RetrogeneDB ID:

retro_hsap_4863

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:75555242..75556244(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000213684
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:LDHB
Ensembl ID:ENSG00000111716
Aliases:LDHB, HEL-S-281, LDH-B, LDH-H, LDHBD, TRG-5
Description:lactate dehydrogenase B [Source:HGNC Symbol;Acc:6541]


Retrocopy-Parental alignment summary:






>retro_hsap_4863
ATAGCAACTCTTAAGGAAAAACTCATTGTACCAGTTGCGGAAGAAGAGGCAACAGTCCAAAACAATAAGATCACTGTAGT
GAGTGTTGGACAAGTTGGTATGGCGTGTGCTATCAGCATTCTGGGAAAATCTCTGGCTGATGAATTTGCTTTTGTGGATG
TTTTGGAAGATAAGCTTAAAGGAGAAATGATGGATCTGCAGCATGGGAGCTTATTTCTCAAGAAGCTTAAAATTGTGGCA
GATAAAGATTATTCTGTGACTGCCAGTTATAAGATTGTAGTGGTAACTTCAGGAGTCCTTCAGCAAGAGGGGGAGAGGCG
TCTCAATTTGGTGCAGAAAAAATGTTAATGTCTTCAAATTCATTATTCCTCAAATTGTCAAGCACACTTCTGATTGCACA
TAATTGTGGTTTCCAACCTAGGGGACATTCTTACGTATGTTACCTGGAAAATAAGTGGATTACTCAAACACCATGTGATT
GGAAGTGGATGTAATCCGGATTCTGCTAGATTTCACTGCCTTATGGATGAAAAATTTGGCATTCATCCCAGCAGCTGCCA
TGGAAGGATTTTGGGGGAACATAGTGACTCAAGTGTGGCTGTGTGGATTGGCATGAATGTGACAGGTTTTTCTCTCCAGG
AATTGAATCCAGAAATAGGAACTGACAATGATAGTGAAAATTGGAAAGAAGTGCATAAGATGGTGGTTGAAAATGCCTAT
GAAGTCAACAAGCTAAATGGATATACCCACTGGGATATTGGATTAAGTGTGGCTGATCTCATTGAATCCATGTTGAAAAA
TCTATCCAGGATTCATCTCGTGTCAACAATGGTAAAGGGGATGTATGGCATCGAGAATGAAGTCTTCCTGAGCCTTCCAT
ATATCCTCAATGCCCGGGGATTAACCAGCGTTATCAACCAGAAGCTAAAGGATGATGAGGTTGCTCAGTTCAAGAAAAGT
ACAGATACCCCGTGGGACATCCAGAAGGACCTAAAAGACCTG

ORF - retro_hsap_4863 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.71 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMATLKEKLIAPVAEEEATVPNNKITVVGVGQVGMACAISILGKSLADELALVDVLEDKLKGEMMDLQHGS
.ATLKEKLI.PVAEEEATV.NNKITVV.VGQVGMACAISILGKSLADE.A.VDVLEDKLKGEMMDLQHGS
RetrocopyIATLKEKLIVPVAEEEATVQNNKITVVSVGQVGMACAISILGKSLADEFAFVDVLEDKLKGEMMDLQHGS
ParentalLFLQTPKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQ-RNVNVFKFIIPQIVKYSPDCI-IIVVS
LFL...KIVADKDYSVTA..KIVVVT.GV.QQEGE.RLNLVQ..NVNVFKFIIPQIVK...DC..IIVVS
RetrocopyLFLKKLKIVADKDYSVTASYKIVVVTSGVLQQEGERRLNLVQ>KNVNVFKFIIPQIVKHTSDCT<IIVVS
ParentalNPVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSSVAVWSGVNVA
N..DILTYVTWK.SGL.KH.VIGSGCN.DSARF..LM.EK.GIHPSSCHG.ILGEH.DSSVAVW.G.NV.
RetrocopyNLGDILTYVTWKISGLLKHHVIGSGCNPDSARFHCLMDEKFGIHPSSCHGRILGEHSDSSVAVWIGMNVT
ParentalGVSLQELNPEMGTDNDSENWKEVHKMVVESAYEVIKLKGYTNWAIGLSVADLIESMLKNLSRIHPVSTMV
G.SLQELNPE.GTDNDSENWKEVHKMVVE.AYEV.KL.GYT.W.IGLSVADLIESMLKNLSRIH.VSTMV
RetrocopyGFSLQELNPEIGTDNDSENWKEVHKMVVENAYEVNKLNGYTHWDIGLSVADLIESMLKNLSRIHLVSTMV
ParentalKGMYGIENEVFLSLPCILNARGLTSVINQKLKDDEVAQLKKSADTLWDIQKDLKDL
KGMYGIENEVFLSLP.ILNARGLTSVINQKLKDDEVAQ.KKS.DT.WDIQKDLKDL
RetrocopyKGMYGIENEVFLSLPYILNARGLTSVINQKLKDDEVAQFKKSTDTPWDIQKDLKDL

