RetrogeneDB ID:

retro_hsap_958

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:8786962..8788256(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000255967
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HADHA
Ensembl ID:ENSG00000084754
Aliases:HADHA, ECHA, GBP, HADH, LCEH, LCHAD, MTPA, TP-ALPHA
Description:hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit [Source:HGNC Symbol;Acc:4801]


Retrocopy-Parental alignment summary:






>retro_hsap_958
ATGGTGGCCTACCGGGCGATTGGCATCCTCAGCCGCTTCTCTGACTTCAGGATCCTCTGATCCCAAGGTTATATACGCCG
CAATTTTACAGAGTCTTCTGCTTTGCTGACCAGAACCCATATTAACTATGGAGTCAAAGGGGATGTGGCAGTTATTCGAA
TTAAATCTTCCACTTCAAAGGTAAATACACTGAGTAAAGAGCTGCATTCAGAGTTCACGGAAGTTATGAATGAAGTCTGG
GCTACTAATCAAATCAGAAATGCTGTCCTTATTTCATCCAAAGCCAGGCCGCTTTATTGCAGGTGCTGATATCAATATGT
TAGCCACTTGCAAGACCCCTCAAGAAGTAACACAGGTATCACAAGAAGCACAGAGAACATTTGAGAAACTTGAAAAGGCC
GCAAAGCCTGTTATAGCTGCCATCAGTGGATCCTGCCTGGGAGGAGGGCTTGAGCTTGCCATTTCATGCCAATACAGAAT
AGCAACAAAAGATGGAAAAACAATATTAGGTGCCCCTGAAGTCTTGCTGGGGATCTTACCAGGAGCAGGAGGCACACAAA
GGCTGCCCAAAATGGTGGGTGTGCCTGCTGTTTTTGACATGATGCTGACTAGTAGAAACATTCATGCAGATAGCGCAAAG
AAAATGGGACTGGTTGACCAATTGGTAGAACCCCTGGGACCGGGAATAAAACCTCCAGAGGAATGGACAATCGAATACCT
GGAAGCAGTTGCAATTACTTTTGCCAAAGGACTAGCTGATAAGAAGATCTCTCCAAAGAGAGACAAGGGATTGGTGGAAA
AATTGACAGCGTACACCATGACTATTCCATTTGTCAGGCAACAGGTTTACAAAAAAGTGGAAGAAAAAGTGCAAAAGGAG
ACTAAAGGCCTTTATCCTGCACCTCTGAAAATAATTGACGTGGTAAAGACTGGAATTGAGCGAGGGATTGATGCTGGTTA
TCTCTCTGAATCTCAGAAATTTGGATAGCTTGCAATGACCAGTGAATCAAAGGCCTTGATGGGTCTCTACCATGGTCAGG
TCTTGTGCAAGAAGAATAAATTTGGAGCACCACAGAAGGATGTTAAGCGTCTGGCTATTCTTGGTGAAGGGCTGAAGGGA
GCAGGCATCACCCAAGTCTCTGTGGATAAGAGGCTAAAGACTATACTTAAAGATGCCACACTCACTAGGCTAGGCCAAGG
ACAGCAACAAGTGTTCAAAGGATTGAATGATAAAGTGAATAAGAAAGCTCTAACATCATTTGTAAGGGATTCCATCTTCA
GCAACTTGACTGGG

