RetrogeneDB ID:

retro_hsap_1140

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:88176897..88178345(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000258128
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MKRN1
Ensembl ID:ENSG00000133606
Aliases:MKRN1, RNF61
Description:makorin ring finger protein 1 [Source:HGNC Symbol;Acc:7112]


Retrocopy-Parental alignment summary:






>retro_hsap_1140
ATGGCGGAGGCTGCAGCTCTCAGACCAACAGCCACAACATCAGGGGCGGCAGTGGCGGCAGCGGCGGCGGCGGCAGCAGC
GGCCTCCCCTACCAGGATCCCCACAGTCACCATTCTGTCCCCAGGGGGCAGGCGAGGGGGCCGCGGCAGCGATGGCAGCG
GCGGCAGCTGGACTAAACAGGTCACCTGCAGGTATTTTATGCATGGGGTTTATAAGGAAGGAGATAACTGTTGCAAGTTG
CATGACCTCTCTGACAGTCCGTATAATGTAGTGTACAAGAGTTTGCAGCCAGGGTACTGTATTTATGGAGACTGCTGCAG
ATATGAACATAGCAAGCCATTGAAACAGAAAGAAGCAACTGCTACAGAGCTAACTACAAAGTCATCCCTTGCTGCTTCCT
CAAGTCTCTCATGGATAGTCGGACCACTTGTTGAAATGAATACGGGTGAAGCTGAGTCAAGAAATTCAAACTTTGTAACT
GTAGGAGCAGGTTCAGAGGGCTGGGTGAATGCTGTTGAGTTTGTTCCTGGGCAACCCTACTGTGGCCGCACTGCGCCTTC
CTGCACTGAAGCACCCCTGCAGGGCTCAGTGACCAAGGAAGAATCAGAGAAAGAGCAAACTGCCGTGGAAACAAAGAAGC
AGCTGTGCCCCTATGCTGCAGTGGGAGAGTGCCGATATCGGGAGAACTTGTGTGTATATGGAGATTCGTGTGACATGTGT
GGCTGCAGGTCCTGCATCTGATGGATGCTGCCCAGAGATCACAGCATATAAAATCATGCTTTGAGGCCCATGAGAAAGAC
AGGGAGCTCTCATTTGCTGTGCAGCGCAGCGAGGAAATGGTGTGTGAGAGCTGCATGGAGATGATCTATGAGAAAGCCAA
CCCCAGACAGCACCGCTTCGGGATCCTCTCCAACTGCAACCACACCTACTGTCTTAAGTGCATTCGCAAGTGGAGGAGTG
CTAAGCAGTTTGAGAGCAAGATCATAAAGTCCTGCCCAGAATGTCGGATCACATCTAACTTTGTCGTTCCAAGTGAGTAC
TGTGTGGAGGAGAAAGAAGAGAAGCAGAAACTCATTCTGAAATACAAGGAGGCAATGAGCAACAAGGCGTGCAGGTATTT
TGATGAAGGACATGGGAGCTGCCCGTTTGGAGGGAACGGTTTTTATAAGCATGTGTACCCTGATGGCCGTAGAGAGGAGC
CACAGAGACAGAAGGTGGGAACATCAAGCAGATACCCGGCCCAATGAAGGAACCACTTCTGGGAACTCATTGAGGAAAGA
GAGAACAGCAGCCCCTTTGACAACGATGAAGAAGAGGTTGTCACCTTTGAGCTGGGTGAGTTGTTGCTTATGCTTTTGGC
TGCAGTTGGGGACGATGAACTAACAGACTCTGAAGATGAGAGCGACTTGTTTCATGAGGAGCTGGAAGATTTTTATGACT
TGGATCTA

ORF - retro_hsap_1140 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.77 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAEAAT--PGTTATTSGAGAAAATAAAASPTPIPTVTAPSLGAGGGGGGSDGSGGGWTKQVTCRYFMHGV
MAEAA...P..T................SPT.IPTVT..S.G...GG.GSDGSGG.WTKQVTCRYFMHGV
RetrocopyMAEAAALRPTATTXXXXXXXXXXXXXXXSPTRIPTVTILSPGGRRGGRGSDGSGGSWTKQVTCRYFMHGV
ParentalCKEGDNCRYSHDLSDSPYSVVCKYFQRGYCIYGDRCRYEHSKPLKQEEATATELTTKSSLAASSSLSSIV
.KEGDNC...HDLSDSPY.VV.K..Q.GYCIYGD.CRYEHSKPLKQ.EATATELTTKSSLAASSSLS.IV
RetrocopyYKEGDNCCKLHDLSDSPYNVVYKSLQPGYCIYGDCCRYEHSKPLKQKEATATELTTKSSLAASSSLSWIV
ParentalGPLVEMNTGEAESRNSNFATVGAGSEDWVNAIEFVPGQPYCGRTAPSCTEAPLQGSVTKEESEKEQTAVE
GPLVEMNTGEAESRNSNF.TVGAGSE.WVNA.EFVPGQPYCGRTAPSCTEAPLQGSVTKEESEKEQTAVE
RetrocopyGPLVEMNTGEAESRNSNFVTVGAGSEGWVNAVEFVPGQPYCGRTAPSCTEAPLQGSVTKEESEKEQTAVE
ParentalTKKQLCPYAAVGECRYGEN-CVYLHGDSCDMCG-LQVLHPMDAAQRSQHIKSCIEAHEKDMELSFAVQRS
TKKQLCPYAAVGECRY.EN.CVY..GDSCDMCG.LQVLH.MDAAQRSQHIKSC.EAHEKD.ELSFAVQRS
RetrocopyTKKQLCPYAAVGECRYRENLCVY--GDSCDMCG<LQVLHLMDAAQRSQHIKSCFEAHEKDRELSFAVQRS
ParentalKDMVCGICMEVVYEKANPSERRFGILSNCNHTYCLKCIRKWRSAKQFESKIIKSCPECRITSNFVIPSEY
..MVC..CME..YEKANP...RFGILSNCNHTYCLKCIRKWRSAKQFESKIIKSCPECRITSNFV.PSEY
RetrocopyEEMVCESCMEMIYEKANPRQHRFGILSNCNHTYCLKCIRKWRSAKQFESKIIKSCPECRITSNFVVPSEY
ParentalWVEEKEEKQKLILKYKEAMSNKACRYFDEGRGSCPFGGNCFYKHAYPDGRREEPQRQKVGTSSRYRAQRR
.VEEKEEKQKLILKYKEAMSNKACRYFDEG.GSCPFGGN.FYKH.YPDGRREEPQRQKVGTSSRY.AQ.R
RetrocopyCVEEKEEKQKLILKYKEAMSNKACRYFDEGHGSCPFGGNGFYKHVYPDGRREEPQRQKVGTSSRYPAQ*R
ParentalNHFWELIEERENSNPFDNDEEEVVTFELGEMLLMLLAAGGDDELTDSEDEWDLFHDELEDFYDLDL
NHFWELIEERENS.PFDNDEEEVVTFELGE.LLMLLAA.GDDELTDSEDE.DLFH.ELEDFYDLDL
RetrocopyNHFWELIEERENSSPFDNDEEEVVTFELGELLLMLLAAVGDDELTDSEDESDLFHEELEDFYDLDL