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 .08 RPM 598 .39 RPM
bodymap2_adrenal 0 .00 RPM 335 .41 RPM
bodymap2_brain 0 .00 RPM 756 .97 RPM
bodymap2_breast 0 .00 RPM 668 .04 RPM
bodymap2_colon 0 .00 RPM 417 .25 RPM
bodymap2_heart 0 .02 RPM 1184 .37 RPM
bodymap2_kidney 0 .00 RPM 1122 .52 RPM
bodymap2_liver 0 .00 RPM 14 .05 RPM
bodymap2_lung 0 .00 RPM 203 .06 RPM
bodymap2_lymph_node 0 .00 RPM 301 .55 RPM
bodymap2_ovary 0 .06 RPM 551 .47 RPM
bodymap2_prostate 0 .00 RPM 360 .57 RPM
bodymap2_skeletal_muscle 0 .00 RPM 95 .69 RPM
bodymap2_testis 0 .02 RPM 334 .30 RPM
bodymap2_thyroid 0 .02 RPM 608 .48 RPM
bodymap2_white_blood_cells 0 .00 RPM 387 .95 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4863 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4863 retrocopy.

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_201226769 libraries735 libraries314 libraries11 libraries0 libraries

The graphical summary, for retro_hsap_4863 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_4863 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4863 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3237
Gorilla gorilla retro_ggor_3033
Pongo abelii retro_pabe_3780
Parental genes homology:
Parental genes homology involve 14 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000161754 retrocopies
retro_amel_1316, retro_amel_814, retro_amel_882, retro_amel_977,
Canis familiaris ENSCAFG000000121959 retrocopies
retro_cfam_1068, retro_cfam_111, retro_cfam_1674, retro_cfam_17, retro_cfam_1700, retro_cfam_174, retro_cfam_1836, retro_cfam_701, retro_cfam_93,
Echinops telfairi ENSETEG000000199551 retrocopy
retro_etel_850,
Felis catus ENSFCAG000000126391 retrocopy
retro_fcat_462,
Homo sapiens ENSG00000111716 1 retrocopy
retro_hsap_4863 ,
Homo sapiens ENSG000001343335 retrocopies
retro_hsap_2097, retro_hsap_2285, retro_hsap_3021, retro_hsap_323, retro_hsap_4231,
Homo sapiens ENSG000001668002 retrocopies
retro_hsap_42, retro_hsap_905,
Macropus eugenii ENSMEUG000000048251 retrocopy
retro_meug_311,
Myotis lucifugus ENSMLUG000000121551 retrocopy
retro_mluc_202,
Macaca mulatta ENSMMUG000000026794 retrocopies
retro_mmul_212, retro_mmul_303, retro_mmul_308, retro_mmul_315,
Monodelphis domestica ENSMODG000000177861 retrocopy
retro_mdom_1484,
Mustela putorius furoENSMPUG000000001725 retrocopies
retro_mputfur_1300, retro_mputfur_1561, retro_mputfur_492, retro_mputfur_539, retro_mputfur_549,
Sus scrofa ENSSSCG000000005761 retrocopy
retro_sscr_37,
Tarsius syrichta ENSTSYG000000137597 retrocopies
retro_tsyr_1130, retro_tsyr_1532, retro_tsyr_1860, retro_tsyr_2051, retro_tsyr_334, retro_tsyr_64, retro_tsyr_986,

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 = 0.18 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .09 RPM
CEU_NA11930 0 .10 RPM
CEU_NA12004 0 .11 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .18 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .06 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .05 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .06 RPM
TSI_NA20513 0 .10 RPM
TSI_NA20518 0 .17 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .06 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .05 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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