RetrogeneDB ID:

retro_hsap_4013

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:144077326..144077899(+)
Located in intron of:ENSG00000247317
Retrocopy
information
Ensembl ID:ENSG00000253971
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CDC42
Ensembl ID:ENSG00000070831
Aliases:CDC42, CDC42Hs, G25K
Description:cell division cycle 42 [Source:HGNC Symbol;Acc:1736]


Retrocopy-Parental alignment summary:






>retro_hsap_4013
ATGCAGACAATTAAGTGTGTTTTTGTGGGCAATGGTGCTGTTGGTAAAACATGTCTCCTGATATCCTACACAACAAACAA
ATTTCCATCAAAATATGTACCAACTGTTTTTGACAACTATGCAGTCACTGTTATGATTGGTGGAGAAACATATACTCTTG
GACTTTTTGATACTGCAGGGCAAGACGATGATGACAGATTATGACCGCTGAGTTATCTACAAACAGATGTATTTCCAGTC
TGTTTTTCAGTGGTCTCTCCATCTTCATTTGAAAATGTGAAAGGAAAGTGGGTGTCTAAGATAACTCACCACTGTCCAAA
GACTCATTTCTTGCTTGTTGGGACCCTAATTCATCTCAGAGATGACCCCTCTACTATTGAGAAACTTGCCAAGAACAAAC
AGAAGCCCACCACTCCAGAGACTGCTGAAAAGCTGATCCGTGACCTGAAGGCTGTCAGGTATGTGGTGTGTTCTGCACTC
ACACAGAAAGGCCTAAGGAATGTATTTGATGAAGCAATATTGGCTTCCCTGGAGCCTCCAGAACTGAAGAAGAGCCACAG
GTGTGTGCTGCTA

ORF - retro_hsap_4013 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.96 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMQTIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAGQEDYDRLRPL
MQTIKCV.VG.GAVGKTCLLISYTTNKFPS.YVPTVFDNYAVTVMIGGE.YTLGLFDTAGQ.D.DRL.PL
RetrocopyMQTIKCVFVGNGAVGKTCLLISYTTNKFPSKYVPTVFDNYAVTVMIGGETYTLGLFDTAGQDDDDRL*PL
ParentalSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLRDDPSTIEKLAKNKQKPITPE
SY.QTDVF.VCFSVVSPSSFENVK.KWV..ITHHCPKT.FLLVGT.I.LRDDPSTIEKLAKNKQKP.TPE
RetrocopySYLQTDVFPVCFSVVSPSSFENVKGKWVSKITHHCPKTHFLLVGTLIHLRDDPSTIEKLAKNKQKPTTPE
ParentalTAEKLARDLKAVKYVECSALTQKGLKNVFDEAILAALEPPEPKKSRRCVLL
TAEKL.RDLKAV.YV.CSALTQKGL.NVFDEAILA.LEPPE.KKS.RCVLL
RetrocopyTAEKLIRDLKAVRYVVCSALTQKGLRNVFDEAILASLEPPELKKSHRCVLL

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 397 .02 RPM
bodymap2_adrenal 0 .00 RPM 299 .65 RPM
bodymap2_brain 0 .02 RPM 209 .16 RPM
bodymap2_breast 0 .00 RPM 331 .19 RPM
bodymap2_colon 0 .00 RPM 227 .18 RPM
bodymap2_heart 0 .00 RPM 123 .43 RPM
bodymap2_kidney 0 .12 RPM 207 .82 RPM
bodymap2_liver 0 .00 RPM 90 .92 RPM
bodymap2_lung 0 .00 RPM 331 .80 RPM
bodymap2_lymph_node 0 .00 RPM 187 .27 RPM
bodymap2_ovary 0 .15 RPM 321 .54 RPM
bodymap2_prostate 0 .00 RPM 218 .41 RPM
bodymap2_skeletal_muscle 0 .00 RPM 105 .94 RPM
bodymap2_testis 0 .00 RPM 229 .71 RPM
bodymap2_thyroid 0 .00 RPM 229 .89 RPM
bodymap2_white_blood_cells 0 .00 RPM 576 .79 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4013 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4013 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4013 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4013 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4013 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 16 parental genes, and 60 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000147075 retrocopies
retro_cfam_1587, retro_cfam_1970, retro_cfam_2189, retro_cfam_88, retro_cfam_89,
Choloepus hoffmanni ENSCHOG0000000530610 retrocopies
retro_chof_103, retro_chof_1044, retro_chof_1195, retro_chof_1853, retro_chof_2055, retro_chof_2105, retro_chof_2331, retro_chof_2407, retro_chof_50, retro_chof_800,
Callithrix jacchus ENSCJAG000000059126 retrocopies
retro_cjac_1275, retro_cjac_1808, retro_cjac_1826, retro_cjac_2251, retro_cjac_751, retro_cjac_911,
Cavia porcellus ENSCPOG000000065434 retrocopies
retro_cpor_1168, retro_cpor_286, retro_cpor_33, retro_cpor_887,
Equus caballus ENSECAG000000191801 retrocopy
retro_ecab_11,
Felis catus ENSFCAG000000048534 retrocopies
retro_fcat_129, retro_fcat_1421, retro_fcat_1579, retro_fcat_896,
Homo sapiens ENSG00000070831 6 retrocopies
retro_hsap_2775, retro_hsap_2968, retro_hsap_3028, retro_hsap_3404, retro_hsap_3848, retro_hsap_4013 ,
Homo sapiens ENSG000001197293 retrocopies
retro_hsap_1333, retro_hsap_2158, retro_hsap_2316,
Homo sapiens ENSG000001362386 retrocopies
retro_hsap_1256, retro_hsap_1925, retro_hsap_28, retro_hsap_3036, retro_hsap_3072, retro_hsap_4910,
Myotis lucifugus ENSMLUG000000133654 retrocopies
retro_mluc_1076, retro_mluc_1864, retro_mluc_2456, retro_mluc_905,
Monodelphis domestica ENSMODG000000160783 retrocopies
retro_mdom_18, retro_mdom_181, retro_mdom_537,
Mustela putorius furoENSMPUG000000159992 retrocopies
retro_mputfur_308, retro_mputfur_957,
Oryctolagus cuniculus ENSOCUG000000099861 retrocopy
retro_ocun_60,
Otolemur garnettii ENSOGAG000000142611 retrocopy
retro_ogar_131,
Sorex araneus ENSSARG000000051843 retrocopies
retro_sara_10, retro_sara_220, retro_sara_3,
Sus scrofa ENSSSCG000000035201 retrocopy
retro_sscr_899,

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 = 0.17 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .07 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .09 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .10 RPM
GBR_HG00131 0 .17 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .09 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .09 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .08 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .12 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .10 RPM

Indel association:

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





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