RetrogeneDB ID:

retro_hsap_120

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:20852515..20853174(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000215520
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS4X
Ensembl ID:ENSG00000198034
Aliases:None
Description:ribosomal protein S4, X-linked [Source:HGNC Symbol;Acc:10424]


Retrocopy-Parental alignment summary:






>retro_hsap_120
AGCAGCTCAAAGCAATGGATGCTGGAGACACTGACTGGTGTGTCTGCTCCTCATCCATCCACCAGTCCCCACAAGCTGAG
AGTATGTCTCCTCCTCATCATTTTTCCTAAGAAACAGAATTAAGTATGCCCTGATCAGAGATGAACTAAAGATTTGGATG
CTGCGGCTCATTAAGATTGACGACAAGGTCCAAACTGATAGAACCTACCCTGCTGGATTCAAAGATGTCATCATCATTGA
CAAGACCAGAGAGAATGTCCGTCTGACCTGTAACATCAGGGTCACTTTGCCATTCACCGTATTACAGCTGAGGAGGCCAA
GTACAAATTGTGCAAAGTGAGAAAAATCTTGCGGCTACAAAAGGAATCCCTCATCTGGTAACCAATGATGCTGGCACCAT
CCGCTACCCTGGTCCCCTCATCAAGGTGAATGACATCATTCAGATTGATTTGGATACTGGCAAGAGTACCGATGTCATCA
AGTTTGATACTGGTAACCTGTGGATGGTGACTGGAGGTGCGAACCTGGGAAGAATTGGTGTGATTACCAACAGAGAGAGG
CACCCTGGATCTTTTGATGTGGTTCATGTGAAAGATGCCAACAGCAACAGCTTTGCCACCTGGCTTTCCAGCATTTTTGT
TATTGGCAAGGGCAACAAA

ORF - retro_hsap_120 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.23 %
Parental protein coverage: 84.03 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIF-LRNRLKYALTGDEVKKICMQRFIKIDGKVRTDIT
...K.WML..LTGV.AP.PST.PHKLR.CL.LIIF.LRNR.KYAL..DE.K.I.M.R.IKID.KV.TD.T
RetrocopySSSKQWMLETLTGVSAPHPSTSPHKLRVCLLLIIF>LRNRIKYALIRDELK-IWMLRLIKIDDKVQTDRT
ParentalYPAGFMDVISIDKTGENFRLIYDTK-GRFAVHRITPEEAKYKLCKVRKIF-VGTKGIPHLVTHDARTIRY
YPAGF.DVI.IDKT.EN.RL......G.FA.HRIT.EEAKYKLCKVRKI....TKGIPHLVT.DA.TIRY
RetrocopyYPAGFKDVIIIDKTRENVRLTCNIR<GHFAIHRITAEEAKYKLCKVRKIL<AATKGIPHLVTNDAGTIRY
ParentalPDPLIKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFA
P.PLIKVND.IQIDL.TGK.TD.IKFDTGNL.MVTGGANLGRIGVITNRERHPGSFDVVHVKDAN.NSFA
RetrocopyPGPLIKVNDIIQIDLDTGKSTDVIKFDTGNLWMVTGGANLGRIGVITNRERHPGSFDVVHVKDANSNSFA
ParentalTRLSNIFVIGKGNK
T.LS.IFVIGKGNK
RetrocopyTWLSSIFVIGKGNK

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 1077 .78 RPM
bodymap2_adrenal 0 .00 RPM 994 .39 RPM
bodymap2_brain 0 .00 RPM 249 .47 RPM
bodymap2_breast 0 .00 RPM 912 .87 RPM
bodymap2_colon 0 .00 RPM 1472 .93 RPM
bodymap2_heart 0 .00 RPM 215 .90 RPM
bodymap2_kidney 0 .00 RPM 575 .10 RPM
bodymap2_liver 0 .00 RPM 226 .26 RPM
bodymap2_lung 0 .00 RPM 826 .90 RPM
bodymap2_lymph_node 0 .00 RPM 1412 .13 RPM
bodymap2_ovary 0 .02 RPM 2009 .69 RPM
bodymap2_prostate 0 .00 RPM 1321 .94 RPM
bodymap2_skeletal_muscle 0 .00 RPM 719 .78 RPM
bodymap2_testis 0 .02 RPM 641 .02 RPM
bodymap2_thyroid 0 .00 RPM 887 .86 RPM
bodymap2_white_blood_cells 0 .00 RPM 1229 .94 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_120 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_120 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_120 retrocopy 5' end.