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 106 .41 RPM
bodymap2_adrenal 0 .02 RPM 102 .47 RPM
bodymap2_brain 0 .00 RPM 85 .79 RPM
bodymap2_breast 0 .00 RPM 98 .97 RPM
bodymap2_colon 0 .00 RPM 157 .66 RPM
bodymap2_heart 0 .00 RPM 74 .12 RPM
bodymap2_kidney 0 .10 RPM 80 .86 RPM
bodymap2_liver 0 .00 RPM 33 .27 RPM
bodymap2_lung 0 .00 RPM 121 .84 RPM
bodymap2_lymph_node 0 .00 RPM 110 .87 RPM
bodymap2_ovary 0 .00 RPM 100 .41 RPM
bodymap2_prostate 0 .00 RPM 118 .23 RPM
bodymap2_skeletal_muscle 0 .02 RPM 109 .15 RPM
bodymap2_testis 1 .00 RPM 265 .36 RPM
bodymap2_thyroid 0 .00 RPM 135 .98 RPM
bodymap2_white_blood_cells 0 .00 RPM 237 .73 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1140 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1140 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_298641827 libraries1 library0 libraries0 libraries1 library

The graphical summary, for retro_hsap_1140 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_1140 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1140 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_776
Pongo abelii retro_pabe_947
Parental genes homology:
Parental genes homology involve 19 parental genes, and 47 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000083062 retrocopies
retro_btau_401, retro_btau_943,
Canis familiaris ENSCAFG000000039532 retrocopies
retro_cfam_2157, retro_cfam_253,
Choloepus hoffmanni ENSCHOG000000110153 retrocopies
retro_chof_173, retro_chof_2357, retro_chof_89,
Callithrix jacchus ENSCJAG000000134742 retrocopies
retro_cjac_210, retro_cjac_2991,
Cavia porcellus ENSCPOG000000009481 retrocopy
retro_cpor_109,
Dasypus novemcinctus ENSDNOG000000195642 retrocopies
retro_dnov_1011, retro_dnov_388,
Felis catus ENSFCAG000000249421 retrocopy
retro_fcat_67,
Homo sapiens ENSG00000133606 4 retrocopies
retro_hsap_1140 , retro_hsap_4197, retro_hsap_4676, retro_hsap_4859,
Gorilla gorilla ENSGGOG000000239774 retrocopies
retro_ggor_119, retro_ggor_2813, retro_ggor_3031, retro_ggor_381,
Microcebus murinus ENSMICG000000021141 retrocopy
retro_mmur_1184,
Macaca mulatta ENSMMUG000000104203 retrocopies
retro_mmul_191, retro_mmul_2597, retro_mmul_76,
Mus musculus ENSMUSG000000299221 retrocopy
retro_mmus_2663,
Nomascus leucogenys ENSNLEG000000019214 retrocopies
retro_nleu_1027, retro_nleu_2167, retro_nleu_33, retro_nleu_939,
Otolemur garnettii ENSOGAG000000098772 retrocopies
retro_ogar_3468, retro_ogar_424,
Pongo abelii ENSPPYG000000180573 retrocopies
retro_pabe_3435, retro_pabe_3776, retro_pabe_947,
Pan troglodytes ENSPTRG000000197665 retrocopies
retro_ptro_2849, retro_ptro_3106, retro_ptro_3234, retro_ptro_75, retro_ptro_776,
Sus scrofa ENSSSCG000000164982 retrocopies
retro_sscr_43, retro_sscr_637,
Tarsius syrichta ENSTSYG000000099963 retrocopies
retro_tsyr_1256, retro_tsyr_1525, retro_tsyr_508,
Tursiops truncatus ENSTTRG000000095282 retrocopies
retro_ttru_1064, retro_ttru_1128,

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 = 0.1 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 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 .03 RPM
CEU_NA12873 0 .03 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 .03 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .02 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 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .10 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .07 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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