RetrogeneDB ID:

retro_hsap_1386

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:14:19719545..19720552(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000257573
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TOMM40
Ensembl ID:ENSG00000130204
Aliases:TOMM40, C19orf1, D19S1177E, PER-EC1, PEREC1, TOM40
Description:translocase of outer mitochondrial membrane 40 homolog (yeast) [Source:HGNC Symbol;Acc:18001]


Retrocopy-Parental alignment summary:






>retro_hsap_1386
CCGCCACCTCCGCCCTCGCCGCCGGGCTTCACGCTGCCGCCGCTGAGAGGCGGCCTGGGCGCCGGCACCACTAGGAGTCG
AGGTTCGGAACGGACCCCCGGGGCTGCAACCGCCAGCGCCTCAGGGGCCGCCGAGGATGGGGCCTGCGGCTGCCTGCCCA
ACCCGGGCACATTCCAGGAGTGCCACCGGAGGTGTAAGGAGCTGTTTCCCATTCAGATGGAGGGTGTCAAGCTCACAGTC
AACAAAGGGTTGAGTAACCGTTTCCAGGTGAACCACACAGTAGCCCTCAGCGCAATCGGGGAGTCCAACTACCACTTCGG
GGTCACGTATGTGGGGACAAAGCAGCTGAGTCCCACAGAGGCGTTCCCTGTACTGGTAGGTGACATGGACAACAGCGGCA
GTCTCCACGCTCAGGTCATTCACCAGCTGGGCCCCGGTCTCAGGTCCAAGATGGCCATCCAGACCCAGCAGTCGAAGTTT
GTGAACTGGCAGGTGGACGGGGAGTATCGGGGCTCTGACTCACAGCAGCCGTCACCCTGGGGATCCCAGACGTCCTCGTG
GGTTCAAGAATTCTCGAAGCCCACTACCTCCAGAGCATCAGGCCTTGCCTGGCCCTGGGCGGAGAGCTGGTCTACAACCG
GCGGCCTGGGGACGAGGGCACTGTCACGTCTCTAGCTGGGAAATACACATTGAACAACTGGTTGGCAACGGTAACGTTGA
GCCAGGCGGGCATGCACGCAACATACTACCACAAAGCCAGTGACCAGTTGCAGGTGGGTGTGGATTTTCAGGCCAGCACA
AGGATGCAGGATACCAGCGTCTCCTTCAGGTACCAGCTGGACCTGCCCAAGGCCAACCTCCTCTTCAAAGGCTCTGTGGA
TAGCAACTGGATCGTGGGTGCCACGCTGGAGAAGAAGCTCCAGCTCCTGCCCCTGACGCTGGCCCTTGGGGCCTTCCTGA
ATCACCGCAAGAACAAGTTCCAGTGTGGCTCTGGACTCACCATCGGC

ORF - retro_hsap_1386 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.28 %
Parental protein coverage: 93.07 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPPPPPSPPGFTLPPLGGSLGAGTSTSRSSERTPGAATASASGAAEDGACGCLPNPGTFEECHRKCKELFP
PPPPPSPPGFTLPPL.G.LGAGT..SR.SERTPGAATASASGAAEDGACGCLPNPGTF.ECHR.CKELFP
RetrocopyPPPPPSPPGFTLPPLRGGLGAGTTRSRGSERTPGAATASASGAAEDGACGCLPNPGTFQECHRRCKELFP
ParentalIQMEGVKLTVNKGLSNHFQVNHTVALSTIGESNYHFGVTYVGTKQLSPTEAFPVLVGDMDNSGSLNAQVI
IQMEGVKLTVNKGLSN.FQVNHTVALS.IGESNYHFGVTYVGTKQLSPTEAFPVLVGDMDNSGSL.AQVI
RetrocopyIQMEGVKLTVNKGLSNRFQVNHTVALSAIGESNYHFGVTYVGTKQLSPTEAFPVLVGDMDNSGSLHAQVI
ParentalHQLGPGLRSKMAIQTQQSKFVNWQVDGEYRGSD-FTAAVTLGNPDVLVGSGILVAHYLQSITPCLALGGE
HQLGPGLRSKMAIQTQQSKFVNWQVDGEYRGSD..TAAVTLG.PDVLVGS.IL.AHYLQSI.PCLALGGE
RetrocopyHQLGPGLRSKMAIQTQQSKFVNWQVDGEYRGSD<LTAAVTLGIPDVLVGSRILEAHYLQSIRPCLALGGE
ParentalLVYHRRPGEEGTVMSLAGKYTLNNWLATVTLGQAGMHATYYHKASDQLQVGVEFEASTRMQDTSVSFGYQ
LVY.RRPG.EGTV.SLAGKYTLNNWLATVTL.QAGMHATYYHKASDQLQVGV.F.ASTRMQDTSVSF.YQ
RetrocopyLVYNRRPGDEGTVTSLAGKYTLNNWLATVTLSQAGMHATYYHKASDQLQVGVDFQASTRMQDTSVSFRYQ
ParentalLDLPKANLLFKGSVDSNWIVGATLEKKLPPLPLTLALGAFLNHRKNKFQCGFGLTIG
LDLPKANLLFKGSVDSNWIVGATLEKKL..LPLTLALGAFLNHRKNKFQCG.GLTIG
RetrocopyLDLPKANLLFKGSVDSNWIVGATLEKKLQLLPLTLALGAFLNHRKNKFQCGSGLTIG

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 .12 RPM 23 .56 RPM
bodymap2_adrenal 0 .08 RPM 42 .52 RPM
bodymap2_brain 0 .07 RPM 22 .57 RPM
bodymap2_breast 0 .08 RPM 15 .64 RPM
bodymap2_colon 0 .00 RPM 19 .86 RPM
bodymap2_heart 0 .00 RPM 12 .96 RPM
bodymap2_kidney 0 .00 RPM 27 .28 RPM
bodymap2_liver 0 .00 RPM 28 .86 RPM
bodymap2_lung 0 .00 RPM 14 .01 RPM
bodymap2_lymph_node 0 .09 RPM 17 .31 RPM
bodymap2_ovary 0 .02 RPM 33 .00 RPM
bodymap2_prostate 0 .00 RPM 18 .20 RPM
bodymap2_skeletal_muscle 0 .02 RPM 34 .01 RPM
bodymap2_testis 0 .02 RPM 32 .16 RPM
bodymap2_thyroid 0 .02 RPM 28 .27 RPM
bodymap2_white_blood_cells 0 .00 RPM 10 .10 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1386 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1386 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1386 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1386 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1386 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 8 parental genes, and 13 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000130204 5 retrocopies
retro_hsap_1300, retro_hsap_1386 , retro_hsap_2321, retro_hsap_2537, retro_hsap_3159,
Microcebus murinus ENSMICG000000140411 retrocopy
retro_mmur_420,
Myotis lucifugus ENSMLUG000000289281 retrocopy
retro_mluc_697,
Nomascus leucogenys ENSNLEG000000017262 retrocopies
retro_nleu_2368, retro_nleu_2542,
Oryctolagus cuniculus ENSOCUG000000235821 retrocopy
retro_ocun_1143,
Pan troglodytes ENSPTRG000000111261 retrocopy
retro_ptro_39,
Ictidomys tridecemlineatus ENSSTOG000000090191 retrocopy
retro_itri_150,
Drosophila melanogaster FBgn00160411 retrocopy
retro_dmel_74,

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 = 0.26 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .26 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .13 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .02 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 .02 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .03 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 .00 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .04 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 .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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