RetrogeneDB ID:

retro_hsap_4918

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:Y:3550800..3551906(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000232927
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:USP12
Ensembl ID:ENSG00000152484
Aliases:USP12, UBH1, USP12L1
Description:ubiquitin specific peptidase 12 [Source:HGNC Symbol;Acc:20485]


Retrocopy-Parental alignment summary:






>retro_hsap_4918
ATGGAAATCCTAATGACAGTCTCCAAATTCGCCTCCATCTGTACCATGGGCGCCAATGCTTCGGCGTTAGAGAAAGAGAT
TGGTCCAGAACAGTTTCCGGTCAACGAGCATTATTTTGGATTAGTCAATTTTGGGAATACCTGCTACTGCAATTCAGTTC
TTCAAGCACTTATTTTTGTCGTCCGTTTCGGGAAAAAGTTCTTGCATATAAGAGTCAACCTAGGAAAAAGGAGAGCTTTC
TTACATGCTTAGCAGATCTCTTCCACAGCATAGCCACTCAGAAGAAAAAGGTTGGAGTAATACCTCCGAAGAAGTTCATC
ACAAGATTACAGAAATAAAATGAGCTTTTCGACAACTACATGCAACAAGATGCCCATGAATTCTTAAATTACCTACTAAA
TACAATTGGTGATATTTTACAAGAAGAGAGAAAGCAGGAAAAACAAAATGGTCGCTAACCTAATGATAATATTGATAATG
AAAATAATAGCAGCACACCAGACCCAACGTGGGTTCATGAGATTTTTTGGGGAACGTTAACTAATGAAACCAGAAGTCTT
ACTTGCGAAACTATAAGCAGCAAAGATGAAGATTTTTTAGACCTTTCTGTTGACGTGGAACAAAATACATCAATTACTCA
CTGCTTAAGGGGTTTCAGCAACACAGAAACTCTATGCAGTTAATACAAGTATTACTGTGAAGAGTGTCGCAGCAAACAGG
AAGCACACAAACAGATGAAAGTTTAAAAACTGCCCATGATTCTAGCTCTACACTTGAAGAGATTTAAATATATGGATCAA
CTTCATCGATATACAAAACTCTCTTACCGGGTGGTTTTTCCTTTAGAACTTCGTCTATTTAACACTTCAGGTGATGCCAC
CAATCCAGACAGAATGTACGACCTTGTTGCTGTTGTGGTTCACTGTGGAAGTGGTCCCAATCGAGGCCATTATATTGCGA
TAGTTAAGAGTCATGATTTTTGATTGTTGTTTGATGAGACATTGTAGAAAAATAGATACACAAGCTATTGAAGAATTCTA
CGGGTTGACATCAGATACTCAAAGAACTCTGAGTCTGGTTACATCCTTTTCTATCAGTCTCGGGAC

