RetrogeneDB ID:

retro_hsap_41

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:96761301..96762468(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000163114
Aliases:PDHA2, PDHAL
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:PDHA1
Ensembl ID:ENSG00000131828
Aliases:PDHA1, PDHA, PDHCE1A, PHE1A
Description:pyruvate dehydrogenase (lipoamide) alpha 1 [Source:HGNC Symbol;Acc:8806]


Retrocopy-Parental alignment summary:






>retro_hsap_41
ATGCTGGCCGCCTTCATCTCCCGCGTGTTGAGGCGAGTTGCCCAGAAATCAGCTCGCAGAGTGCTGGTGGCATCCCGTAA
CTCCTCAAATGACGCTACATTTGAAATTAAGAAATGTGATCTTTATCTGTTGGAAGAGGGTCCCCCTGTCACTACAGTGC
TCACTAGGGCGGAGGGGCTTAAATACTACAGGATGATGCTGACTGTTCGCCGCATGGAATTGAAGGCAGATCAGCTGTAC
AAACAGAAATTCATTCGCGGTTTCTGTCACCTGTGCGATGGTCAGGAAGCTTGTTGCGTGGGCCTTGAGGCCGGCATAAA
CCCCTCGGATCACGTCATTACATCCTATAGGGCTCATGGTGTGTGCTATACTCGGGGACTTTCTGTCCGATCCATTCTCG
CAGAGCTGACGGGAAGAAGAGGAGGTTGTGCTAAAGGAAAAGGAGGATCGATGCATATGTATACCAAGAACTTCTATGGG
GGCAATGGCATCGTCGGTGCACAGGGCCCCCTGGGCGCTGGCATTGCTCTGGCCTGTAAATATAAAGGAAACGATGAGAT
CTGTTTGACTTTATATGGGGATGGCGCTGCGAATCAGGGGCAGATAGCCGAAGCTTTCAATATGGCAGCTTTATGGAAAT
TACCTTGTGTTTTCATCTGTGAGAATAACCTATATGGAATGGGAACATCTACTGAGAGAGCAGCAGCCAGCCCTGATTAC
TACAAGAGGGGCAATTTTATCCCTGGGCTAAAGGTCGATGGAATGGATGTTCTGTGTGTTCGTGAGGCAACAAAATTTGC
AGCTAACTACTGTAGATCTGGAAAGGGGCCCATACTGATGGAGCTGCAAACCTACCGTTATCATGGACACAGTATGAGTG
ATCCTGGAGTCAGTTATCGTACACGAGAAGAAATTCAGGAAGTAAGAAGTAAGAGGGATCCTATAATAATTCTCCAAGAT
AGAATGGTAAACAGCAAGCTCGCCACTGTGGAAGAATTAAAGGAAATTGGGGCTGAGGTGAGGAAAGAAATTGATGATGC
TGCCCAGTTTGCTACCACTGATCCTGAGCCACATTTGGAAGAATTAGGCCATCACATCTACAGCAGTGATTCATCTTTTG
AAGTTCGTGGTGCAAATCCATGGATCAAGTTTAAGTCCGTCAGTTAA

ORF - retro_hsap_41 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.82 %
Parental protein coverage: 99.23 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMLAA-VSRVLSGASQKPASRVLVASRNFANDATFEIKKCDLHRLEEGPPVTTVLTREDGLKYYRMMQTVR
MLAA..SRVL....QK.A.RVLVASRN..NDATFEIKKCDL..LEEGPPVTTVLTR..GLKYYRMM.TVR
RetrocopyMLAAFISRVLRRVAQKSARRVLVASRNSSNDATFEIKKCDLYLLEEGPPVTTVLTRAEGLKYYRMMLTVR
ParentalRMELKADQLYKQKIIRGFCHLCDGQEACCVGLEAGINPTDHLITAYRAHGFTFTRGLSVREILAELTGRK
RMELKADQLYKQK.IRGFCHLCDGQEACCVGLEAGINP.DH.IT.YRAHG...TRGLSVR.ILAELTGR.
RetrocopyRMELKADQLYKQKFIRGFCHLCDGQEACCVGLEAGINPSDHVITSYRAHGVCYTRGLSVRSILAELTGRR
ParentalGGCAKGKGGSMHMYAKNFYGGNGIVGAQVPLGAGIALACKYNGKDEVCLTLYGDGAANQGQIFEAYNMAA
GGCAKGKGGSMHMY.KNFYGGNGIVGAQ.PLGAGIALACKY.G.DE.CLTLYGDGAANQGQI.EA.NMAA
RetrocopyGGCAKGKGGSMHMYTKNFYGGNGIVGAQGPLGAGIALACKYKGNDEICLTLYGDGAANQGQIAEAFNMAA
ParentalLWKLPCIFICENNRYGMGTSVERAAASTDYYKRGDFIPGLRVDGMDILCVREATRFAAAYCRSGKGPILM
LWKLPC.FICENN.YGMGTS.ERAAAS.DYYKRG.FIPGL.VDGMD.LCVREAT.FAA.YCRSGKGPILM
RetrocopyLWKLPCVFICENNLYGMGTSTERAAASPDYYKRGNFIPGLKVDGMDVLCVREATKFAANYCRSGKGPILM
ParentalELQTYRYHGHSMSDPGVSYRTREEIQEVRSKSDPIMLLKDRMVNSNLASVEELKEIDVEVRKEIEDAAQF
ELQTYRYHGHSMSDPGVSYRTREEIQEVRSK.DPI..L.DRMVNS.LA.VEELKEI..EVRKEI.DAAQF
RetrocopyELQTYRYHGHSMSDPGVSYRTREEIQEVRSKRDPIIILQDRMVNSKLATVEELKEIGAEVRKEIDDAAQF
ParentalATADPEPPLEELGYHIYSSDPPFEVRGANQWIKFKSVS
AT.DPEP.LEELG.HIYSSD..FEVRGAN.WIKFKSVS
RetrocopyATTDPEPHLEELGHHIYSSDSSFEVRGANPWIKFKSVS

