RetrogeneDB ID:

retro_hsap_740

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:127355642..127356540(-)
Located in intron of:ENSG00000175018
Retrocopy
information
Ensembl ID:ENSG00000214297
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ALDOA
Ensembl ID:ENSG00000149925
Aliases:ALDOA, ALDA, GSD12, HEL-S-87p
Description:aldolase A, fructose-bisphosphate [Source:HGNC Symbol;Acc:414]


Retrocopy-Parental alignment summary:






>retro_hsap_740
GAACTTGCCACCACCAGCACCATGCCCTACCGATATCCAGCATTGACCCTGGAGCAGAAGAAGGAGCTGTCTGACATCGC
TCACCGCATCGTGGCACTGGGCAAGGGCATCCTGGCTGCAGATGAGTCCACTGGGAGCATTGCCAAGCGGCTGCAGTCCC
TTAACGCCGAGAACACCAAAGAGAACTGGCGCTTCTACTGTCAGCTGCTGCTGACAGCTGACGACTGCGTGAACCCCTGC
ATCGGGGACGTCATCCTCTTCCACCAGACACTCTACCAGAAGAAGGATGATGGGCGTCCTTTCCCCCAAGTTGTCATGTC
CAAGGGTGGTGTTGGGGGCAGCAAGGTAGACAAGGGCGTGGTCTCCCTTGCAGGGACAAATGGCGAGACCACCACCCAAG
GGTTGTATGGGCTGTCTGAGTGCTGTGCCCAGTACAAGAAGGATGGAGCTGACTTCACCAAGTGGCATTGTGTTCTGAAG
ATTGGGGAACACACCCCCTCAGCCCTTGCCGTCATGGAAAATACCAACGTCCTGGCCTGTCATGCCAGCATCTGCTAGCA
GAGTGGCATTGTGCCCATTGCGGAGCCTGAGATCCCCCCTAATGGGGACCATGACTTGAAGCACTGCCAGTGTGTGACCA
AGAAGGTGCTGACTGCTGTCTACAAGGCTCTGAGTGATCAACACATCTATCTTGGAGGGCATCTTGCTGAACCCCAGCAT
GGTCACCCCAGGCCATCCCTGCATCCAGAAGTTTTCTCACGAGGAGATTGCCATGGTGACTGTCACAACGCTGCACCGCA
CAGTGCCCCCCGCTGTCCCTGGGATCACATTCCTGTCTGGAGGCCAGAATGAGGAGGAGGCATCCATCAACCTCAACGCC
ATTAACAAGTGCTCCCTG

ORF - retro_hsap_740 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84. %
Parental protein coverage: 71.53 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalELATTSTMPYQYPALTPEQKKELSDIAHRIVAPGKGILAADESTGSIAKRLQSIGTENTEENRRFYRQLL
ELATTSTMPY.YPALT.EQKKELSDIAHRIVA.GKGILAADESTGSIAKRLQS...ENT.EN.RFY.QLL
RetrocopyELATTSTMPYRYPALTLEQKKELSDIAHRIVALGKGILAADESTGSIAKRLQSLNAENTKENWRFYCQLL
ParentalLTADDRVNPCIGGVILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSE
LTADD.VNPCIG.VILFH.TLYQK.DDGRPFPQV..SKGGV.G.KVDKGVV.LAGTNGETTTQGL.GLSE
RetrocopyLTADDCVNPCIGDVILFHQTLYQKKDDGRPFPQVVMSKGGVGGSKVDKGVVSLAGTNGETTTQGLYGLSE
ParentalRCAQYKKDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQ
.CAQYKKDGADF.KW.CVLKIGEHTPSALA.MEN.NVLA..ASIC.Q.GIVPI.EPEI.P.GDHDLK.CQ
RetrocopyCCAQYKKDGADFTKWHCVLKIGEHTPSALAVMENTNVLACHASIC*QSGIVPIAEPEIPPNGDHDLKHCQ
ParentalYVTEKVLAAVYKALSDHHIY-LEGTLLKPNMVTPGHACTQKFSHEEIAMATVTALRRTVPPAVTGITFLS
.VT.KVL.AVYKALSD.HIY.LEG.LL.P.MVTPGH.C.QKFSHEEIAM.TVT.L.RTVPPAV.GITFLS
RetrocopyCVTKKVLTAVYKALSDQHIY>LEGILLNPSMVTPGHPCIQKFSHEEIAMVTVTTLHRTVPPAVPGITFLS
ParentalGGQSEEEASINLNAINKCPL
GGQ.EEEASINLNAINKC.L
RetrocopyGGQNEEEASINLNAINKCSL

