RetrogeneDB ID:

retro_hsap_1361

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:14:69550114..69552103(+)
Located in intron of:ENSG00000139990
Retrocopy
information
Ensembl ID:ENSG00000259165
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DDX18
Ensembl ID:ENSG00000088205
Aliases:DDX18, MrDb
Description:DEAD (Asp-Glu-Ala-Asp) box polypeptide 18 [Source:HGNC Symbol;Acc:2741]


Retrocopy-Parental alignment summary:






>retro_hsap_1361
ATGTCTCACCTGCTGATGAAACTCCTACGCAAGAAGATCAAGAAGTGGAACCTCAAACTGCGGCAGTGGAACCTAAAGTT
GCAGGGGGCCTCAAATCTGACCCTGTCCGAAACTCAAAATACAGATGTGTCTGAAGAAACAACGGGAGGTGGAAAGGTTA
AAAAATCAAAACATTCTATGAATGTGGGCTTATCAGATGCTCAAAATGGAGATGTGTCTCAAGAAGCAGTGGAAAATATA
AAAGTTAAAAAATCTCCCCAGAAATCCACCGTATTAACCAATGGAGAAGCAGCAATGCAGTCTCCTAATTCAGAATCAAA
AAAGAAGAGAAAAATGGTGAATGATGCTGAGTCTGATACAAAAAAAGCAAAAACTGAAAACAAAGGGGAATCTGAAGAAG
AAAGTGCCAAGTCTCCTAAAGAAACAGAAAATAATGTTGAGAAGCCAGATGATGAAGATGACAGTGAGATGCCCAGCCTG
CCCCTGGGACTGACAGGAGCTTTTGAGGATACTTCATTTGCTTCTTATGTAATCTTGTCAATGAAAACACTCTGAAGGCA
ATAAAAGAAATGGGTTTTACAAACGTGACTGAAATTCAGCATAAAAGTATCAGACCACCTCTGGAAGGCAGGGATCTTCT
TGCAGCTACAAAAACCGTCAGTGGTAAAACCCCAGCTTTTCTCATCCTGCAGCTGAACTCATTGTTAAGTTAAATTTCAT
GCCCAGGAATGGAACAGGGGTCCTTATTCTCTCACCTACTAGAGAACTAGCCATGCAAACTTTTGGTGTTCTTAAGGAGC
TAATGAGTCACCACGTGCATACCTATGGGTTGATAATGGGTGGCAGTAATAGATCTGCTGAAGCACAGAAACTTGCTAAT
GGGATCAACATCACTGTGGTCACACCAGGCTGTCTGCTGGACCATATGCAGAATATCCCAGGGTTTATGTATAAAAATCT
GCAGTGTCTGGTTATCGATGAAGCTGATCGTATCTTGGATGTTGAGTTTGAAGAGGAATTAAAACAAATTATTAAACTTT
TGCCAACACGTAGACAGACGATGCTCTTTTCTGCCACCCAAACTTGAAAAGTTGAAGGCCCGGCAAGGATTTCTCTGAAA
AAGGAGCCATTGTATGTTGGTGTTGATGACGATAAAGCTAATGCAACAGTGGATGGTCTTGAGCAGGGATATGTTGTTTG
TCCTTCTGAAAAGAGATTCCTTCTACTCTTTACATTCCTTAAGAAGAACCAAAAAAAGAAGCTTATGGCCTTCTTTTCAT
CTTGTATGTCCGTGAAATACCACTATGAGTTGCTGAACTACATTGATTTGCCCATCTTGGCCATTCATGGAAAGCAAAAG
CAAAATAAGCATACGACCACATTCTTCCAGTTCTGCAATGCAGATTCAGGAACACTATTGTGTACAGATGTGGCAGCAAG
AGAACTGGACATTACTGAAGTCAACTGGATTGTTCAGTATGACCCTCCGGATGACCCTAAGGAATAATATTCATCGTGTG
GGTAGAACAGCCAGAGACCTAAATGGGAGAAGGCATGCCTTGCTCATTTTGCACCCAGAAGAATTGGGTTTTCTTCACTA
CCTGAAATGATCCAAGGTTCCATTAAGTGAATTTGACTTTTCCTGGTCTAAAATTTCTGACATTCAGTCTCAGCTTGAGA
AATTGATTCAAAAGAACTACTTTTTTCATAAGTCAGCTCAGGAAGCATATAAATCATACATACAAACCTACGATTCCCAT
TCTCTGAAACAGATCTTTAATGTTTAATAACTTAAATTTGCCTCAAGTTGCTGTCATTGGTTTCAAGGTGCCTCCCTTTG
TTGATCTGAACGTCAACAGCAATGAAGGCAAGCAGAAAAAGCGAGTAGGCAGTGGTGGATTTGGCTACCAGAAAACCAAG
AAAGTTGAGAAGTCCAAAATCTTTAAACATATTAGCAAGCAAACATCCAACCGCAGGCAGTTCTCTCAC