ORF - retro_hsap_4918 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.65 %
Parental protein coverage: 100. %
Number of stop codons detected: 5
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMEILMTVSKFASICTMGANASALEKEIGPEQFPVNEHYFGLVNFGNTCYCNSVLQAL-YFCRPFREKVLA
MEILMTVSKFASICTMGANASALEKEIGPEQFPVNEHYFGLVNFGNTCYCNSVLQAL.YFCRPFREKVLA
RetrocopyMEILMTVSKFASICTMGANASALEKEIGPEQFPVNEHYFGLVNFGNTCYCNSVLQAL<YFCRPFREKVLA
ParentalYKSQPRKKESLLTCLADLFHSIATQKKKVGVIPPKKFITRLRKENELFDNYMQQDAHEFLNYLLNTIADI
YKSQPRKKES.LTCLADLFHSIATQKKKVGVIPPKKFITRL.K.NELFDNYMQQDAHEFLNYLLNTI.DI
RetrocopyYKSQPRKKESFLTCLADLFHSIATQKKKVGVIPPKKFITRLQK*NELFDNYMQQDAHEFLNYLLNTIGDI
ParentalLQEERKQEKQNGRLPNGNIDNENNNSTPDPTWVHEIFQGTLTNETRCLTCETISSKDEDFLDLSVDVEQN
LQEERKQEKQNGR.PN.NIDNENN.STPDPTWVHEIF.GTLTNETR.LTCETISSKDEDFLDLSVDVEQN
RetrocopyLQEERKQEKQNGR*PNDNIDNENNSSTPDPTWVHEIFWGTLTNETRSLTCETISSKDEDFLDLSVDVEQN
ParentalTSITHCLRGFSNTETLCSEYKYYCEECRSKQEAHKRMKVKKLPMILALHLKRFKYMDQLHRYTKLSYRVV
TSITHCLRGFSNTETLCS.YKYYCEECRSKQEAHK.MKV.KLPMILALHLKRFKYMDQLHRYTKLSYRVV
RetrocopyTSITHCLRGFSNTETLCS*YKYYCEECRSKQEAHKQMKV*KLPMILALHLKRFKYMDQLHRYTKLSYRVV
ParentalFPLELRLFNTSGDATNPDRMYDLVAVVVHCGSGPNRGHYIAIVKSHDFWLLFDD-DIVE-KIDAQAIEEF
FPLELRLFNTSGDATNPDRMYDLVAVVVHCGSGPNRGHYIAIVKSHDF.LLFD..DIVE.KID.QAIEEF
RetrocopyFPLELRLFNTSGDATNPDRMYDLVAVVVHCGSGPNRGHYIAIVKSHDF*LLFDE<DIVE<KIDTQAIEEF
ParentalYGLTSD-ISKNSESGYILFYQSRD
YGLTSD..SKNSESGYILFYQSRD
RetrocopyYGLTSD<YSKNSESGYILFYQSRD

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 55 .16 RPM
bodymap2_adrenal 0 .00 RPM 56 .00 RPM
bodymap2_brain 0 .00 RPM 75 .95 RPM
bodymap2_breast 0 .00 RPM 60 .04 RPM
bodymap2_colon 0 .00 RPM 175 .55 RPM
bodymap2_heart 0 .00 RPM 38 .23 RPM
bodymap2_kidney 0 .00 RPM 68 .93 RPM
bodymap2_liver 0 .00 RPM 25 .35 RPM
bodymap2_lung 0 .00 RPM 91 .79 RPM
bodymap2_lymph_node 0 .00 RPM 46 .82 RPM
bodymap2_ovary 0 .00 RPM 47 .17 RPM
bodymap2_prostate 0 .00 RPM 113 .19 RPM
bodymap2_skeletal_muscle 0 .00 RPM 26 .61 RPM
bodymap2_testis 0 .00 RPM 87 .86 RPM
bodymap2_thyroid 0 .00 RPM 66 .46 RPM
bodymap2_white_blood_cells 0 .00 RPM 58 .96 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4918 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4918 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4918 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4918 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4918 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4726
Pan troglodytes retro_ptro_3143
Gorilla gorilla retro_ggor_2937
Pongo abelii retro_pabe_3672
Parental genes homology:
Parental genes homology involve 9 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000193445 retrocopies
retro_cjac_2734, retro_cjac_3901, retro_cjac_3964, retro_cjac_3965, retro_cjac_4011,
Homo sapiens ENSG00000152484 4 retrocopies
retro_hsap_2328, retro_hsap_3266, retro_hsap_4726, retro_hsap_4918 ,
Microcebus murinus ENSMICG000000062692 retrocopies
retro_mmur_1167, retro_mmur_1187,
Macaca mulatta ENSMMUG000000214251 retrocopy
retro_mmul_937,
Nomascus leucogenys ENSNLEG000000003233 retrocopies
retro_nleu_1817, retro_nleu_1995, retro_nleu_2426,
Otolemur garnettii ENSOGAG000000306391 retrocopy
retro_ogar_2897,
Pongo abelii ENSPPYG000000052323 retrocopies
retro_pabe_2110, retro_pabe_2705, retro_pabe_3672,
Pan troglodytes ENSPTRG000000057273 retrocopies
retro_ptro_1701, retro_ptro_2209, retro_ptro_3143,
Tupaia belangeri ENSTBEG000000129602 retrocopies
retro_tbel_3285, retro_tbel_4692,

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 = 0.03 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 .03 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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