RetrogeneDB ID:

retro_hsap_1827

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:17:33841954..33842205(-)
Located in intron of:ENSG00000205045
Retrocopy
information
Ensembl ID:ENSG00000255987
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TOMM20
Ensembl ID:ENSG00000173726
Aliases:TOMM20, MAS20, MOM19, TOM20
Description:translocase of outer mitochondrial membrane 20 homolog (yeast) [Source:HGNC Symbol;Acc:20947]


Retrocopy-Parental alignment summary:






>retro_hsap_1827
CTGGGTCGGAACGGAGCCATCGCCGCTGGAGTATTCGGGGCCCTTTTCATCGGGTACTGCATCTACTTCGACCGCAAAAG
ACTGAAGTGACCCCAACTTAAAGAATAGGCGTCCAGAATAAAGAAAGAAACAGAAGCTGGCCGAGGAGTGAGTTGAGCTT
TCCAAGTTAGCTGACCTTAAAGATGCTGAAGCTGTCCAGAAATTCTTCCTGGAAGAGATATAGCTTTGGTGAAGAGATCC
TAGCTAAAGGT

ORF - retro_hsap_1827 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.65 %
Parental protein coverage: 57.24 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVGRNSAIAAGVCGALFIGYCIYFDRKRR-SDPNFKNRLRERRKKQKLAKERAGLSKLPDLKDAEAVQKFF
.GRN.AIAAGV.GALFIGYCIYFDRKR..SDPN.KNR..E.RKKQKLA.E...LSKL.DLKDAEAVQKFF
RetrocopyLGRNGAIAAGVFGALFIGYCIYFDRKRL>SDPNLKNRRPE*RKKQKLAEE*VELSKLADLKDAEAVQKFF
ParentalLEEI-QLGEELLAQG
LEEI...GEE.LA.G
RetrocopyLEEI>SFGEEILAKG

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 197 .17 RPM
bodymap2_adrenal 0 .90 RPM 189 .40 RPM
bodymap2_brain 0 .00 RPM 608 .93 RPM
bodymap2_breast 0 .33 RPM 272 .90 RPM
bodymap2_colon 0 .04 RPM 283 .81 RPM
bodymap2_heart 0 .18 RPM 158 .84 RPM
bodymap2_kidney 0 .15 RPM 167 .22 RPM
bodymap2_liver 0 .02 RPM 76 .17 RPM
bodymap2_lung 0 .33 RPM 188 .06 RPM
bodymap2_lymph_node 1 .53 RPM 115 .98 RPM
bodymap2_ovary 0 .17 RPM 273 .58 RPM
bodymap2_prostate 0 .00 RPM 295 .39 RPM
bodymap2_skeletal_muscle 0 .00 RPM 137 .92 RPM
bodymap2_testis 0 .15 RPM 186 .00 RPM
bodymap2_thyroid 0 .09 RPM 319 .83 RPM
bodymap2_white_blood_cells 2 .01 RPM 167 .21 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1827 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1827 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1827 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1827 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1827 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1166
Macaca mulatta retro_mmul_1255
Parental genes homology:
Parental genes homology involve 18 parental genes, and 97 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000005625 retrocopies
retro_btau_1025, retro_btau_1147, retro_btau_1357, retro_btau_492, retro_btau_533,
Choloepus hoffmanni ENSCHOG000000023837 retrocopies
retro_chof_1381, retro_chof_1699, retro_chof_2252, retro_chof_2497, retro_chof_2511, retro_chof_415, retro_chof_901,
Callithrix jacchus ENSCJAG000000181273 retrocopies
retro_cjac_1860, retro_cjac_2420, retro_cjac_918,
Echinops telfairi ENSETEG000000176934 retrocopies
retro_etel_1224, retro_etel_130, retro_etel_1514, retro_etel_559,
Homo sapiens ENSG00000173726 5 retrocopies
retro_hsap_1827 , retro_hsap_1906, retro_hsap_3866, retro_hsap_4702, retro_hsap_796,
Gorilla gorilla ENSGGOG000000251845 retrocopies
retro_ggor_1395, retro_ggor_2166, retro_ggor_2606, retro_ggor_2923, retro_ggor_656,
Loxodonta africana ENSLAFG000000154991 retrocopy
retro_lafr_436,
Myotis lucifugus ENSMLUG000000162181 retrocopy
retro_mluc_644,
Macaca mulatta ENSMMUG000000071362 retrocopies
retro_mmul_1255, retro_mmul_273,
Monodelphis domestica ENSMODG000000084526 retrocopies
retro_mdom_1112, retro_mdom_1172, retro_mdom_1297, retro_mdom_1527, retro_mdom_1568, retro_mdom_838,
Mus musculus ENSMUSG0000009390412 retrocopies
retro_mmus_1437, retro_mmus_1669, retro_mmus_1698, retro_mmus_1990, retro_mmus_2026, retro_mmus_2141, retro_mmus_3142, retro_mmus_3311, retro_mmus_3637, retro_mmus_3655, retro_mmus_457, retro_mmus_935,
Pongo abelii ENSPPYG000000000994 retrocopies
retro_pabe_1497, retro_pabe_1553, retro_pabe_3650, retro_pabe_708,
Pan troglodytes ENSPTRG000000021275 retrocopies
retro_ptro_1166, retro_ptro_1252, retro_ptro_2634, retro_ptro_3124, retro_ptro_554,
Rattus norvegicus ENSRNOG000000199804 retrocopies
retro_rnor_1191, retro_rnor_1958, retro_rnor_1983, retro_rnor_2103,
Sarcophilus harrisii ENSSHAG000000158763 retrocopies
retro_shar_272, retro_shar_512, retro_shar_669,
Ictidomys tridecemlineatus ENSSTOG000000275643 retrocopies
retro_itri_248, retro_itri_71, retro_itri_820,
Tupaia belangeri ENSTBEG0000000382726 retrocopies
retro_tbel_1483, retro_tbel_2215, retro_tbel_2239, retro_tbel_2240, retro_tbel_2340, retro_tbel_2348, retro_tbel_2440, retro_tbel_2472, retro_tbel_2548, retro_tbel_2610, retro_tbel_2619, retro_tbel_3000, retro_tbel_3182, retro_tbel_3204, retro_tbel_3674, retro_tbel_3687, retro_tbel_3729, retro_tbel_3808, retro_tbel_3895, retro_tbel_3949, retro_tbel_4068, retro_tbel_4096, retro_tbel_4136, retro_tbel_4596, retro_tbel_4625, retro_tbel_600,
Vicugna pacos ENSVPAG000000039801 retrocopy
retro_vpac_252,

