RetrogeneDB ID:

retro_hsap_4798

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:27445837..27446348(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000235642
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PTP4A1
Ensembl ID:ENSG00000112245
Aliases:PTP4A1, HH72, PRL-1, PRL1, PTP(CAAX1), PTPCAAX1
Description:protein tyrosine phosphatase type IVA, member 1 [Source:HGNC Symbol;Acc:9634]


Retrocopy-Parental alignment summary:






>retro_hsap_4798
ATGGCTAGAATGAACCTCCCTGCTTCTGTGGACATTGCATACAAAAATGTGAGATTTCTTATTACACACAACCCAACCAA
TACCTACTTTAATAGATTCTTACAGGAACTTAAGCAGGATGGAGTTACCACCATAGTAAGAGTATGAAAAGCAACTTACA
ACATTGCTCTTTTAGAGAAGGGAAGCATCCAGGTTCCGGACTGGCCTTTTGATGATGGTACAGCACCATCCAGCCAGATA
ATTGATAACTGGTTAAAACTTATGAAAAATAAATTTCATGAAGATCCTGGTTGTTGTATTGCAATTCACTGTGTTGTAGG
TTTTGGGTGAGCTCCAGTTGCTAGTTGCCCTAGCTTTAATTGAAGGTGGAATGAAATATGAAAATGTAGTACAGTTCATC
AGATAAAAGTGACATGGAACTTTTAACAGCAAACAACTTTTGTATTTGGAGAAATATTGTCTTAAAATATGCTTGCACCT
CAGAAATCCCAGAAATAACTGTTTCCTTCAG

ORF - retro_hsap_4798 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.09 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMARMNRPAPVEVTYKNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATYDTTLVEKEGIHVLDWPF
MARMN.PA.V...YKN.RFLITHNPTN...N.F..ELK..GVTTIVRV..ATY...L.EK..I.V.DWPF
RetrocopyMARMNLPASVDIAYKNVRFLITHNPTNTYFNRFLQELKQDGVTTIVRV*KATYNIALLEKGSIQVPDWPF
ParentalDDGAPPSNQIVDDWLSLVKIKFREEPGCCIAVHCVAGLGRAPV-LVALALIEGGMKYEDAVQFIRQKRRG
DDG..PS.QI.D.WL.L.K.KF.E.PGCCIA.HCV.G.G.APV.LVALALIEGGMKYE..VQFIR.K..G
RetrocopyDDGTAPSSQIIDNWLKLMKNKFHEDPGCCIAIHCVVGFG*APV>LVALALIEGGMKYENVVQFIR*K*HG
ParentalAFNSKQLLYLEKYRPKMRLRFKDSNGHRNNCCIQ
.FNSKQLLYLEKY..K..L........RNNC..Q
RetrocopyTFNSKQLLYLEKYCLKICLHLRNP---RNNCFLQ