ORF - retro_hsap_958 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.11 %
Parental protein coverage: 56.49 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMVACRAIGILSRFSAFRILRSRGYICRNFTGSSALLTRTHINYGVKGDVAVVRINSPNSKVNTLSKELHS
MVA.RAIGILSRFS.FRIL.S.GYI.RNFT.SSALLTRTHINYGVKGDVAV.RI.S..SKVNTLSKELHS
RetrocopyMVAYRAIGILSRFSDFRIL*SQGYIRRNFTESSALLTRTHINYGVKGDVAVIRIKSSTSKVNTLSKELHS
ParentalEFSEVMNEIWASDQIRSAVLISSK-PGCFIAGADINMLAACKTLQEVTQLSQEAQRIVEKLEKSTKPIVA
EF.EVMNE.WA..QIR.AVLISSK.PG.FIAGADINMLA.CKT.QEVTQ.SQEAQR..EKLEK..KP..A
RetrocopyEFTEVMNEVWATNQIRNAVLISSK>PGRFIAGADINMLATCKTPQEVTQVSQEAQRTFEKLEKAAKPVIA
ParentalAINGSCLGGGLEVAISCQYRIATKDRKTVLGTPEVLLGALPGAGGTQRLPKMVGVPAALDMMLTGRSIRA
AI.GSCLGGGLE.AISCQYRIATKD.KT.LG.PEVLLG.LPGAGGTQRLPKMVGVPA..DMMLT.R.I.A
RetrocopyAISGSCLGGGLELAISCQYRIATKDGKTILGAPEVLLGILPGAGGTQRLPKMVGVPAVFDMMLTSRNIHA
ParentalDRAKKMGLVDQLVEPLGPGLKPPEERTIEYLEEVAITFAKGLADKKISPKRDKGLVEKLTAYAMTIPFVR
D.AKKMGLVDQLVEPLGPG.KPPEE.TIEYLE.VAITFAKGLADKKISPKRDKGLVEKLTAY.MTIPFVR
RetrocopyDSAKKMGLVDQLVEPLGPGIKPPEEWTIEYLEAVAITFAKGLADKKISPKRDKGLVEKLTAYTMTIPFVR
ParentalQQVYKKVEEKVRKQTKGLYPAPLKIIDVVKTGIEQGSDAGYLCESQKFGELVMTKESKALMGLYHGQVLC
QQVYKKVEEKV.K.TKGLYPAPLKIIDVVKTGIE.G.DAGYL.ESQKFG.L.MT.ESKALMGLYHGQVLC
RetrocopyQQVYKKVEEKVQKETKGLYPAPLKIIDVVKTGIERGIDAGYLSESQKFG*LAMTSESKALMGLYHGQVLC
ParentalKKNKFGAPQKDVKHLAILGAGLMGAGIAQVSVDKGLKTILKDATLTALDRGQQQVFKGLNDKVKKKALTS
KKNKFGAPQKDVK.LAILG.GL.GAGI.QVSVDK.LKTILKDATLT.L..GQQQVFKGLNDKV.KKALTS
RetrocopyKKNKFGAPQKDVKRLAILGEGLKGAGITQVSVDKRLKTILKDATLTRLGQGQQQVFKGLNDKVNKKALTS
ParentalFERDSIFSNLTG
F.RDSIFSNLTG
RetrocopyFVRDSIFSNLTG

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 404 .34 RPM
bodymap2_adrenal 0 .00 RPM 212 .08 RPM
bodymap2_brain 0 .00 RPM 141 .04 RPM
bodymap2_breast 0 .10 RPM 291 .95 RPM
bodymap2_colon 0 .00 RPM 263 .14 RPM
bodymap2_heart 0 .13 RPM 603 .51 RPM
bodymap2_kidney 0 .00 RPM 247 .42 RPM
bodymap2_liver 0 .00 RPM 201 .44 RPM
bodymap2_lung 0 .09 RPM 167 .60 RPM
bodymap2_lymph_node 0 .00 RPM 164 .12 RPM
bodymap2_ovary 0 .02 RPM 264 .59 RPM
bodymap2_prostate 0 .00 RPM 255 .25 RPM
bodymap2_skeletal_muscle 0 .07 RPM 560 .70 RPM
bodymap2_testis 0 .02 RPM 229 .03 RPM
bodymap2_thyroid 0 .13 RPM 278 .83 RPM
bodymap2_white_blood_cells 0 .00 RPM 294 .16 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_958 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_958 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_29833815 libraries184 libraries192 libraries359 libraries279 libraries

The graphical summary, for retro_hsap_958 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_958 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_958 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_664
Gorilla gorilla retro_ggor_772
Macaca mulatta retro_mmul_787
Parental genes homology:
Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000069721 retrocopy
retro_dnov_1863,
Homo sapiens ENSG00000084754 1 retrocopy
retro_hsap_958 ,
Homo sapiens ENSG000001387961 retrocopy
retro_hsap_1571,
Gorilla gorilla ENSGGOG000000049181 retrocopy
retro_ggor_772,
Macaca mulatta ENSMMUG000000043802 retrocopies
retro_mmul_1987, retro_mmul_787,
Mustela putorius furoENSMPUG000000085461 retrocopy
retro_mputfur_705,
Nomascus leucogenys ENSNLEG000000016162 retrocopies
retro_nleu_1588, retro_nleu_772,
Pongo abelii ENSPPYG000000125832 retrocopies
retro_pabe_2576, retro_pabe_817,
Pan troglodytes ENSPTRG000000117322 retrocopies
retro_ptro_2109, retro_ptro_664,
Ictidomys tridecemlineatus ENSSTOG000000015931 retrocopy
retro_itri_681,

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 = 0.08 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 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 .03 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 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 .02 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .08 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 .03 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 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 .02 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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