RetrogeneDB ID:

retro_hsap_31

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:120181538..120183215(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000182890
Aliases:GLUD2, GDH2, GLUDP1
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:GLUD1
Ensembl ID:ENSG00000148672
Aliases:GLUD1, GDH, GDH1, GLUD
Description:glutamate dehydrogenase 1 [Source:HGNC Symbol;Acc:4335]


Retrocopy-Parental alignment summary:






>retro_hsap_31
ATGTACCGCTACCTGGCCAAAGCGCTGCTGCCGTCCCGGGCCGGGCCCGCTGCCCTGGGCTCCGCGGCCAACCACTCGGC
CGCGTTGCTGGGCCGGGGCCGCGGACAGCCCGCCGCCGCCTCGCAGCCGGGGCTCGCATTGGCCGCCCGGCGCCACTACA
GCGAGTTGGTGGCCGACCGCGAGGACGACCCCAACTTCTTCAAGATGGTGGAGGGCTTCTTCGATCGCGGCGCCAGCATC
GTGGAGGACAAGTTGGTGAAGGACCTGAGGACCCAGGAAAGCGAGGAGCAGAAGCGGAACCGGGTGCGCGGCATCCTGCG
GATCATCAAGCCCTGCAACCATGTGCTGAGTCTCTCCTTCCCCATCCGGCGCGACGACGGCTCCTGGGAGGTCATCGAAG
GCTACCGGGCCCAGCACAGCCAGCACCGCACGCCCTGCAAGGGAGGTATCCGTTACAGCACTGATGTGAGTGTAGATGAA
GTAAAAGCTTTGGCTTCTCTGATGACATACAAGTGTGCAGTGGTTGATGTGCCGTTTGGGGGTGCTAAAGCTGGTGTTAA
GATCAATCCCAAGAACTATACCGAAAATGAATTGGAAAAGATCACAAGGAGGTTCACCATGGAGCTAGCAAAGAAGGGCT
TTATTGGTCCTGGCGTTGATGTGCCTGCTCCAGACATGAACACAGGTGAGCGGGAGATGTCCTGGATTGCTGATACCTAT
GCCAGCACCATAGGGCACTATGATATTAATGCACACGCCTGTGTTACTGGTAAACCCATCAGCCAAGGGGGAATCCATGG
ACGCATCTCTGCTACTGGCCGTGGTGTCTTCCATGGGATTGAAAACTTCATCAATGAAGCTTCTTACATGAGCATTTTAG
GAATGACACCAGGGTTTAGAGATAAAACATTTGTTGTTCAGGGATTTGGTAATGTGGGCCTACACTCTATGAGATATTTA
CATCGTTTTGGTGCTAAATGTATTGCTGTTGGTGAGTCTGATGGGAGTATATGGAATCCAGATGGTATTGACCCAAAGGA
ACTGGAAGACTTCAAATTGCAACATGGGTCCATTCTGGGCTTCCCCAAGGCAAAGCCCTATGAAGGAAGCATCTTGGAGG
TCGACTGTGACATACTGATCCCAGCTGCCACTGAGAAGCAGTTGACCAAATCCAACGCACCCAGAGTCAAAGCCAAGATC
ATTGCTGAAGGTGCCAATGGGCCAACAACTCCAGAAGCTGATAAGATCTTCCTGGAGAGAAACATTTTGGTTATTCCAGA
TCTCTACTTGAATGCTGGAGGAGTGACAGTATCTTACTTTGAGTGGCTGAAGAATCTAAATCATGTCAGCTATGGCCGTT
TGACCTTCAAATATGAAAGGGATTCTAACTACCACTTGCTCCTGTCTGTTCAAGAGAGTTTAGAAAGAAAATTTGGAAAG
CATGGTGGAACTATTCCCATTGTACCCACGGCAGAGTTCCAAGACAGTATATCGGGTGCATCTGAGAAAGACATTGTGCA
CTCTGCCTTGGCATACACAATGGAGCGTTCTGCCAGGCAAATTATGCACACAGCCATGAAGTATAACCTGGGATTGGACC
TGAGAACAGCTGCCTATGTCAATGCCATTGAAAAAGTCTTCAAAGTGTACAGTGAAGCTGGTGTGACCTTCACATAG