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 154 .47 RPM
bodymap2_adrenal 0 .00 RPM 89 .27 RPM
bodymap2_brain 0 .00 RPM 181 .05 RPM
bodymap2_breast 0 .00 RPM 173 .45 RPM
bodymap2_colon 0 .00 RPM 228 .41 RPM
bodymap2_heart 0 .00 RPM 79 .53 RPM
bodymap2_kidney 0 .00 RPM 185 .48 RPM
bodymap2_liver 0 .00 RPM 559 .50 RPM
bodymap2_lung 0 .00 RPM 237 .75 RPM
bodymap2_lymph_node 0 .00 RPM 95 .53 RPM
bodymap2_ovary 0 .00 RPM 290 .37 RPM
bodymap2_prostate 0 .00 RPM 448 .99 RPM
bodymap2_skeletal_muscle 0 .00 RPM 1088 .60 RPM
bodymap2_testis 0 .00 RPM 127 .47 RPM
bodymap2_thyroid 0 .00 RPM 234 .26 RPM
bodymap2_white_blood_cells 0 .00 RPM 140 .87 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4798 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4798 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4798 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4798 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4798 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3190
Gorilla gorilla retro_ggor_2986
Pongo abelii retro_pabe_3732
Sus scrofa retro_sscr_1186
Equus caballus retro_ecab_10
Parental genes homology:
Parental genes homology involve 27 parental genes, and 122 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000024383 retrocopies
retro_amel_1102, retro_amel_1344, retro_amel_1590,
Bos taurus ENSBTAG000000022753 retrocopies
retro_btau_1051, retro_btau_1186, retro_btau_859,
Canis familiaris ENSCAFG000000024903 retrocopies
retro_cfam_1832, retro_cfam_206, retro_cfam_593,
Callithrix jacchus ENSCJAG000000017433 retrocopies
retro_cjac_2812, retro_cjac_4144, retro_cjac_910,
Dipodomys ordii ENSDORG000000099606 retrocopies
retro_dord_148, retro_dord_244, retro_dord_355, retro_dord_375, retro_dord_696, retro_dord_92,
Erinaceus europaeus ENSEEUG000000064773 retrocopies
retro_eeur_227, retro_eeur_626, retro_eeur_687,
Echinops telfairi ENSETEG000000081836 retrocopies
retro_etel_1485, retro_etel_1681, retro_etel_1698, retro_etel_18, retro_etel_2153, retro_etel_668,
Felis catus ENSFCAG000000011993 retrocopies
retro_fcat_1439, retro_fcat_335, retro_fcat_969,
Homo sapiens ENSG00000112245 5 retrocopies
retro_hsap_2171, retro_hsap_3212, retro_hsap_479, retro_hsap_4798 , retro_hsap_807,
Homo sapiens ENSG000001840074 retrocopies
retro_hsap_1069, retro_hsap_1754, retro_hsap_4331, retro_hsap_944,
Gorilla gorilla ENSGGOG000000225217 retrocopies
retro_ggor_1723, retro_ggor_2180, retro_ggor_2251, retro_ggor_2986, retro_ggor_452, retro_ggor_662, retro_ggor_763,
Latimeria chalumnae ENSLACG000000071831 retrocopy
retro_lcha_90,
Loxodonta africana ENSLAFG000000065728 retrocopies
retro_lafr_1054, retro_lafr_1120, retro_lafr_1133, retro_lafr_328, retro_lafr_670, retro_lafr_7, retro_lafr_780, retro_lafr_939,
Myotis lucifugus ENSMLUG000000011621 retrocopy
retro_mluc_264,
Macaca mulatta ENSMMUG000000027771 retrocopy
retro_mmul_1720,
Monodelphis domestica ENSMODG000000187015 retrocopies
retro_mdom_1630, retro_mdom_1864, retro_mdom_363, retro_mdom_729, retro_mdom_927,
Mustela putorius furoENSMPUG000000031181 retrocopy
retro_mputfur_17,
Mus musculus ENSMUSG0000002606410 retrocopies
retro_mmus_1192, retro_mmus_1830, retro_mmus_1874, retro_mmus_1891, retro_mmus_2138, retro_mmus_2876, retro_mmus_2985, retro_mmus_3053, retro_mmus_3527, retro_mmus_575,
Nomascus leucogenys ENSNLEG000000004406 retrocopies
retro_nleu_1111, retro_nleu_1159, retro_nleu_1681, retro_nleu_169, retro_nleu_407, retro_nleu_893,
Oryctolagus cuniculus ENSOCUG000000063114 retrocopies
retro_ocun_225, retro_ocun_226, retro_ocun_24, retro_ocun_26,
Pongo abelii ENSPPYG000000167435 retrocopies
retro_pabe_2058, retro_pabe_255, retro_pabe_2660, retro_pabe_3732, retro_pabe_721,
Pan troglodytes ENSPTRG000000183144 retrocopies
retro_ptro_1657, retro_ptro_2239, retro_ptro_3190, retro_ptro_360,
Rattus norvegicus ENSRNOG000000117714 retrocopies
retro_rnor_1591, retro_rnor_2798, retro_rnor_494, retro_rnor_827,
Rattus norvegicus ENSRNOG000000463704 retrocopies
retro_rnor_2349, retro_rnor_2868, retro_rnor_612, retro_rnor_971,
Tupaia belangeri ENSTBEG0000000995614 retrocopies
retro_tbel_1216, retro_tbel_1392, retro_tbel_2167, retro_tbel_2236, retro_tbel_23, retro_tbel_2549, retro_tbel_2570, retro_tbel_2611, retro_tbel_3144, retro_tbel_3295, retro_tbel_3424, retro_tbel_4074, retro_tbel_4123, retro_tbel_869,
Tarsius syrichta ENSTSYG000000046322 retrocopies
retro_tsyr_1011, retro_tsyr_1152,
Tursiops truncatus ENSTTRG000000041296 retrocopies
retro_ttru_34, retro_ttru_450, retro_ttru_571, retro_ttru_642, retro_ttru_643, retro_ttru_69,

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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