RetrogeneDB ID:

retro_hsap_1816

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:17:25410080..25411073(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000265646
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TUFM
Ensembl ID:ENSG00000178952
Aliases:TUFM, COXPD4, EF-TuMT, EFTU, P43
Description:Tu translation elongation factor, mitochondrial [Source:HGNC Symbol;Acc:12420]


Retrocopy-Parental alignment summary:






>retro_hsap_1816
ATGACCACAATGGCGGCTGCCACCTTGCTGCGCGCGACGCCTCACTTCAGCGGTCTCGCTGCCGGCCGGACCTTCCTGCT
GCAGGGTCTGCTGCTGCTGCTGAAAGCCCTGGCATTGCCTCTCTTGTGCCACGGCCTGGCTGTGGGGGCCAAGAAGACTT
AACGTGTGTGAGAAGCCACATGTGAATGTGGGTACCATCGGCCATGTGGACCATGGCAAGACCAAACTGATTGCAGCTAT
CACAAAGATTCTAGCCGAGGGAGGTGGGGCTAAGTTCAAGAAGTACAAGGAGATTGACAATGCCCCCAGAGGAGCAAGCT
CCAGGTATCACCATCAGTGTGGCTCATGTGGAGTATAGCACTGTCGCCCACCACTATGCCCACACAGACAGCCCGGGTCA
TGCAGATTATGTTAAGTATATGATCACGGGCACCACACCCCTTGACGGCTGCCTCCTGGTGGTAGCAGCCAATGACAGCC
CCATGCCCTAGACCCGAGAGCACTTATTACTGGCCAAATAGATTGGGGTGGAGCATGTGGTGGTGTATGTGAACAAGGCT
GATGCTGTCCAGGACTCTGAGATGGTGGAGCTGGTGGAACTGGAGATTCAGGAGCTGTTCACTGAGTTTGGCTATAAAGG
GGAGGAGACCCCAGTCATTGTAGGCTCTACTGTCTGCCCTTGAGGGTCGGGACCCTGAGTTAGGTCTGAAGTCTGTGCAG
AAGCTACTGGATGCTGTGGACACTTACATCCCAGTGCCTGCCCGTGACCTGGAGAAGCCTTTCCTGCTGACTGTAGAGGC
AGTGTACTCCATGTCTGGCCATGGCACCATGGTGACAGGTATGCTAGAGCATGACATTTTAAAGAAAGGAGACAAGCGTG
AGCTCCTAGGACATAATAAGAACATCTGCACTGTGCTGACAGGCATTGAGATGTTCCACAAGAGCCTGGAGAGGGCCGAG
GCTGGAGATAACCTCAGGGCCCTGGTCCGAGGG

ORF - retro_hsap_1816 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.13 %
Parental protein coverage: 72.75 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMTTMAAATLLRATPHFSGLAAGRTFLLQGLLRLLKAPALPLLCRGLAVEAKKT-YVRDKPHVNVGTIGHV
MTTMAAATLLRATPHFSGLAAGRTFLLQGLL.LLKA.ALPLLC.GLAV.AKKT..V..KPHVNVGTIGHV
RetrocopyMTTMAAATLLRATPHFSGLAAGRTFLLQGLLLLLKALALPLLCHGLAVGAKKT>NVCEKPHVNVGTIGHV
ParentalDHGKTTLTAAITKILAEGGGAKFKKYEEIDNAP-EERARGITINAAHVEYSTAARHYAHTDCPGHADYVK
DHGKT.L.AAITKILAEGGGAKFKKY.EIDNAP.EE.A.GITI..AHVEYST.A.HYAHTD.PGHADYVK
RetrocopyDHGKTKLIAAITKILAEGGGAKFKKYKEIDNAP>EEQAPGITISVAHVEYSTVAHHYAHTDSPGHADYVK
ParentalNMITGTAPLDGCILVVAANDGPMPQTREHLLLARQIGVEHVVVYVNKADAVQDSEMVELVELEIRELLTE
.MITGT.PLDGC.LVVAAND.PMP.TREHLLLA..IGVEHVVVYVNKADAVQDSEMVELVELEI.EL.TE
RetrocopyYMITGTTPLDGCLLVVAANDSPMP*TREHLLLAK*IGVEHVVVYVNKADAVQDSEMVELVELEIQELFTE
ParentalFGY-KGEETPVIVGSALCALEGRDPELGLKSVQKLLDAVDTYIPVPARDLEKPFLLPVEAVYSVPGRGTV
FGY.KG...P......L.ALEGRDPELGLKSVQKLLDAVDTYIPVPARDLEKPFLL.VEAVYS..G.GT.
RetrocopyFGY>KGRR-PQSL*ALLSALEGRDPELGLKSVQKLLDAVDTYIPVPARDLEKPFLLTVEAVYSMSGHGTM
ParentalVTGTLERGILKKGDECELLGHSKNIRTVVTGIEMFHKSLERAEAGDNLGALVRG
VTG.LE..ILKKGD..ELLGH.KNI.TV.TGIEMFHKSLERAEAGDNL.ALVRG
RetrocopyVTGMLEHDILKKGDKRELLGHNKNICTVLTGIEMFHKSLERAEAGDNLRALVRG

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 83 .55 RPM
bodymap2_adrenal 0 .00 RPM 103 .39 RPM
bodymap2_brain 0 .00 RPM 60 .15 RPM
bodymap2_breast 0 .00 RPM 83 .15 RPM
bodymap2_colon 0 .00 RPM 77 .96 RPM
bodymap2_heart 0 .00 RPM 99 .45 RPM
bodymap2_kidney 0 .00 RPM 134 .92 RPM
bodymap2_liver 0 .00 RPM 115 .31 RPM
bodymap2_lung 0 .00 RPM 82 .98 RPM
bodymap2_lymph_node 0 .00 RPM 93 .27 RPM
bodymap2_ovary 0 .00 RPM 86 .21 RPM
bodymap2_prostate 0 .00 RPM 85 .70 RPM
bodymap2_skeletal_muscle 0 .00 RPM 130 .04 RPM
bodymap2_testis 0 .00 RPM 122 .47 RPM
bodymap2_thyroid 0 .00 RPM 110 .54 RPM
bodymap2_white_blood_cells 0 .00 RPM 85 .96 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_1816 in 1 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CMI POLR2A 17:25407977..25412362

EST - click to see more details

No EST(s) were mapped for retro_hsap_1816 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1816 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1816 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1816 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1174
Parental genes homology:
Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Dipodomys ordii ENSDORG000000164741 retrocopy
retro_dord_278,
Homo sapiens ENSG00000178952 1 retrocopy
retro_hsap_1816 ,
Macropus eugenii ENSMEUG000000111311 retrocopy
retro_meug_1783,
Monodelphis domestica ENSMODG000000155641 retrocopy
retro_mdom_384,
Mus musculus ENSMUSG000000738381 retrocopy
retro_mmus_10,
Ornithorhynchus anatinus ENSOANG000000131141 retrocopy
retro_oana_36,
Oryctolagus cuniculus ENSOCUG000000026831 retrocopy
retro_ocun_333,
Pan troglodytes ENSPTRG000000079391 retrocopy
retro_ptro_1174,
Rattus norvegicus ENSRNOG000000186041 retrocopy
retro_rnor_1134,
Vicugna pacos ENSVPAG000000095411 retrocopy
retro_vpac_346,
Drosophila melanogaster FBgn00331841 retrocopy
retro_dmel_52,

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 = 0.07 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 .07 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 .02 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 .03 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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