ORF - retro_hsap_31 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.7 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMYRYLGEALLLSRAGPAALGSASADSAALLGWARGQPAAAPQPGLALAARRHYSEAVADREDDPNFFKMV
MYRYL..ALL.SRAGPAALGSA...SAALLG..RGQPAAA.QPGLALAARRHYSE.VADREDDPNFFKMV
RetrocopyMYRYLAKALLPSRAGPAALGSAANHSAALLGRGRGQPAAASQPGLALAARRHYSELVADREDDPNFFKMV
ParentalEGFFDRGASIVEDKLVEDLRTRESEEQKRNRVRGILRIIKPCNHVLSLSFPIRRDDGSWEVIEGYRAQHS
EGFFDRGASIVEDKLV.DLRT.ESEEQKRNRVRGILRIIKPCNHVLSLSFPIRRDDGSWEVIEGYRAQHS
RetrocopyEGFFDRGASIVEDKLVKDLRTQESEEQKRNRVRGILRIIKPCNHVLSLSFPIRRDDGSWEVIEGYRAQHS
ParentalQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMELA
QHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYT.NELEKITRRFTMELA
RetrocopyQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTENELEKITRRFTMELA
ParentalKKGFIGPGIDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGI
KKGFIGPG.DVPAPDM.TGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGI
RetrocopyKKGFIGPGVDVPAPDMNTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGI
ParentalENFINEASYMSILGMTPGFGDKTFVVQGFGNVGLHSMRYLHRFGAKCIAVGESDGSIWNPDGIDPKELED
ENFINEASYMSILGMTPGF.DKTFVVQGFGNVGLHSMRYLHRFGAKCIAVGESDGSIWNPDGIDPKELED
RetrocopyENFINEASYMSILGMTPGFRDKTFVVQGFGNVGLHSMRYLHRFGAKCIAVGESDGSIWNPDGIDPKELED
ParentalFKLQHGSILGFPKAKPYEGSILEADCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLER
FKLQHGSILGFPKAKPYEGSILE.DCDILIPAA.EKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLER
RetrocopyFKLQHGSILGFPKAKPYEGSILEVDCDILIPAATEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLER
ParentalNIMVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIPIVPT
NI.VIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLL.SVQESLERKFGKHGGTIPIVPT
RetrocopyNILVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLLSVQESLERKFGKHGGTIPIVPT
ParentalAEFQDRISGASEKDIVHSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKVFKVYNEAGVTFT
AEFQD.ISGASEKDIVHS.LAYTMERSARQIM.TAMKYNLGLDLRTAAYVNAIEKVFKVY.EAGVTFT
RetrocopyAEFQDSISGASEKDIVHSALAYTMERSARQIMHTAMKYNLGLDLRTAAYVNAIEKVFKVYSEAGVTFT

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 1 .15 RPM 183 .51 RPM
bodymap2_adrenal 1 .08 RPM 138 .43 RPM
bodymap2_brain 2 .72 RPM 430 .52 RPM
bodymap2_breast 1 .83 RPM 174 .09 RPM
bodymap2_colon 0 .72 RPM 189 .68 RPM
bodymap2_heart 1 .07 RPM 106 .82 RPM
bodymap2_kidney 2 .75 RPM 252 .70 RPM
bodymap2_liver 4 .52 RPM 1016 .55 RPM
bodymap2_lung 1 .09 RPM 263 .63 RPM
bodymap2_lymph_node 0 .88 RPM 131 .94 RPM
bodymap2_ovary 0 .40 RPM 174 .11 RPM
bodymap2_prostate 0 .85 RPM 199 .35 RPM
bodymap2_skeletal_muscle 0 .60 RPM 83 .03 RPM
bodymap2_testis 7 .81 RPM 131 .61 RPM
bodymap2_thyroid 0 .49 RPM 160 .20 RPM
bodymap2_white_blood_cells 0 .79 RPM 200 .46 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_31 in 5 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CFW POLR2A X:120181417..120181529
ENCFF002CFX POLR2A X:120181406..120181630
ENCFF002DAE POLR2A X:120181360..120181670
ENCFF002DBO POLR2A X:120181287..120181671
ENCFF002DBP POLR2A X:120181351..120181681

EST - click to see more details

4 EST(s) were mapped to retro_hsap_31 retrocopy
EST ID Start End Identity Match Mis-match Score
BU166908 120181448 120182196 97.4 739 5 724
CN290035 120181479 120182009 99.7 528 2 526
DB457851 120181469 120181960 99.8 489 1 488
HY003742 120181465 120181980 99.9 513 1 512

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_1968621009 libraries532 libraries253 libraries29 libraries6 libraries