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 = 3.1 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .60 RPM
CEU_NA11843 0 .17 RPM
CEU_NA11930 0 .98 RPM
CEU_NA12004 0 .68 RPM
CEU_NA12400 0 .95 RPM
CEU_NA12751 1 .00 RPM
CEU_NA12760 1 .17 RPM
CEU_NA12827 0 .66 RPM
CEU_NA12872 0 .41 RPM
CEU_NA12873 1 .12 RPM
FIN_HG00183 1 .10 RPM
FIN_HG00277 1 .07 RPM
FIN_HG00315 0 .28 RPM
FIN_HG00321 1 .30 RPM
FIN_HG00328 0 .69 RPM
FIN_HG00338 0 .34 RPM
FIN_HG00349 1 .00 RPM
FIN_HG00375 0 .86 RPM
FIN_HG00377 0 .98 RPM
FIN_HG00378 1 .23 RPM
GBR_HG00099 2 .18 RPM
GBR_HG00111 0 .49 RPM
GBR_HG00114 1 .37 RPM
GBR_HG00119 1 .20 RPM
GBR_HG00131 1 .21 RPM
GBR_HG00133 0 .92 RPM
GBR_HG00134 1 .94 RPM
GBR_HG00137 0 .99 RPM
GBR_HG00142 0 .50 RPM
GBR_HG00143 1 .15 RPM
TSI_NA20512 1 .58 RPM
TSI_NA20513 1 .72 RPM
TSI_NA20518 0 .64 RPM
TSI_NA20532 0 .78 RPM
TSI_NA20538 1 .80 RPM
TSI_NA20756 1 .45 RPM
TSI_NA20765 1 .45 RPM
TSI_NA20771 1 .11 RPM
TSI_NA20786 0 .76 RPM
TSI_NA20798 1 .59 RPM
YRI_NA18870 2 .67 RPM
YRI_NA18907 0 .76 RPM
YRI_NA18916 0 .27 RPM
YRI_NA19093 1 .85 RPM
YRI_NA19099 1 .78 RPM
YRI_NA19114 1 .31 RPM
YRI_NA19118 1 .76 RPM
YRI_NA19213 2 .51 RPM
YRI_NA19214 3 .10 RPM
YRI_NA19223 2 .47 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).





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