RetrogeneDB ID:

retro_hsap_128

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:27503241..27503765(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000229985
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL18A
Ensembl ID:ENSG00000105640
Aliases:RPL18A, L18A
Description:ribosomal protein L18a [Source:HGNC Symbol;Acc:10311]


Retrocopy-Parental alignment summary:






>retro_hsap_128
AAGGCCTTGGGCACACTATGAGAGTACAAGGTGGTGGGTCGCTGCCTGCCCACCCCCAAATGCCACACACCGCCCCTCTA
CCGCATGGGAATCTTTGCGCCTAATCATGTCGTCGCCGAGTCCCGCTTCTGGTACTTCGTATCTCAGTTAAAGAAGATGA
AGAAGTTTTCAGGGGAGATTGTCTACTGTGGGCCGGTGTTTGAGAAGTTCCCCTGGGGGTGAAGAACTTCGGCATCTGGC
TGCACTATGACTCCCGGAGCGGCATCCACAACATGTACTGAGAATACTGGGACCTGAACACCGCGGGCGCTGTCACCCAG
TGCTACCGAGACATGGGCGCCCGGCACCGCGCCTGGACCCATTCCATCCAGATCACGAAGGTGGAGGCGATCGCAGCCAG
CAAGTGCCCGCGGCCGGCCGTCAAGCAGTTCCACGACTCCAAGATCAAGTTTCCGCTACCCCACCGGGTCCTGCGCTGTC
AGCACAAGCCACACTTCACCACCCGGAGACCCAACACCTTCTTC

ORF - retro_hsap_128 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.5 %
Parental protein coverage: 99.43 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalKASGTLREYKVVGRCLPTPKCHTPPLYRMRIFAPNHVVAKSRFWYFVSQLKKMKKSSGEIVYCGQVFEKS
KA.GTL.EYKVVGRCLPTPKCHTPPLYRM.IFAPNHVVA.SRFWYFVSQLKKMKK.SGEIVYCG.VFEK.
RetrocopyKALGTL*EYKVVGRCLPTPKCHTPPLYRMGIFAPNHVVAESRFWYFVSQLKKMKKFSGEIVYCGPVFEKF
ParentalP-LRVKNFGIWLRYDSRSGTHNMYREYRDLTTAGAVTQCYRDMGARHRARAHSIQIMKVEEIAASKCRRP
P.L.VKNFGIWL.YDSRSG.HNMY.EY.DL.TAGAVTQCYRDMGARHRA..HSIQI.KVE.IAASKC.RP
RetrocopyP<LGVKNFGIWLHYDSRSGIHNMY*EYWDLNTAGAVTQCYRDMGARHRAWTHSIQITKVEAIAASKCPRP
ParentalAVKQFHDSKIKFPLPHRVLRRQHKPRFTTKRPNTFF
AVKQFHDSKIKFPLPHRVLR.QHKP.FTT.RPNTFF
RetrocopyAVKQFHDSKIKFPLPHRVLRCQHKPHFTTRRPNTFF

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 326 .50 RPM
bodymap2_adrenal 0 .00 RPM 199 .33 RPM
bodymap2_brain 0 .00 RPM 47 .79 RPM
bodymap2_breast 0 .00 RPM 170 .88 RPM
bodymap2_colon 0 .00 RPM 309 .01 RPM
bodymap2_heart 0 .00 RPM 49 .01 RPM
bodymap2_kidney 0 .00 RPM 71 .33 RPM
bodymap2_liver 0 .00 RPM 66 .31 RPM
bodymap2_lung 0 .00 RPM 224 .42 RPM
bodymap2_lymph_node 0 .00 RPM 309 .26 RPM
bodymap2_ovary 0 .00 RPM 335 .13 RPM
bodymap2_prostate 0 .00 RPM 267 .99 RPM
bodymap2_skeletal_muscle 0 .00 RPM 173 .98 RPM
bodymap2_testis 0 .00 RPM 150 .67 RPM
bodymap2_thyroid 0 .00 RPM 178 .37 RPM
bodymap2_white_blood_cells 0 .00 RPM 300 .59 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_128 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_128 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_128 retrocopy 5' end.