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 414 .63 RPM
bodymap2_adrenal 0 .00 RPM 310 .42 RPM
bodymap2_brain 0 .00 RPM 494 .96 RPM
bodymap2_breast 0 .00 RPM 729 .27 RPM
bodymap2_colon 0 .00 RPM 537 .79 RPM
bodymap2_heart 0 .00 RPM 941 .55 RPM
bodymap2_kidney 0 .00 RPM 462 .62 RPM
bodymap2_liver 0 .00 RPM 91 .82 RPM
bodymap2_lung 0 .00 RPM 375 .30 RPM
bodymap2_lymph_node 0 .00 RPM 321 .74 RPM
bodymap2_ovary 0 .00 RPM 360 .07 RPM
bodymap2_prostate 0 .00 RPM 714 .44 RPM
bodymap2_skeletal_muscle 0 .00 RPM 3134 .22 RPM
bodymap2_testis 0 .00 RPM 297 .92 RPM
bodymap2_thyroid 0 .00 RPM 807 .73 RPM
bodymap2_white_blood_cells 0 .00 RPM 514 .11 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_740 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_740 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_2218368 libraries496 libraries855 libraries88 libraries22 libraries

The graphical summary, for retro_hsap_740 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_740 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_740 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_526
Gorilla gorilla retro_ggor_621
Pongo abelii retro_pabe_636
Parental genes homology:
Parental genes homology involve 16 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000082212 retrocopies
retro_cfam_190, retro_cfam_631,
Callithrix jacchus ENSCJAG000000068741 retrocopy
retro_cjac_1803,
Cavia porcellus ENSCPOG000000074341 retrocopy
retro_cpor_951,
Echinops telfairi ENSETEG000000192301 retrocopy
retro_etel_20,
Homo sapiens ENSG00000149925 1 retrocopy
retro_hsap_740 ,
Gorilla gorilla ENSGGOG000000139791 retrocopy
retro_ggor_621,
Myotis lucifugus ENSMLUG000000112103 retrocopies
retro_mluc_1172, retro_mluc_2634, retro_mluc_808,
Macaca mulatta ENSMMUG000000009831 retrocopy
retro_mmul_2596,
Monodelphis domestica ENSMODG000000156964 retrocopies
retro_mdom_1236, retro_mdom_1356, retro_mdom_528, retro_mdom_96,
Mus musculus ENSMUSG000000306953 retrocopies
retro_mmus_2160, retro_mmus_42, retro_mmus_90,
Nomascus leucogenys ENSNLEG000000021521 retrocopy
retro_nleu_133,
Oryctolagus cuniculus ENSOCUG000000063291 retrocopy
retro_ocun_1550,
Ochotona princeps ENSOPRG000000097601 retrocopy
retro_opri_914,
Pongo abelii ENSPPYG000000072441 retrocopy
retro_pabe_636,
Pan troglodytes ENSPTRG000000079831 retrocopy
retro_ptro_526,
Rattus norvegicus ENSRNOG000000236477 retrocopies
retro_rnor_1343, retro_rnor_1541, retro_rnor_1796, retro_rnor_1807, retro_rnor_226, retro_rnor_2791, retro_rnor_536,

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 = 0.12 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .10 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .07 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .12 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .02 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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