RetrogeneDB ID:

retro_hsap_2875

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:162204395..162204737(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000241874
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TOMM22
Ensembl ID:ENSG00000100216
Aliases:TOMM22, 1C9-2, MST065, MSTP065, TOM22
Description:translocase of outer mitochondrial membrane 22 homolog (yeast) [Source:HGNC Symbol;Acc:18002]


Retrocopy-Parental alignment summary:






>retro_hsap_2875
ATGGCTGCTGCTGTCACTGCTACTTTTGCTGTGGAACCCCTGTCCCCAAACTAATTGCTCCCGAAAAGCAATGTGCAGAA
GACTAAGTAGGAGCTGGAAGAGAATGATGAGGAGAAGCTAGATGAAAGCATGCCGAAGAGACCATGGGGCCTAACCAAGA
TATTTGCATATAGGGTCCAGTCTGCAGCCACAGCCACTTTTGATATCTCCCTTCTTATGGCTCAAAACATGCACAGGTTT
TCCAGGTCATCCTTGTGGACTGGGGTTACTTCCAATATAATCCTCGTTTTTCATGTTGTCTTTGAGGCTGAGAAGTTACA
AATGGAGCAACAGCAGATACTT

ORF - retro_hsap_2875 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.28 %
Parental protein coverage: 80.28 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAAAVAAAGAGEPQSPDELLPKGDAEKPEEELEEDDDEELDETLSERLWGLTEMFPERVRSAAGATFDLS
MAAAV.A..A.EP.SP..LLPK....K...ELEE.D.E.LDE....R.WGLT..F..RV.SAA.ATFD.S
RetrocopyMAAAVTATFAVEPLSPN*LLPKSNVQKTK*ELEENDEEKLDESMPKRPWGLTKIFAYRVQSAATATFDIS
ParentalLFVAQKMYRFSRAALWIGTTSFMILVLPVVFETEKLQMEQQQQL
L..AQ.M.RFSR..LW.G.TS..ILV..VVFE.EKLQMEQQQ.L
RetrocopyLLMAQNMHRFSRSSLWTGVTSNIILVFHVVFEAEKLQMEQQQIL

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 28 .25 RPM
bodymap2_adrenal 0 .00 RPM 36 .85 RPM
bodymap2_brain 0 .00 RPM 21 .80 RPM
bodymap2_breast 0 .00 RPM 31 .40 RPM
bodymap2_colon 0 .00 RPM 30 .34 RPM
bodymap2_heart 0 .00 RPM 30 .77 RPM
bodymap2_kidney 0 .00 RPM 34 .60 RPM
bodymap2_liver 0 .00 RPM 35 .34 RPM
bodymap2_lung 0 .00 RPM 30 .12 RPM
bodymap2_lymph_node 0 .00 RPM 39 .42 RPM
bodymap2_ovary 0 .00 RPM 31 .77 RPM
bodymap2_prostate 0 .00 RPM 59 .67 RPM
bodymap2_skeletal_muscle 0 .00 RPM 38 .39 RPM
bodymap2_testis 0 .00 RPM 43 .36 RPM
bodymap2_thyroid 0 .00 RPM 28 .23 RPM
bodymap2_white_blood_cells 0 .00 RPM 53 .55 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2875 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2875 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2875 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2875 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2875 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Macaca mulatta retro_mmul_1459
Parental genes homology:
Parental genes homology involve 23 parental genes, and 85 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000106923 retrocopies
retro_amel_542, retro_amel_58, retro_amel_867,
Canis familiaris ENSCAFG000000013832 retrocopies
retro_cfam_1817, retro_cfam_197,
Callithrix jacchus ENSCJAG000000117315 retrocopies
retro_cjac_1220, retro_cjac_1230, retro_cjac_3675, retro_cjac_498, retro_cjac_94,
Cavia porcellus ENSCPOG000000059631 retrocopy
retro_cpor_754,
Equus caballus ENSECAG000000103591 retrocopy
retro_ecab_334,
Erinaceus europaeus ENSEEUG000000064281 retrocopy
retro_eeur_29,
Echinops telfairi ENSETEG000000005447 retrocopies
retro_etel_123, retro_etel_1477, retro_etel_154, retro_etel_1753, retro_etel_190, retro_etel_2025, retro_etel_599,
Homo sapiens ENSG00000100216 6 retrocopies
retro_hsap_1249, retro_hsap_2875 , retro_hsap_3003, retro_hsap_4928, retro_hsap_633, retro_hsap_907,
Gorilla gorilla ENSGGOG000000132304 retrocopies
retro_ggor_3084, retro_ggor_554, retro_ggor_734, retro_ggor_980,
Macropus eugenii ENSMEUG000000029011 retrocopy
retro_meug_855,
Microcebus murinus ENSMICG000000117923 retrocopies
retro_mmur_1549, retro_mmur_408, retro_mmur_892,
Myotis lucifugus ENSMLUG000000037612 retrocopies
retro_mluc_2116, retro_mluc_543,
Macaca mulatta ENSMMUG000000003648 retrocopies
retro_mmul_1020, retro_mmul_1113, retro_mmul_1459, retro_mmul_241, retro_mmul_2426, retro_mmul_2438, retro_mmul_2532, retro_mmul_498,
Mustela putorius furoENSMPUG000000131562 retrocopies
retro_mputfur_1038, retro_mputfur_1254,
Mus musculus ENSMUSG000000224272 retrocopies
retro_mmus_1884, retro_mmus_2496,
Nomascus leucogenys ENSNLEG000000151596 retrocopies
retro_nleu_2116, retro_nleu_2142, retro_nleu_2249, retro_nleu_375, retro_nleu_454, retro_nleu_617,
Otolemur garnettii ENSOGAG000000295839 retrocopies
retro_ogar_1153, retro_ogar_1294, retro_ogar_1905, retro_ogar_2022, retro_ogar_2067, retro_ogar_214, retro_ogar_3111, retro_ogar_3328, retro_ogar_792,
Pongo abelii ENSPPYG000000118256 retrocopies
retro_pabe_1041, retro_pabe_1088, retro_pabe_1968, retro_pabe_2489, retro_pabe_563, retro_pabe_782,
Pan troglodytes ENSPTRG000000143746 retrocopies
retro_ptro_1583, retro_ptro_2031, retro_ptro_2117, retro_ptro_461, retro_ptro_627, retro_ptro_860,
Rattus norvegicus ENSRNOG000000140584 retrocopies
retro_rnor_1323, retro_rnor_2280, retro_rnor_548, retro_rnor_549,
Sus scrofa ENSSSCG000000000971 retrocopy
retro_sscr_310,
Tupaia belangeri ENSTBEG000000156834 retrocopies
retro_tbel_1810, retro_tbel_2901, retro_tbel_2922, retro_tbel_3041,
Vicugna pacos ENSVPAG000000014851 retrocopy
retro_vpac_586,

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 ) 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 .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 .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 .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 .00 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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