RetrogeneDB ID:

retro_hsap_29

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:13:52602940..52605241(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000253797
Aliases:UTP14C, 2700066J21Rik, KIAA0266, UTP14B
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:UTP14A
Ensembl ID:ENSG00000156697
Aliases:UTP14A, NYCO16, SDCCAG16, dJ537K23.3
Description:UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast) [Source:HGNC Symbol;Acc:10665]


Retrocopy-Parental alignment summary:






>retro_hsap_29
ATGAATGTGAACCAGGTTGCAGAGAATCTGGCTTTGAGCCACCAGGAAGAACTAGTGGATTTGCCAAAAAACTACCCCTT
GAGTGAAAATGAAGATGAGGGGGACAGTGATGGAGAGAGAAAGCATCAAAAGCTTCTGGAAGCAATCATTTCCCTTGATG
GAAAGAATAGGCGGAAATTGGCTGAGAGGTCTGAGGCTAGTCTGAAAGTGTCAGAGTTCAGTGTCAGTTCTGAAGGATCA
GGAGAAAAGCTGGGCCTTGCAGATCTGCTTGAGCCCGTTAAAACTTCATCTTCTTTGGCCACTGTAAAAAAGCAACTGAA
TAGAGTCAAATCAAAGAAGGTGGTGGAGTTACCTCTTAACAAAGAAAAAATTGAACAGATCCACAGAGAAGTAGCATTCA
GTAAAACCTCACAGGTCCTCTCCAAATGGGACCCTATCATCCTGAAGAACCAGCAGGCAGAGCAGCTGGTTTTTCCCCTG
GGGAAGGAGCAGCCAGCCATTGCTCCCATTGAACATGCGCTCAGTGGCTGGAAGGCAAGAACTCCCCTGGAGCAGGAAAT
TTTTAACCTCCTCCATAAGAACAAGCAGCCAGTGACAGATCCTTTACTGACTCCCATGGAAAAGGCCTCTCTCCAAGCCA
TGAGCCTGGAAGAGGCAAAGATGCACCGAGCAGAGCTTCAGAGGGCTCGGGCTCTGCAGTCCTACTATGAGGCCAAGGCT
CGAAAAGAGAAGAAAATCAAAAGTAAAAAGTATCACAAAGTCGTGAAGAAAGGAAAGGCCAAGAAAGCCTTAAAAGAGTT
TGAGCAGCTACAGAAGGTTAATCCAACTGTGGCACTGGAAGAAATGGAAAAAATTGAAAATGCCAGAATGATGGAAAGAA
TGAGCCTTAAGCACCAAAACAGTGGGAAATGGGCCAAGTCAAAGGCAATTATGGCCAAATATGACCTGGAGGCTCGCCAA
GCTATGCAGGAACAGTTGGCCAAGAACAAAGAACTGACACAGAAACTCCAGGTAGCCTCTGAGAGTGAGGAAGAGGAGGG
AGGCACAGAAGTGGAAGAACTCCTTGTCCCTCATGTAGCGAATGAAGTGCAGATGAATGTGGACGGACCGAATCCCTGGA
TGTTCAGGAGCTGCACCAGTGACACCAAAGAGGCTGCAACACAGGAGGACCCTGAGCAAGTGCCAGAGCTTGCAGCTCAT
GAGGTTTCTGCAAGTGAGGCAGAAGAAAGACCAGTGGCAGAGGAAGAAATTTTGTTGAGAGAATTTGAGGAAAGGCAATC
CCTTAGAAAAAGATCTGAGCTCAACCAGGATGCTGAGCCAGCAAGCAGTCAAGAAACAAAAGATTCTAGCAGCCAGGAGG
TGCTGTCCGAATTGAGGGCACTATCTCAGAAATTGAAGGAAAAACATCAGTCCAGGAAGCAAAAAGCAAGTTCAGAGGGG
ACTGTTCCCCAGGTCCAGAGAGAGGAACCTGCCCCAGAAGAAGCGGAACCCCTATTGCTACAGAGGTCAGAGAGAGTACA
AACTCTGGAAGAGCTAGAAGAGCTGGGAAAAGAAGATTGTTTTCAAAATAAGGAGCTTCCCAGACCTGTGTTAGAAGGAC
AGCAGTCAGAGAGGACCCCAAATAATCGGCCTGATGCCCCTAAGGAGAAGAAAGAGAAGGAGCAACTGATCAACCTACAG
AACTTCCTGACCACACAGTCTCCTTCCGTGAGGTCTTTGGCAGTTCCCACAATAATAGAGGAGCTGGAAGATGAAGAGGA
GAGAGACCAAAGGCAGATGATAAAGGAAGCTTTTGCTGGGGATGATGTCATCAGAGATTTCTTGAAAGAGAAGAGGGAAG
CTGTGGAGGCGAGTAAGCCAAAGGACGTGGACCTGACACTACCTGGCTGGGGCGAGTGGGGTGGTGTGGGCCTAAAGCCC
AGTGCCAAGAAAAGACGCCAGTTTCTCATTAAAGCCCCTGAGGGTCCTCCAAGAAAAGATAAGAATTTGCCAAATGTGAT
TATCAGTGAGAAGCGCAACATCCACGCAGCAGCTCATCAGGTACAAGTGCTTCCATATCCATTTACCCACCATCGGCAAT
TTGAAAGGACCATCCAGACCCCTATAGGATCCACATGGAACACCCAGAGGGCTTTCCAAAAGCTGACTACTCCCAAGGTC
GTCACCAAGCCAGGCCATATCATTAAGCCCATAAAAGCAGAGGATGTGGGCTACCAGTCTTCCTCAAGGTCAGACCTGCC
TGTCATACAGAGGAATCCAAAACGAATCACCACACGTCACAATAAAGAAGAAAAACTGTAG

