensembl ID:ENSG00000248590
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GLDC
Ensembl ID:ENSG00000178445
Aliases:GLDC, GCE, GCSP, HYGN1
Description:glycine dehydrogenase (decarboxylating) [Source:HGNC Symbol;Acc:4313]


Retrocopy-Parental alignment summary:






>retro_hsap_2932
ATGCAGTCCTGTGCCAGGGCGTTGGGGCTGCTCCTGGGCCGCGGGGTCGGGGGCGGCCGCCGCCTGGCTGGGGGATCGGG
GCTGTGCTGGGCGCCGTGGGGCCGGGACAGCAGCAGTGCCGGCGGGGACAGCGCCGCGGCTGGGGCCTCGCGCCTCCTGG
AGCGCCTTCTGCCCAGACACGACGACTTCGCTCGGAGGCACATCGGCCCTGGGGACAAAGACCAGAGAGAGATGCTGCAG
ATCTTGGGGCTGGCGAGCATTGATGAATTGATCGAGAAGACGGTCCCTGCCAACATCCATTTGAAAAGACCCTTGAAAAT
GGAAGACCCTGTTTGTGAAAATGAAATCCTTGCAACTCTGCATGCCATTTCAAGCAAAAACCAGATCTGGAGATCCTATA
TTGGCATGGGCTATTGTAACTGCTCAGTGCCACAGACGATTTTGCGGAACTTACTGGAGAACTCAGGATGGATCACCCAG
TATACTCCATACCAGCCTGAGGTGTCTCAGGGGAGGCTGGAGAGTTTACTCAACTACCAGACCATGGTGTGTGACATCAC
AGGCCTGGACATGGCCAGTGCATCCCTGCTGGATGAGGGACTGCGGCTGCAGAGGCGCTGCAGCTGTGCTACAGACACAA
GAGGAGGAAATTTTTTGTTGACCCCCATTGCCACCCACAGACAATAGCTGTTGTCCAGACTCGAGCCAAATATACTGGAG
TCCTCATTGAGCTGAAGTTACCCTGTGAAATGGACTTCAGTGGAAAAGATGTCAGCGGAGTGTTGTTCCAGTACCCAGAC
ACGGAGGGGAAGGTGGAAGACTTTACGGAACTCGTGGAGAGAGCTCATCAGAGTGGGAGCCTGGCCTGCTGTGTGTGCTA
CTGACCTTTTAGCTTTGTGCATCTTGAGGCCACCGGGAGAATTTGGGGTAGACATCGCCTTGGGCAGCTCCCAGAGATTT
GGAGTGCCACTGGGCTATGGGGGACCCCACGCAGCATTTTTTGCCGTCCGAGAAAGCTTGGTGAGAATGATGCCTGGAAG
AATGGTGGGGGCAACAAGAGACGCCACTGGGAAAGAAGTGTATTGTCTTGCTCTTCAAACCAGGGAGCAACACACTGAGA
GAGACATGGCTACCAGCAACATCTGTACAGCTCAGGCCCTCTTGGCGAATATGGCAGCCATGTTTGCAATCTACCATGGT
TCCCATGGGCTGGAGCATATTGCTAGGAGAGTACATAATGCCACTTTGATTTTGCCAGAAGGTCTCAAGCGAGCAGGGCA
TCAACTCCAGCATGACGTGTTCTTTGATACCTTGAAGATTCAGTGTGGCTGCTCAGTGAAGGAGGTCTTGGGCAGGGCCG
CTCAGCGGCAGATCAATTTTCGGCTTTTTGAGGATGGCACACTTGGTATTTCTCTTGATGAAACAGTCAATGAAAAAGAT
CTGGACGATTTGTTGCGGATCTTTGTTTGTGAGTCATCTGCAGAACTGGTTGCTGAAAGCATGGGAGAGGAGTGCAGAGG
TATTCCAGGGTCTGTGTTCAAGAGGACCAGCCCGTTCCTCACCCATCAAGTGTTCAACAGCTACCACTCTGAAACAAATA
TTGTCCGGTATATGAAGAAACTGGAAAATAAAGACATTTCCCTTGTTCACAGCATGATTCCACTGGGATCCTGCACCATG
AAACTGAACAGTTCGTCTGAACTCGCACCTATCACATGGAAAGAATTTGCAAACATCCACCCCTTTGTGCCTCTGGACCA
AGCTCAAGGATATCAGCAGCTTTTCTGAGAGCTTGAGAAGGATTTGTGTGAACTCACAGGTTATGACCAGGTCTGTTTCC
AGCCAAACAGGGGAGCCCAGGGAGAATATGCTGGACTGGCCACTATCCGAGCCTACTTAAACCAGAAAGGAGAGGGGCAC
AGAACGGTTTGCCTCATTCTGAAATCAACACATGGGACCAACCCAACAAGTGCCCACATGGCAGGCATGAAGATTCAGCC
TGTGGAGGTGGATAAATGTGGGAATATCAATGCAGTTCACCTCAAGGCCATGGTGGATAAGCACAAGGAGAACCTAGCAG
CCATCATGATTACATACCCATCCACCAATGGGGTGTTTGAAGAGAACATCAGTGACGTGTGTGACCTCATCCATCAACAT
GGAGGATAGGTCTACCTAGACGGGGCAAATATGAACGCTCAGGTGGGAATCTGTCGCCCTGGAGACTTTGGGTCTGATGT
CTCGCACCTAAATCTTCACAAGACCTTCTGCATTCCCCACAGAGGAGGTGGTCCTGGCATGGGGCCCATTGGCGTAAGAA
ATACCTTGCCCCGTTTTTGCCCAATCATCCCATCATTTCACTAAAGCGGAATGAGGATGCCTGTCCTGTGGGAACCGTCA
GTGCGGCCCCATGGGGCTCCAGTTCCATCTTGCCCATTTCCTGGGCTTATATCAAGATGATGGGAGGCAAGGGCCTTAAA
CAAGCCACGGAAACTGCGATATTAAATGCCAACTACATGGCCAAGCGATTAGAAAAACACTACAGAATTCTTTTCAGGGG
TGCAAGAGGTTATGTGGGTCATGAATTTATTTTGGACACGAGACCCTTCAAAAAGTCTGCAAATATTGAGGCAGTGGATG
TGGCCAAGAGACTCCAGGATTATGGATTTCACGCCCCTATCATGCCCTGGCCTGTGGCAGGGACCCTCATGGTTGAGCCC
ACTGAGTCGGAGGACAAGGCAGAGCTGGACAGATTCTGTGATGCCATGATCAGCATTCGGCAGGAAGTTGCTGACATTGA
GGAGGGCCGCATCGACCCCAGGGTCAATCCGCTGAAGATGTCTCCACACTCCCTGACCTGCGTTATATCTTCCCACTGGG
ACCGGCCTTATATTCCAGAGAGGTGGCAGCATTCCCACTCCCCTTCGTGAAACCAGAGAACAAATTCTGGCCAGTGATTG
CCCGGATTGATGACATATATGGAGATCAGCACCTGGTTTGTACCTGCCCACCCATGGAAGTTTATGAGTTGCCATTTTCT
GAACAAAAGAGGGCCTCTTCT