The graphical summary, for retro_hsap_31 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_31 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_31 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3162
Pongo abelii retro_pabe_79
Parental genes homology:
Parental genes homology involve 20 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000075402 retrocopies
retro_btau_1413, retro_btau_1741,
Canis familiaris ENSCAFG000000160951 retrocopy
retro_cfam_747,
Choloepus hoffmanni ENSCHOG000000011011 retrocopy
retro_chof_2002,
Callithrix jacchus ENSCJAG000000116331 retrocopy
retro_cjac_2830,
Dipodomys ordii ENSDORG000000097671 retrocopy
retro_dord_400,
Equus caballus ENSECAG000000073712 retrocopies
retro_ecab_886, retro_ecab_919,
Echinops telfairi ENSETEG000000196382 retrocopies
retro_etel_141, retro_etel_2024,
Homo sapiens ENSG00000148672 1 retrocopy
retro_hsap_31 ,
Gorilla gorilla ENSGGOG000000157701 retrocopy
retro_ggor_2954,
Loxodonta africana ENSLAFG000000120591 retrocopy
retro_lafr_504,
Microcebus murinus ENSMICG000000165261 retrocopy
retro_mmur_524,
Monodelphis domestica ENSMODG000000027561 retrocopy
retro_mdom_124,
Nomascus leucogenys ENSNLEG000000116581 retrocopy
retro_nleu_36,
Otolemur garnettii ENSOGAG000000036411 retrocopy
retro_ogar_2757,
Procavia capensis ENSPCAG000000086621 retrocopy
retro_pcap_11,
Pongo abelii ENSPPYG000000028273 retrocopies
retro_pabe_3109, retro_pabe_3213, retro_pabe_79,
Pan troglodytes ENSPTRG000000027114 retrocopies
retro_ptro_3162, retro_ptro_3283, retro_ptro_3285, retro_ptro_3290,
Ictidomys tridecemlineatus ENSSTOG000000128431 retrocopy
retro_itri_737,
Tarsius syrichta ENSTSYG000000015781 retrocopy
retro_tsyr_313,
Tursiops truncatus ENSTTRG000000081451 retrocopy
retro_ttru_950,

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 = 1.12 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .53 RPM
CEU_NA11843 0 .14 RPM
CEU_NA11930 1 .11 RPM
CEU_NA12004 0 .15 RPM
CEU_NA12400 1 .12 RPM
CEU_NA12751 0 .70 RPM
CEU_NA12760 0 .76 RPM
CEU_NA12827 0 .47 RPM
CEU_NA12872 0 .30 RPM
CEU_NA12873 0 .38 RPM
FIN_HG00183 0 .63 RPM
FIN_HG00277 0 .48 RPM
FIN_HG00315 0 .25 RPM
FIN_HG00321 0 .39 RPM
FIN_HG00328 0 .17 RPM
FIN_HG00338 0 .32 RPM
FIN_HG00349 0 .60 RPM
FIN_HG00375 0 .20 RPM
FIN_HG00377 0 .23 RPM
FIN_HG00378 0 .17 RPM
GBR_HG00099 0 .41 RPM
GBR_HG00111 0 .17 RPM
GBR_HG00114 0 .13 RPM
GBR_HG00119 0 .22 RPM
GBR_HG00131 0 .14 RPM
GBR_HG00133 0 .22 RPM
GBR_HG00134 0 .24 RPM
GBR_HG00137 0 .19 RPM
GBR_HG00142 0 .39 RPM
GBR_HG00143 0 .48 RPM
TSI_NA20512 0 .06 RPM
TSI_NA20513 0 .24 RPM
TSI_NA20518 0 .42 RPM
TSI_NA20532 0 .20 RPM
TSI_NA20538 0 .14 RPM
TSI_NA20756 0 .32 RPM
TSI_NA20765 0 .15 RPM
TSI_NA20771 0 .45 RPM
TSI_NA20786 0 .21 RPM
TSI_NA20798 0 .31 RPM
YRI_NA18870 0 .85 RPM
YRI_NA18907 0 .49 RPM
YRI_NA18916 0 .38 RPM
YRI_NA19093 0 .42 RPM
YRI_NA19099 0 .35 RPM
YRI_NA19114 0 .47 RPM
YRI_NA19118 0 .25 RPM
YRI_NA19213 0 .17 RPM
YRI_NA19214 0 .32 RPM
YRI_NA19223 0 .20 RPM

Indel association:

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





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