ORF - retro_hsap_29 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.22 %
Parental protein coverage: 99.35 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMTANRLAESLLALSQQEELADLPKDYLLSESEDEGDNDGERKHQKLLEAISSLDGKNRRKLAERSEASLK
M..N..AE.L.ALS.QEEL.DLPK.Y.LSE.EDEGD.DGERKHQKLLEAI.SLDGKNRRKLAERSEASLK
RetrocopyMNVNQVAENL-ALSHQEELVDLPKNYPLSENEDEGDSDGERKHQKLLEAIISLDGKNRRKLAERSEASLK
ParentalVSEFNVSSEGSGEKLVLADLLEPVKTSSSLATVKKQLSRVKSKKTVELPLNKEEIERIHREVAFNKTAQV
VSEF.VSSEGSGEKL.LADLLEPVKTSSSLATVKKQL.RVKSKK.VELPLNKE.IE.IHREVAF.KT.QV
RetrocopyVSEFSVSSEGSGEKLGLADLLEPVKTSSSLATVKKQLNRVKSKKVVELPLNKEKIEQIHREVAFSKTSQV
ParentalLSKWDPVVLKNRQAEQLVFPLEKEEPAIAPIEHVLSGWKARTPLEQEIFNLLHKNKQPVTDPLLTPVEKA
LSKWDP..LKN.QAEQLVFPL.KE.PAIAPIEH.LSGWKARTPLEQEIFNLLHKNKQPVTDPLLTP.EKA
RetrocopyLSKWDPIILKNQQAEQLVFPLGKEQPAIAPIEHALSGWKARTPLEQEIFNLLHKNKQPVTDPLLTPMEKA
ParentalSLRAMSLEEAKMRRAELQRARALQSYYEAKARREKKIKSKKYHKVVKKGKAKKALKEFEQLRKVNPAAAL
SL.AMSLEEAKM.RAELQRARALQSYYEAKAR.EKKIKSKKYHKVVKKGKAKKALKEFEQL.KVNP..AL
RetrocopySLQAMSLEEAKMHRAELQRARALQSYYEAKARKEKKIKSKKYHKVVKKGKAKKALKEFEQLQKVNPTVAL
ParentalEELEKIEKARMMERMSLKHQNSGKWAKSKAIMAKYDLEARQAMQEQLSKNKELTQKLQVASESEEEEGGT
EE.EKIE.ARMMERMSLKHQNSGKWAKSKAIMAKYDLEARQAMQEQL.KNKELTQKLQVASESEEEEGGT
RetrocopyEEMEKIENARMMERMSLKHQNSGKWAKSKAIMAKYDLEARQAMQEQLAKNKELTQKLQVASESEEEEGGT
ParentalEDVEELLVPDVVNEVQMNADGPNPWMLRSCTSDTKEAATQEDPEQLPELEAHGVSESEGEERPVAEEEIL
E.VEELLVP.V.NEVQMN.DGPNPWM.RSCTSDTKEAATQEDPEQ.PEL.AH.VS.SE.EERPVAEEEIL
RetrocopyE-VEELLVPHVANEVQMNVDGPNPWMFRSCTSDTKEAATQEDPEQVPELAAHEVSASEAEERPVAEEEIL
ParentalLREFEERRSLRKRSELSQDAEPAGSQETKDSGSQEVLSELRVLSQKLKENHQSRKQKASSEGTIPQVQRE