ORF - retro_hsap_1361 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.09 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMSHLPMKLLRKKIEKRNLKLRQRNLKFQGASNLTLSETQNGDVSEETMGSRKVKKSKQKPMNVGLSETQN
MSHL.MKLLRKKI.K.NLKLRQ.NLK.QGASNLTLSETQN.DVSEET.G..KVKKSK...MNVGLS..QN
RetrocopyMSHLLMKLLRKKIKKWNLKLRQWNLKLQGASNLTLSETQNTDVSEETTGGGKVKKSKHS-MNVGLSDAQN
ParentalGGMSQEAVGNIKVTKSPQKSTVLTNGEAAMQSSNSESKKKKKKKRKMVNDAEPDTKKAKTENKGKSEEES
G..SQEAV.NIKV.KSPQKSTVLTNGEAAMQS.NSES....KKKRKMVNDAE.D.........G.SEEES
RetrocopyGDVSQEAVENIKVKKSPQKSTVLTNGEAAMQSPNSES----KKKRKMVNDAESDXXXXXXXXXGESEEES
ParentalAETTKETENNVEKPDNDEDESEVPSLPLGLTGAFEDTSFAS-LCNLVNENTLKAIKEMGFTNMTEIQHKS
A...KETENNVEKPD.DED.SE.PSLPLGLTGAFEDTSFAS.LCNLVNENTLKAIKEMGFTN.TEIQHKS
RetrocopyAKSPKETENNVEKPD-DEDDSEMPSLPLGLTGAFEDTSFAS<LCNLVNENTLKAIKEMGFTNVTEIQHKS
ParentalIRPLLEGRDLLAAAKTGSGKTLAFLI-PAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHH
IRP.LEGRDLLAA.KT.SGKT.AFLI.PA.ELIVKL.FMPRNGTGVLILSPTRELAMQTFGVLKELM.HH
RetrocopyIRPPLEGRDLLAATKTVSGKTPAFLI<PAAELIVKLNFMPRNGTGVLILSPTRELAMQTFGVLKELMSHH
ParentalVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELK
VHTYGLIMGGSNRSAEAQKL.NGINI.V.TPG.LLDHMQN.PGFMYKNLQCLVIDEADRILDV.FEEELK
RetrocopyVHTYGLIMGGSNRSAEAQKLANGINITVVTPGCLLDHMQNIPGFMYKNLQCLVIDEADRILDVEFEEELK
ParentalQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEPLYVGVDDDKANATVDGLEQGYVVCPSEKRFLLLFT
QIIKLLPTRRQTMLFSATQT.KVE..ARISLKKEPLYVGVDDDKANATVDGLEQGYVVCPSEKRFLLLFT
RetrocopyQIIKLLPTRRQTMLFSATQT*KVEGPARISLKKEPLYVGVDDDKANATVDGLEQGYVVCPSEKRFLLLFT
ParentalFLKKNRKKKLMVFFSSCMSVKYHYELLNYIDLPVLAIHGKQKQNKRTTTFFQFCNADSGTLLCTDVAARG
FLKKN.KKKLM.FFSSCMSVKYHYELLNYIDLP.LAIHGKQKQNK.TTTFFQFCNADSGTLLCTDVAAR.
RetrocopyFLKKNQKKKLMAFFSSCMSVKYHYELLNYIDLPILAIHGKQKQNKHTTTFFQFCNADSGTLLCTDVAARE
ParentalLDIPEVDWIVQYDPPDDPKE-YIHRVGRTARGLNGRGHALLILRPEELGFLRYLKQSKVPLSEFDFSWSK
LDI.EV.WIVQYDPPDDPKE..IHRVGRTAR.LNGR.HALLIL.PEELGFL.YLK.SKVPLSEFDFSWSK
RetrocopyLDITEVNWIVQYDPPDDPKE>NIHRVGRTARDLNGRRHALLILHPEELGFLHYLK*SKVPLSEFDFSWSK
ParentalISDIQSQLEKLIEKNYFLHKSAQEAYKSYIRAYDSHSLKQIFNV-NNLNLPQVALSFGFKVPPFVDLNVN
ISDIQSQLEKLI.KNYF.HKSAQEAYKSYI..YDSHSLKQIFNV.NNLNLPQVA...GFKVPPFVDLNVN
RetrocopyISDIQSQLEKLIQKNYFFHKSAQEAYKSYIQTYDSHSLKQIFNV>NNLNLPQVAV-IGFKVPPFVDLNVN
ParentalSNEGKQKKRGGGGGFGYQKTKKVEKSKIFKHISKKSSDSRQFSH
SNEGKQKKR.G.GGFGYQKTKKVEKSKIFKHISK..S..RQFSH
RetrocopySNEGKQKKRVGSGGFGYQKTKKVEKSKIFKHISKQTSNRRQFSH