Lab - click to see more details

retro_hsap_120 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_120 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_131
Gorilla gorilla retro_ggor_223
Pongo abelii retro_pabe_493
Parental genes homology:
Parental genes homology involve 22 parental genes, and 210 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000146011 retrocopy
retro_acar_82,
Bos taurus ENSBTAG000000188005 retrocopies
retro_btau_119, retro_btau_125, retro_btau_146, retro_btau_33, retro_btau_76,
Canis familiaris ENSCAFG000000171512 retrocopies
retro_cfam_165, retro_cfam_194,
Callithrix jacchus ENSCJAG000000041922 retrocopies
retro_cjac_19, retro_cjac_361,
Cavia porcellus ENSCPOG000000063373 retrocopies
retro_cpor_1023, retro_cpor_1075, retro_cpor_31,
Equus caballus ENSECAG000000108526 retrocopies
retro_ecab_34, retro_ecab_435, retro_ecab_443, retro_ecab_614, retro_ecab_757, retro_ecab_850,
Homo sapiens ENSG000001298241 retrocopy
retro_hsap_1704,
Homo sapiens ENSG00000198034 19 retrocopies
retro_hsap_1070, retro_hsap_1151, retro_hsap_120 , retro_hsap_1204, retro_hsap_1792, retro_hsap_1868, retro_hsap_2026, retro_hsap_2051, retro_hsap_2052, retro_hsap_2270, retro_hsap_2437, retro_hsap_2443, retro_hsap_3162, retro_hsap_3423, retro_hsap_3519, retro_hsap_3986, retro_hsap_4051, retro_hsap_656, retro_hsap_875,
Macropus eugenii ENSMEUG0000000796916 retrocopies
retro_meug_131, retro_meug_141, retro_meug_1644, retro_meug_1732, retro_meug_1814, retro_meug_194, retro_meug_2098, retro_meug_2121, retro_meug_228, retro_meug_562, retro_meug_628, retro_meug_673, retro_meug_843, retro_meug_872, retro_meug_972, retro_meug_999,
Meleagris gallopavo ENSMGAG000000096711 retrocopy
retro_mgal_3,
Microcebus murinus ENSMICG0000001660658 retrocopies
retro_mmur_1107, retro_mmur_1108, retro_mmur_1123, retro_mmur_1136, retro_mmur_1168, retro_mmur_1208, retro_mmur_1209, retro_mmur_1229, retro_mmur_1231, retro_mmur_1257, retro_mmur_1268, retro_mmur_1334, retro_mmur_1411, retro_mmur_1416, retro_mmur_1430, retro_mmur_1442, retro_mmur_1454, retro_mmur_1467, retro_mmur_1471, retro_mmur_1519, retro_mmur_1578, retro_mmur_1584, retro_mmur_1599, retro_mmur_1600, retro_mmur_1611, retro_mmur_166, retro_mmur_241, retro_mmur_281, retro_mmur_289, retro_mmur_293, retro_mmur_347, retro_mmur_363, retro_mmur_390, retro_mmur_510, retro_mmur_511, retro_mmur_521, retro_mmur_523, retro_mmur_530, retro_mmur_54, retro_mmur_551, retro_mmur_591, retro_mmur_609, retro_mmur_619, retro_mmur_663, retro_mmur_665, retro_mmur_687, retro_mmur_767, retro_mmur_784, retro_mmur_828, retro_mmur_840, retro_mmur_917, retro_mmur_918, retro_mmur_931, retro_mmur_943, retro_mmur_946, retro_mmur_949, retro_mmur_96, retro_mmur_995,
Monodelphis domestica ENSMODG000000110701 retrocopy
retro_mdom_238,
Mustela putorius furoENSMPUG0000000529411 retrocopies
retro_mputfur_1044, retro_mputfur_1176, retro_mputfur_1325, retro_mputfur_1326, retro_mputfur_1393, retro_mputfur_160, retro_mputfur_205, retro_mputfur_48, retro_mputfur_725, retro_mputfur_876, retro_mputfur_988,
Mus musculus ENSMUSG0000003132013 retrocopies
retro_mmus_1092, retro_mmus_1686, retro_mmus_2052, retro_mmus_2197, retro_mmus_2487, retro_mmus_2541, retro_mmus_2916, retro_mmus_3025, retro_mmus_3702, retro_mmus_499, retro_mmus_797, retro_mmus_92, retro_mmus_987,
Nomascus leucogenys ENSNLEG0000001812125 retrocopies
retro_nleu_1127, retro_nleu_1226, retro_nleu_1361, retro_nleu_142, retro_nleu_1442, retro_nleu_1907, retro_nleu_1908, retro_nleu_2089, retro_nleu_2256, retro_nleu_244, retro_nleu_2461, retro_nleu_2495, retro_nleu_2587, retro_nleu_2613, retro_nleu_2640, retro_nleu_2646, retro_nleu_2776, retro_nleu_2801, retro_nleu_2932, retro_nleu_2967, retro_nleu_2968, retro_nleu_486, retro_nleu_500, retro_nleu_560, retro_nleu_947,
Otolemur garnettii ENSOGAG000000118082 retrocopies
retro_ogar_121, retro_ogar_229,
Pongo abelii ENSPPYG0000002046224 retrocopies
retro_pabe_1005, retro_pabe_1401, retro_pabe_1472, retro_pabe_1524, retro_pabe_1586, retro_pabe_1657, retro_pabe_1673, retro_pabe_1702, retro_pabe_1784, retro_pabe_1948, retro_pabe_2455, retro_pabe_2629, retro_pabe_2836, retro_pabe_2923, retro_pabe_3275, retro_pabe_3325, retro_pabe_340, retro_pabe_493, retro_pabe_579, retro_pabe_580, retro_pabe_679, retro_pabe_891, retro_pabe_921, retro_pabe_954,
Pan troglodytes ENSPTRG000000220259 retrocopies
retro_ptro_1280, retro_ptro_131, retro_ptro_1366, retro_ptro_1367, retro_ptro_1408, retro_ptro_2276, retro_ptro_3032, retro_ptro_728, retro_ptro_784,
Pan troglodytes ENSPTRG000000224701 retrocopy
retro_ptro_1153,
Rattus norvegicus ENSRNOG000000032011 retrocopy
retro_rnor_135,
Sus scrofa ENSSSCG000000124055 retrocopies
retro_sscr_1070, retro_sscr_563, retro_sscr_580, retro_sscr_665, retro_sscr_973,
Vicugna pacos ENSVPAG000000109524 retrocopies
retro_vpac_244, retro_vpac_460, retro_vpac_604, retro_vpac_653,

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 = 0.04 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 .04 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).



Copyright © RetrogeneDB 2014-2017