RetrogeneDB ID:

retro_hsap_905

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:83525501..83526488(-)
Located in intron of:ENSG00000150672
Retrocopy
information
Ensembl ID:ENSG00000250257
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:LDHAL6A
Ensembl ID:ENSG00000166800
Aliases:LDHAL6A, LDH6A
Description:lactate dehydrogenase A-like 6A [Source:HGNC Symbol;Acc:28335]


Retrocopy-Parental alignment summary:






>retro_hsap_905
ATGGTAACTATCCAGAATGAATTTATTGAGAATTTTGCTTCAGAGGAGGTTATTCACCACAGTAAGGTCTCCATTATAAG
AACTGGATCAGTTAGCATGGCCCGTGCAATCACCATGTTATTAAAAGACTTGAGGGATGAAGTTGCCTTTGTAGCTGTTG
ATAATGGTGAATTGAAGGGTGTGAGACAATGGATCTTAAACATGGCAGTCTTTTCCTAAAACTGCCAGATAGTGCTTCCA
GCAAAGATTATCTCATCTCTGCAAACTCCAACCTAGTGATTATCACATCAGGTGCATGCCAGGAAAAAGGTGAAACACTT
TAATTTAGTCAGTCTAAATGTGGCCATCGTTAAATTAATGATGTCTAATATTACTCAATATAGTCCTGCTGCAAATTGAT
AGTTTCCAGTCCAGTGGATATCTTAATTTATGTAGCTTAGAAATTGAGTACATTTTTCAAAACCCATATTATTGGAAATG
GCTGTAATCTGGACACTGCCCATTTCCATTTCTTGACTGTGCAAGTGCTTGGAATCCACTCTGGAAGCTGCCATGGGTGG
ATCTTTGGAGAGCATGGGGACTCAAGTGTTCCTGTGTGGAGTGGAGTGAACATTGCTGGTGTCCCTCTGAAGGATCTAAA
CTCAGATAAAGGAATTGATCAAGATCTAGAGCAAGGGGGAAAATGTCCACAAAGAAGTGATTGCCAGTGCTTATGAAATT
ATGAAAATGAAAGGTTATACTTCTTGGGCCATTGGCCCATCTGTAACAGATTGAACAGAAAGCATTTTAGAGAATCCTAG
GAGAGCGCATTCAGTTTCCACATAATTAAGGGCCTCTATGGAATGAATGATGTATTCTTCAGTGTTCCTCGTATCTGAGA
GAGAATGGTCTTGCAGACCTTACACAGGTAAAGCTGACCCTTGAAGATGTGGCCCATTTGTAAAGGAGCACAGAAACACT
TTGGGAATTCAGAAGAAGCTCAAGCTT

ORF - retro_hsap_905 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65. %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 7


Retrocopy - Parental Gene Alignment:

ParentalMATIKSELIKNFAEEEAIHHNKISIVGTGSVGVACAISILLKGLSDELVLVDVDEGK-LKG-ETMDLQHG
M.TI..E.I.NFA.EE.IHH.K.SI..TGSV..A.AI..LLK.L.DE...V.VD.G....G.ETMDL.HG
RetrocopyMVTIQNEFIENFASEEVIHHSKVSIIRTGSVSMARAITMLLKDLRDEVAFVAVDNGE<IEGCETMDLKHG
ParentalSPFMKMPNIVSSKDYLVTANSNLVIITAGARQ-KKGETRLDLVQRNVSIFKLMIPNITQYSPH-CKLLIV
S.F.K.P...SSKDYL..ANSNLVIIT.GA.Q.KK......LV..NV.I.KLM..NITQYSP..CKL.IV
RetrocopySLFLKLPDSASSKDYLISANSNLVIITSGACQ>KKVK-HFNLVSLNVAIVKLMMSNITQYSPA<CKL-IV
ParentalTNPVDILTYVAWKLSGFPKNRVIGSGCNLDSARFRYFIGQRLGIHSESCHGLILGEHGDSSVPVWSGVNI
..PVDIL.YVA.KLS.F.K...IG.GCNLD.A.F.....Q.LGIHS.SCHG.I.GEHGDSSVPVWSGVNI
RetrocopySSPVDILIYVA*KLSTFFKTHIIGNGCNLDTAHFHFLTVQVLGIHSGSCHGWIFGEHGDSSVPVWSGVNI
ParentalAGVPLKDLNPDIGTDKDPEQ-WENVHKKVISSGYEMVKMKGYTSWGISLSVADLTESILKNLRRVHPVST
AGVPLKDLN.D.G.D.D.EQ..ENVHK.VI.S.YE..KMKGYTSW.I..SV.D.TESIL.N.RR.H.VST
RetrocopyAGVPLKDLNSDKGIDQDLEQ>GENVHKEVIASAYEIMKMKGYTSWAIGPSVTD*TESILENPRRAHSVST
Parental-LSKGLYGINEDIFLSVPCI-LGENGITDLIKVKLTLEEEACLQKSAETLWE-IQKELKL
...KGLYG.N.D.F.SVP.I.L.ENG..DL..VKLTLE..A.L..S.ETLWE.IQK.LKL
Retrocopy<IIKGLYGMN-DVFFSVPRI<LRENGLADLTQVKLTLEDVAHL*RSTETLWE<IQKKLKL

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 .24 RPM
bodymap2_adrenal 0 .00 RPM 0 .84 RPM
bodymap2_brain 0 .21 RPM 0 .59 RPM
bodymap2_breast 0 .00 RPM 0 .16 RPM
bodymap2_colon 0 .00 RPM 0 .04 RPM
bodymap2_heart 0 .00 RPM 0 .06 RPM
bodymap2_kidney 0 .00 RPM 0 .97 RPM
bodymap2_liver 0 .00 RPM 0 .00 RPM
bodymap2_lung 0 .00 RPM 0 .00 RPM
bodymap2_lymph_node 0 .00 RPM 0 .27 RPM
bodymap2_ovary 0 .00 RPM 0 .71 RPM
bodymap2_prostate 0 .00 RPM 0 .00 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .00 RPM
bodymap2_testis 0 .00 RPM 7 .33 RPM
bodymap2_thyroid 0 .00 RPM 0 .79 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .45 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_905 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_905 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_905 retrocopy 5' end.

Lab - click to see more details

retro_hsap_905 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_905 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_779
Macaca mulatta retro_mmul_1111
Equus caballus retro_ecab_933
Parental genes homology:
Parental genes homology involve 10 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000070672 retrocopies
retro_cjac_164, retro_cjac_2180,
Homo sapiens ENSG000001117161 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 ENSG00000166800 2 retrocopies
retro_hsap_42, retro_hsap_905 ,
Macaca mulatta ENSMMUG000000146142 retrocopies
retro_mmul_1111, retro_mmul_261,
Nomascus leucogenys ENSNLEG000000177802 retrocopies
retro_nleu_29, retro_nleu_378,
Otolemur garnettii ENSOGAG000000092611 retrocopy
retro_ogar_2662,
Pongo abelii ENSPPYG000000034352 retrocopies
retro_pabe_203, retro_pabe_779,
Pan troglodytes ENSPTRG000000034231 retrocopy
retro_ptro_62,
Tarsius syrichta ENSTSYG000000080624 retrocopies
retro_tsyr_1811, retro_tsyr_2064, retro_tsyr_2071, retro_tsyr_731,

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

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





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