Lab - click to see more details

retro_hsap_128 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_128 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Macaca mulatta retro_mmul_364
Parental genes homology:
Parental genes homology involve 21 parental genes, and 95 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000031251 retrocopy
retro_acar_86,
Bos taurus ENSBTAG000000158315 retrocopies
retro_btau_145, retro_btau_1586, retro_btau_842, retro_btau_917, retro_btau_922,
Canis familiaris ENSCAFG000000151221 retrocopy
retro_cfam_231,
Callithrix jacchus ENSCJAG000000140067 retrocopies
retro_cjac_1628, retro_cjac_2814, retro_cjac_3192, retro_cjac_3906, retro_cjac_4134, retro_cjac_441, retro_cjac_642,
Cavia porcellus ENSCPOG000000152051 retrocopy
retro_cpor_1478,
Equus caballus ENSECAG000000152581 retrocopy
retro_ecab_745,
Homo sapiens ENSG00000105640 11 retrocopies
retro_hsap_1053, retro_hsap_128 , retro_hsap_135, retro_hsap_1610, retro_hsap_1961, retro_hsap_2254, retro_hsap_2676, retro_hsap_2776, retro_hsap_4129, retro_hsap_4734, retro_hsap_4776,
Gorilla gorilla ENSGGOG000000028708 retrocopies
retro_ggor_1215, retro_ggor_1680, retro_ggor_1868, retro_ggor_1933, retro_ggor_195, retro_ggor_227, retro_ggor_2775, retro_ggor_2940,
Macropus eugenii ENSMEUG000000032282 retrocopies
retro_meug_36, retro_meug_49,
Myotis lucifugus ENSMLUG000000067014 retrocopies
retro_mluc_1671, retro_mluc_1893, retro_mluc_1978, retro_mluc_2191,
Macaca mulatta ENSMMUG000000288446 retrocopies
retro_mmul_1416, retro_mmul_1591, retro_mmul_2233, retro_mmul_2547, retro_mmul_292, retro_mmul_364,
Monodelphis domestica ENSMODG000000191672 retrocopies
retro_mdom_349, retro_mdom_680,
Mustela putorius furoENSMPUG000000157864 retrocopies
retro_mputfur_1007, retro_mputfur_1189, retro_mputfur_1574, retro_mputfur_457,
Mus musculus ENSMUSG000000451288 retrocopies
retro_mmus_1606, retro_mmus_260, retro_mmus_2910, retro_mmus_2924, retro_mmus_326, retro_mmus_346, retro_mmus_937, retro_mmus_951,
Nomascus leucogenys ENSNLEG000000058897 retrocopies
retro_nleu_1087, retro_nleu_1180, retro_nleu_1940, retro_nleu_2261, retro_nleu_2605, retro_nleu_2672, retro_nleu_680,
Otolemur garnettii ENSOGAG000000318284 retrocopies
retro_ogar_1016, retro_ogar_1891, retro_ogar_2226, retro_ogar_2564,
Pongo abelii ENSPPYG0000000972510 retrocopies
retro_pabe_1200, retro_pabe_1319, retro_pabe_1620, retro_pabe_2239, retro_pabe_2302, retro_pabe_3680, retro_pabe_3717, retro_pabe_3802, retro_pabe_482, retro_pabe_487,
Pan troglodytes ENSPTRG000000106863 retrocopies
retro_ptro_1078, retro_ptro_1803, retro_ptro_27,
Rattus norvegicus ENSRNOG000000187956 retrocopies
retro_rnor_108, retro_rnor_1655, retro_rnor_2279, retro_rnor_2362, retro_rnor_2821, retro_rnor_888,
Sarcophilus harrisii ENSSHAG000000004063 retrocopies
retro_shar_435, retro_shar_474, retro_shar_706,
Ictidomys tridecemlineatus ENSSTOG000000077881 retrocopy
retro_itri_694,

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:

The presence of retro_hsap_128 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_128 presence in various populations. Based on Kabza et al. 2015 (PubMed).


# Indel coordinates AFR, African AMR, Ad Mixed American EUR, European EAS, East Asian
ASW YRI LWK MXL PUR CLM CEU IBS GBR FIN TSI JPT CHB CHS
1. 1:27502051..27515700 100 100 100 99.24 100 100 100 100 100 100 100 100 100 100

Indel #1, located at the genomic coordinates 1:27502051..27515700.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 99.24 % Puerto Ricansfrom Puerto Rico PUR 100 % Colombians fromMedellin, Colombia CLM 100 % Americans of AfricanAncestry in SW USA ASW 100 % Yoruba in Ibadan,Nigeria YRI 100 % Luhya in Webuye,Kenya LWK 100 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 100 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 100 % Finnish in Finland FIN 100 % Toscani in Italia TSI 100 % Han Chinese in Bejing,China CHB 100 % Japanese in Tokyo,Japan 100 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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