ORF - retro_hsap_2932 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.74 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMQSCARAWGLRLGRGVGGGRRLAGGSGPCWAPRSRDSSSGGGDSAAAGASRLLERLLPRHDDFARRHIGP
MQSCARA.GL.LGRGVGGGRRLAGGSG.CWAP..RDSSS.GGDSAAAGASRLLERLLPRHDDFARRHIGP
RetrocopyMQSCARALGLLLGRGVGGGRRLAGGSGLCWAPWGRDSSSAGGDSAAAGASRLLERLLPRHDDFARRHIGP
ParentalGDKDQREMLQTLGLASIDELIEKTVPANIRLKRPLKMEDPVCENEILATLHAISSKNQIWRSYIGMGYYN
GDKDQREMLQ.LGLASIDELIEKTVPANI.LKRPLKMEDPVCENEILATLHAISSKNQIWRSYIGMGY.N
RetrocopyGDKDQREMLQILGLASIDELIEKTVPANIHLKRPLKMEDPVCENEILATLHAISSKNQIWRSYIGMGYCN
ParentalCSVPQTILRNLLENSGWITQYTPYQPEVSQGRLESLLNYQTMVCDITGLDMANASLLDEG-TAAAEALQL
CSVPQTILRNLLENSGWITQYTPYQPEVSQGRLESLLNYQTMVCDITGLDMA.ASLLDEG.TAAAEALQL
RetrocopyCSVPQTILRNLLENSGWITQYTPYQPEVSQGRLESLLNYQTMVCDITGLDMASASLLDEG<TAAAEALQL
ParentalCYRHNKRRKFLVDPRCHPQTIAVVQTRAKYTGVLTELKLPCEMDFSGKDVSGVLFQYPDTEGKVEDFTEL
CYRH.KRRKF.VDP.CHPQTIAVVQTRAKYTGVL.ELKLPCEMDFSGKDVSGVLFQYPDTEGKVEDFTEL
RetrocopyCYRH-KRRKFFVDPHCHPQTIAVVQTRAKYTGVLIELKLPCEMDFSGKDVSGVLFQYPDTEGKVEDFTEL
ParentalVERAHQSGSLA-C-CATDLLALCILRPPGEFGVDIALGSSQRFGVPLGYGGPHAAFFAVRESLVRMMPGR
VERAHQSGSLA.C.CATDLLALCILRPPGEFGVDIALGSSQRFGVPLGYGGPHAAFFAVRESLVRMMPGR
RetrocopyVERAHQSGSLACC>CATDLLALCILRPPGEFGVDIALGSSQRFGVPLGYGGPHAAFFAVRESLVRMMPGR
ParentalMVGVTRDATGKEVYRLALQTREQHIRRDKATSNICTAQALLANMAAMFAIYHGSHGLEHIARRVHNATLI
MVG.TRDATGKEVY.LALQTREQH..RD.ATSNICTAQALLANMAAMFAIYHGSHGLEHIARRVHNATLI
RetrocopyMVGATRDATGKEVYCLALQTREQHTERDMATSNICTAQALLANMAAMFAIYHGSHGLEHIARRVHNATLI
ParentalLSEGLKRAGHQLQHDLFFDTLKIQCGCSVKEVLGRAAQRQINFRLFEDGTLGISLDETVNEKDLDDLLWI
L.EGLKRAGHQLQHD.FFDTLKIQCGCSVKEVLGRAAQRQINFRLFEDGTLGISLDETVNEKDLDDLL.I
RetrocopyLPEGLKRAGHQLQHDVFFDTLKIQCGCSVKEVLGRAAQRQINFRLFEDGTLGISLDETVNEKDLDDLLRI