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 .20 RPM 86 .17 RPM
bodymap2_adrenal 0 .57 RPM 106 .48 RPM
bodymap2_brain 0 .19 RPM 58 .67 RPM
bodymap2_breast 0 .12 RPM 74 .57 RPM
bodymap2_colon 0 .00 RPM 91 .59 RPM
bodymap2_heart 0 .09 RPM 34 .01 RPM
bodymap2_kidney 0 .12 RPM 69 .98 RPM
bodymap2_liver 0 .06 RPM 37 .73 RPM
bodymap2_lung 0 .19 RPM 65 .21 RPM
bodymap2_lymph_node 0 .00 RPM 64 .03 RPM
bodymap2_ovary 0 .04 RPM 123 .02 RPM
bodymap2_prostate 0 .40 RPM 96 .02 RPM
bodymap2_skeletal_muscle 0 .00 RPM 31 .87 RPM
bodymap2_testis 0 .08 RPM 84 .58 RPM
bodymap2_thyroid 0 .15 RPM 144 .32 RPM
bodymap2_white_blood_cells 0 .26 RPM 141 .77 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1361 was not detected

EST - click to see more details

2 EST(s) were mapped to retro_hsap_1361 retrocopy
EST ID Start End Identity Match Mis-match Score
AW892944 69550531 69550980 99.6 445 2 441
DB269893 69550481 69551048 100 567 0 567

TSS - click to see more details

No TSS is located nearby retro_hsap_1361 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1361 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1361 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_933
Pongo abelii retro_pabe_1128
Macaca mulatta retro_mmul_2192
Parental genes homology:
Parental genes homology involve 10 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Echinops telfairi ENSETEG000000171662 retrocopies
retro_etel_1919, retro_etel_297,
Homo sapiens ENSG00000088205 6 retrocopies
retro_hsap_1361 , retro_hsap_1579, retro_hsap_3223, retro_hsap_3561, retro_hsap_608, retro_hsap_834,
Gorilla gorilla ENSGGOG000000284204 retrocopies
retro_ggor_1201, retro_ggor_2189, retro_ggor_2402, retro_ggor_535,
Microcebus murinus ENSMICG000000175901 retrocopy
retro_mmur_1560,
Myotis lucifugus ENSMLUG000000176071 retrocopy
retro_mluc_2279,
Macaca mulatta ENSMMUG000000213431 retrocopy
retro_mmul_2192,
Monodelphis domestica ENSMODG000000005331 retrocopy
retro_mdom_414,
Nomascus leucogenys ENSNLEG000000117694 retrocopies
retro_nleu_1377, retro_nleu_1396, retro_nleu_266, retro_nleu_437,
Pongo abelii ENSPPYG000000127964 retrocopies
retro_pabe_1128, retro_pabe_1301, retro_pabe_2670, retro_pabe_744,
Pan troglodytes ENSPTRG000000123915 retrocopies
retro_ptro_1064, retro_ptro_2174, retro_ptro_2419, retro_ptro_448, retro_ptro_933,

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 = 0.32 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .17 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .16 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .11 RPM
CEU_NA12751 0 .22 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .14 RPM
CEU_NA12872 0 .22 RPM
CEU_NA12873 0 .10 RPM
FIN_HG00183 0 .19 RPM
FIN_HG00277 0 .15 RPM
FIN_HG00315 0 .08 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .07 RPM
FIN_HG00377 0 .13 RPM
FIN_HG00378 0 .04 RPM
GBR_HG00099 0 .26 RPM
GBR_HG00111 0 .06 RPM
GBR_HG00114 0 .11 RPM
GBR_HG00119 0 .17 RPM
GBR_HG00131 0 .29 RPM
GBR_HG00133 0 .19 RPM
GBR_HG00134 0 .15 RPM
GBR_HG00137 0 .14 RPM
GBR_HG00142 0 .17 RPM
GBR_HG00143 0 .06 RPM
TSI_NA20512 0 .17 RPM
TSI_NA20513 0 .15 RPM
TSI_NA20518 0 .14 RPM
TSI_NA20532 0 .10 RPM
TSI_NA20538 0 .23 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .10 RPM
TSI_NA20771 0 .09 RPM
TSI_NA20786 0 .05 RPM
TSI_NA20798 0 .25 RPM
YRI_NA18870 0 .07 RPM
YRI_NA18907 0 .17 RPM
YRI_NA18916 0 .13 RPM
YRI_NA19093 0 .08 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .10 RPM
YRI_NA19118 0 .08 RPM
YRI_NA19213 0 .07 RPM
YRI_NA19214 0 .15 RPM
YRI_NA19223 0 .32 RPM

Indel association:

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



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