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 51 .13 RPM
bodymap2_adrenal 0 .04 RPM 51 .81 RPM
bodymap2_brain 0 .00 RPM 61 .46 RPM
bodymap2_breast 0 .00 RPM 102 .47 RPM
bodymap2_colon 0 .00 RPM 51 .43 RPM
bodymap2_heart 0 .00 RPM 238 .15 RPM
bodymap2_kidney 0 .00 RPM 149 .42 RPM
bodymap2_liver 0 .00 RPM 52 .60 RPM
bodymap2_lung 0 .00 RPM 34 .65 RPM
bodymap2_lymph_node 0 .00 RPM 38 .81 RPM
bodymap2_ovary 0 .00 RPM 50 .99 RPM
bodymap2_prostate 0 .00 RPM 61 .04 RPM
bodymap2_skeletal_muscle 0 .00 RPM 97 .80 RPM
bodymap2_testis 68 .57 RPM 37 .59 RPM
bodymap2_thyroid 0 .00 RPM 87 .90 RPM
bodymap2_white_blood_cells 0 .00 RPM 31 .93 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_41 was not detected

EST - click to see more details

10 EST(s) were mapped to retro_hsap_41 retrocopy
EST ID Start End Identity Match Mis-match Score
AI393336 96761616 96761833 100 217 0 217
BU854475 96761264 96761763 95.2 488 11 470
DB065822 96761278 96761860 100 582 0 582
DB459674 96761243 96761875 100 631 0 631
DB461656 96761274 96761745 100 471 0 471
HY026399 96761255 96761691 99.8 435 1 434
HY029492 96761264 96761736 100 472 0 472
HY048052 96761274 96761768 99.8 493 1 492
HY051642 96761248 96761678 99.6 428 2 426
HY053842 96761237 96761715 99.8 477 1 476

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_1471051809 libraries16 libraries1 library0 libraries3 libraries

The graphical summary, for retro_hsap_41 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_41 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_41 has 9 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_79
Gorilla gorilla retro_ggor_59
Pongo abelii retro_pabe_129
Macaca mulatta retro_mmul_123
Callithrix jacchus retro_cjac_27
Mus musculus retro_mmus_63
Oryctolagus cuniculus retro_ocun_264
Bos taurus retro_btau_100
Equus caballus retro_ecab_21
Parental genes homology:
Parental genes homology involve 22 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000167301 retrocopy
retro_amel_400,
Bos taurus ENSBTAG000000198522 retrocopies
retro_btau_100, retro_btau_1807,
Callithrix jacchus ENSCJAG000000054962 retrocopies
retro_cjac_2414, retro_cjac_27,
Dipodomys ordii ENSDORG000000118481 retrocopy
retro_dord_35,
Equus caballus ENSECAG000000019641 retrocopy
retro_ecab_21,
Erinaceus europaeus ENSEEUG000000054851 retrocopy
retro_eeur_580,
Homo sapiens ENSG00000131828 1 retrocopy
retro_hsap_41 ,
Gorilla gorilla ENSGGOG000000135741 retrocopy
retro_ggor_59,
Myotis lucifugus ENSMLUG000000129322 retrocopies
retro_mluc_2363, retro_mluc_323,
Macaca mulatta ENSMMUG000000173361 retrocopy
retro_mmul_123,
Mustela putorius furoENSMPUG000000032691 retrocopy
retro_mputfur_812,
Mus musculus ENSMUSG000000312992 retrocopies
retro_mmus_63, retro_mmus_631,
Nomascus leucogenys ENSNLEG000000098051 retrocopy
retro_nleu_74,
Oryctolagus cuniculus ENSOCUG000000147481 retrocopy
retro_ocun_264,
Pongo abelii ENSPPYG000000201711 retrocopy
retro_pabe_129,
Pan troglodytes ENSPTRG000000217171 retrocopy
retro_ptro_79,
Pteropus vampyrus ENSPVAG000000054201 retrocopy
retro_pvam_1306,
Sarcophilus harrisii ENSSHAG000000153751 retrocopy
retro_shar_84,
Sus scrofa ENSSSCG000000236432 retrocopies
retro_sscr_1015, retro_sscr_281,
Ictidomys tridecemlineatus ENSSTOG000000154331 retrocopy
retro_itri_1529,
Tupaia belangeri ENSTBEG000000143131 retrocopy
retro_tbel_3327,
Tursiops truncatus ENSTTRG000000006601 retrocopy
retro_ttru_1427,

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 = 0.03 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 .03 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 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 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 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 .02 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).



Copyright © RetrogeneDB 2014-2017