ParentalFGCESSAELVAESMGEECRGIPGSVFKRTSPFLTHQVFNSYHSETNIVRYMKKLENKDISLVHSMIPLGS
F.CESSAELVAESMGEECRGIPGSVFKRTSPFLTHQVFNSYHSETNIVRYMKKLENKDISLVHSMIPLGS
RetrocopyFVCESSAELVAESMGEECRGIPGSVFKRTSPFLTHQVFNSYHSETNIVRYMKKLENKDISLVHSMIPLGS
ParentalCTMKLNSSSELAPITWKEFANIHPFVPLDQAQGYQQLFRELEKDLCELTGYDQVCFQPNSGAQGEYAGLA
CTMKLNSSSELAPITWKEFANIHPFVPLDQAQGYQQLF.ELEKDLCELTGYDQVCFQPN.GAQGEYAGLA
RetrocopyCTMKLNSSSELAPITWKEFANIHPFVPLDQAQGYQQLF*ELEKDLCELTGYDQVCFQPNRGAQGEYAGLA
ParentalTIRAYLNQKGEGHRTVCLIPKSAHGTNPASAHMAGMKIQPVEVDKYGNIDAVHLKAMVDKHKENLAAIMI
TIRAYLNQKGEGHRTVCLI.KS.HGTNP.SAHMAGMKIQPVEVDK.GNI.AVHLKAMVDKHKENLAAIMI
RetrocopyTIRAYLNQKGEGHRTVCLILKSTHGTNPTSAHMAGMKIQPVEVDKCGNINAVHLKAMVDKHKENLAAIMI
ParentalTYPSTNGVFEENISDVCDLIHQHGGQVYLDGANMNAQVGICRPGDFGSDVSHLNLHKTFCIPHGGGGPGM
TYPSTNGVFEENISDVCDLIHQHGG.VYLDGANMNAQVGICRPGDFGSDVSHLNLHKTFCIPH.GGGPGM
RetrocopyTYPSTNGVFEENISDVCDLIHQHGG*VYLDGANMNAQVGICRPGDFGSDVSHLNLHKTFCIPHRGGGPGM
ParentalGPIGV-KKHLAPFLPNHPVISLKRNEDACPVGTVSAAPWGSSSILPISWAYIKMMGGKGLKQATETAILN
GPIGV.KK.LAPFLPNHP.ISLKRNEDACPVGTVSAAPWGSSSILPISWAYIKMMGGKGLKQATETAILN
RetrocopyGPIGV<KKYLAPFLPNHPIISLKRNEDACPVGTVSAAPWGSSSILPISWAYIKMMGGKGLKQATETAILN
ParentalANYMAKRLETHYRILFRGARGYVGHEFILDTRPFKKSANIEAVDVAKRLQDYGFHAPTMSWPVAGTLMVE
ANYMAKRLE.HYRILFRGARGYVGHEFILDTRPFKKSANIEAVDVAKRLQDYGFHAP.M.WPVAGTLMVE
RetrocopyANYMAKRLEKHYRILFRGARGYVGHEFILDTRPFKKSANIEAVDVAKRLQDYGFHAPIMPWPVAGTLMVE
ParentalPTESEDKAELDRFCDAMISIRQEIADIEEGRIDPRVNPLKMSPHSLTCVTSSHWDRPYSRE-VAAFPLP-
PTESEDKAELDRFCDAMISIRQE.ADIEEGRIDPRVNPLKMSPHSLTCV.SSHWDRPY..E.....P.P.
RetrocopyPTESEDKAELDRFCDAMISIRQEVADIEEGRIDPRVNPLKMSPHSLTCVISSHWDRPYIPE>GGSIPTP>
ParentalFVKPENKFWPTIARIDDIYGDQHLVCTCPPMEVYESPFSEQKRASS
FVKPENKFWP.IARIDDIYGDQHLVCTCPPMEVYE.PFSEQKRASS
RetrocopyFVKPENKFWPVIARIDDIYGDQHLVCTCPPMEVYELPFSEQKRASS

