RetrogeneDB ID:

retro_hsap_3739

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:63894299..63894894(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000232727
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:YWHAE
Ensembl ID:ENSG00000108953
Aliases:YWHAE, 14-3-3E, HEL2, KCIP-1, MDCR, MDS
Description:tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide [Source:HGNC Symbol;Acc:12851]


Retrocopy-Parental alignment summary:






>retro_hsap_3739
TTCCAAGAAATGGTGTAGTCAATGAAGAAAGTAGCAGGGATGGATGTGGAACTGACAGTTGAAGAAATAAACTTCCCATC
TGTTGCATATAAGAATGTAATTGGAGCTAGAAGAGCCTCCTGGAGAATAATCAGCAGTATTGAACAGAAAGAAGAAAACA
AGGAAGGAGAAGACAAGCTAAAAATGATTTGGGAATATCAGCAAATGATTGAGACTGAGCTAAAGTTACTCTGTTGTGAC
ATTCTGGATGTACTGGACAAAAACCTCATTCCAGCAGCTAACACTGGCGAGTCCAAAGTTTTCTATTATAAAATGAAAGG
GGACTACCACAGGTATCTGGCAGAATTTGCCACAGGAAATGACAGGAAGGAGGCTGTGGAGAACAGCCTAGTGGCTTATA
AAGCTGCTAGTGATATTGCAATGACAGAACTTCCACCAATGCATCCTACTCGCTTAGGTCTTGCTCTCAAATTTTTCTGT
ATTCTACTACGAAATTCTTAATTCCCCTGACCATGCCTGCAGGTTGGCAAAAGCAGCTTTTGATGATACAATTGCAGAAC
TGGATACGCTGAGTGAAGAAAGCTATAAGGACACT

ORF - retro_hsap_3739 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.45 %
Parental protein coverage: 77.65 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalYDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKGGEDKLKMIREYRQMV
..EMV.SMKKVAGMDVELTVEE.N..SVAYKNVIGARRASWRIISSIEQKEENK.GEDKLKMI.EY.QM.
RetrocopyFQEMV*SMKKVAGMDVELTVEEINFPSVAYKNVIGARRASWRIISSIEQKEENKEGEDKLKMIWEYQQMI
ParentalETELKLICCDILDVLDKHLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIA
ETELKL.CCDILDVLDK.LIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEA.ENSLVAYKAASDIA
RetrocopyETELKLLCCDILDVLDKNLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEAVENSLVAYKAASDIA
ParentalMTELPPTHPIRLGLAL-NFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDS
MTELPP.HP.RLGLAL.NFSVFYYEILNSPD.ACRLAKAAFDD.IAELDTLSEESYKD.
RetrocopyMTELPPMHPTRLGLAL>NFSVFYYEILNSPDHACRLAKAAFDDTIAELDTLSEESYKDT

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 .02 RPM 615 .74 RPM
bodymap2_adrenal 0 .02 RPM 358 .22 RPM
bodymap2_brain 0 .26 RPM 1163 .31 RPM
bodymap2_breast 0 .02 RPM 549 .75 RPM
bodymap2_colon 0 .00 RPM 539 .33 RPM
bodymap2_heart 0 .00 RPM 382 .07 RPM
bodymap2_kidney 0 .00 RPM 453 .17 RPM
bodymap2_liver 0 .00 RPM 239 .27 RPM
bodymap2_lung 0 .00 RPM 630 .29 RPM
bodymap2_lymph_node 0 .00 RPM 299 .72 RPM
bodymap2_ovary 0 .02 RPM 588 .39 RPM
bodymap2_prostate 0 .00 RPM 407 .30 RPM
bodymap2_skeletal_muscle 0 .02 RPM 732 .42 RPM
bodymap2_testis 4 .73 RPM 661 .44 RPM
bodymap2_thyroid 0 .04 RPM 749 .48 RPM
bodymap2_white_blood_cells 0 .02 RPM 221 .94 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3739 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3739 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_176594488 libraries605 libraries618 libraries95 libraries23 libraries

The graphical summary, for retro_hsap_3739 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_3739 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3739 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2538
Parental genes homology:
Parental genes homology involve 17 parental genes, and 41 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000056643 retrocopies
retro_btau_1485, retro_btau_372, retro_btau_954,
Choloepus hoffmanni ENSCHOG000000108612 retrocopies
retro_chof_1912, retro_chof_905,
Ciona intestinalis ENSCING000000238561 retrocopy
retro_cint_15,
Ciona savignyi ENSCSAVG000000117232 retrocopies
retro_csav_13, retro_csav_9,
Echinops telfairi ENSETEG000000120562 retrocopies
retro_etel_1762, retro_etel_738,
Homo sapiens ENSG00000108953 4 retrocopies
retro_hsap_2324, retro_hsap_3739 , retro_hsap_3851, retro_hsap_4703,
Homo sapiens ENSG000001343082 retrocopies
retro_hsap_3004, retro_hsap_8,
Homo sapiens ENSG000001649241 retrocopy
retro_hsap_549,
Homo sapiens ENSG000001669134 retrocopies
retro_hsap_4160, retro_hsap_4841, retro_hsap_622, retro_hsap_855,
Gorilla gorilla ENSGGOG000000168401 retrocopy
retro_ggor_2596,
Monodelphis domestica ENSMODG000000101742 retrocopies
retro_mdom_1567, retro_mdom_744,
Nomascus leucogenys ENSNLEG000000006562 retrocopies
retro_nleu_2067, retro_nleu_2868,
Otolemur garnettii ENSOGAG000000061552 retrocopies
retro_ogar_1003, retro_ogar_2144,
Pongo abelii ENSPPYG000000077694 retrocopies
retro_pabe_1644, retro_pabe_1646, retro_pabe_2107, retro_pabe_3219,
Pan troglodytes ENSPTRG000000085215 retrocopies
retro_ptro_1697, retro_ptro_2538, retro_ptro_2624, retro_ptro_2626, retro_ptro_2993,
Ictidomys tridecemlineatus ENSSTOG000000050841 retrocopy
retro_itri_1175,
Vicugna pacos ENSVPAG000000102883 retrocopies
retro_vpac_230, retro_vpac_411, retro_vpac_559,

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 = 0.09 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 .09 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 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 .06 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .04 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 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 .03 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 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 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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