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 0 .20 RPM
bodymap2_adrenal 0 .00 RPM 2 .29 RPM
bodymap2_brain 0 .05 RPM 12 .66 RPM
bodymap2_breast 0 .00 RPM 0 .45 RPM
bodymap2_colon 0 .00 RPM 0 .27 RPM
bodymap2_heart 0 .00 RPM 0 .13 RPM
bodymap2_kidney 0 .17 RPM 75 .67 RPM
bodymap2_liver 0 .61 RPM 91 .00 RPM
bodymap2_lung 0 .00 RPM 0 .70 RPM
bodymap2_lymph_node 0 .00 RPM 4 .29 RPM
bodymap2_ovary 0 .00 RPM 0 .81 RPM
bodymap2_prostate 0 .02 RPM 1 .66 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .29 RPM
bodymap2_testis 0 .06 RPM 13 .12 RPM
bodymap2_thyroid 0 .09 RPM 24 .27 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .41 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2932 was not detected

EST - click to see more details

2 EST(s) were mapped to retro_hsap_2932 retrocopy
EST ID Start End Identity Match Mis-match Score
AW292881 57458876 57459095 99.1 216 2 214
BI006823 57459615 57459732 100 113 0 112

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_1445091571 libraries127 libraries90 libraries38 libraries3 libraries

The graphical summary, for retro_hsap_2932 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_2932 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2932 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2060
Gorilla gorilla retro_ggor_2034
Pongo abelii retro_pabe_2521
Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000178445 1 retrocopy
retro_hsap_2932 ,
Gorilla gorilla ENSGGOG000000045071 retrocopy
retro_ggor_2034,
Macropus eugenii ENSMEUG000000017341 retrocopy
retro_meug_2056,
Pongo abelii ENSPPYG000000192251 retrocopy
retro_pabe_2521,
Pan troglodytes ENSPTRG000000293471 retrocopy
retro_ptro_2060,

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 = 0.26 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .06 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .07 RPM
CEU_NA12760 0 .13 RPM
CEU_NA12827 0 .09 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .26 RPM
FIN_HG00183 0 .19 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .14 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .12 RPM
FIN_HG00338 0 .09 RPM
FIN_HG00349 0 .14 RPM
FIN_HG00375 0 .10 RPM
FIN_HG00377 0 .08 RPM
FIN_HG00378 0 .11 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .09 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .11 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .08 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .14 RPM
TSI_NA20532 0 .14 RPM
TSI_NA20538 0 .18 RPM
TSI_NA20756 0 .09 RPM
TSI_NA20765 0 .12 RPM
TSI_NA20771 0 .23 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .24 RPM
YRI_NA18907 0 .14 RPM
YRI_NA18916 0 .11 RPM
YRI_NA19093 0 .08 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .24 RPM
YRI_NA19118 0 .08 RPM
YRI_NA19213 0 .12 RPM
YRI_NA19214 0 .07 RPM
YRI_NA19223 0 .02 RPM

Indel association:

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



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