LREFEER.SLRKRSEL.QDAEPA.SQETKDS.SQEVLSELR.LSQKLKE.HQSRKQKASSEGT.PQVQRE
RetrocopyLREFEERQSLRKRSELNQDAEPASSQETKDSSSQEVLSELRALSQKLKEKHQSRKQKASSEGTVPQVQRE
ParentalEPAPEEEEPLLLQRPERVQTLEELEELGKEECFQNKELPRPVLEGQQSERTPNNRPDAPKEKKKKEQMID
EPAPEE.EPLLLQR.ERVQTLEELEELGKE.CFQNKELPRPVLEGQQSERTPNNRPDAPKEKK.KEQ.I.
RetrocopyEPAPEEAEPLLLQRSERVQTLEELEELGKEDCFQNKELPRPVLEGQQSERTPNNRPDAPKEKKEKEQLIN
ParentalLQNLLTTQSPSVKSLAVPT-IEELEDEEERNHRQMIKEAFAGDDVIRDFLKEKREAVEASKPKDVDLTLP
LQN.LTTQSPSV.SLAVPT.IEELEDEEER..RQMIKEAFAGDDVIRDFLKEKREAVEASKPKDVDLTLP
RetrocopyLQNFLTTQSPSVRSLAVPTIIEELEDEEERDQRQMIKEAFAGDDVIRDFLKEKREAVEASKPKDVDLTLP
ParentalGWGEWGGVGLKPSAKKRRRFLIKAPEGPPRKDKNLPNVIINEKRNIHAAAHQVRVLPYPFTHHWQFERTI
GWGEWGGVGLKPSAKKRR.FLIKAPEGPPRKDKNLPNVII.EKRNIHAAAHQV.VLPYPFTHH.QFERTI
RetrocopyGWGEWGGVGLKPSAKKRRQFLIKAPEGPPRKDKNLPNVIISEKRNIHAAAHQVQVLPYPFTHHRQFERTI
ParentalQTPIGSTWNTQRAFQKLTTPKVVTKPGHIINPIKAEDVGYRSSSRSDLSVIQRNPKRITTRHKKQLK
QTPIGSTWNTQRAFQKLTTPKVVTKPGHII.PIKAEDVGY.SSSRSDL.VIQRNPKRITTRH.K..K
RetrocopyQTPIGSTWNTQRAFQKLTTPKVVTKPGHIIKPIKAEDVGYQSSSRSDLPVIQRNPKRITTRHNKEEK

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 11 .67 RPM 13 .26 RPM
bodymap2_adrenal 11 .42 RPM 20 .24 RPM
bodymap2_brain 10 .50 RPM 9 .63 RPM
bodymap2_breast 15 .62 RPM 11 .73 RPM
bodymap2_colon 14 .37 RPM 26 .01 RPM
bodymap2_heart 10 .30 RPM 5 .63 RPM
bodymap2_kidney 18 .94 RPM 10 .73 RPM
bodymap2_liver 8 .79 RPM 7 .61 RPM
bodymap2_lung 7 .33 RPM 7 .28 RPM
bodymap2_lymph_node 12 .66 RPM 11 .71 RPM
bodymap2_ovary 24 .12 RPM 25 .89 RPM
bodymap2_prostate 13 .48 RPM 24 .53 RPM
bodymap2_skeletal_muscle 5 .93 RPM 17 .99 RPM
bodymap2_testis 13 .22 RPM 12 .95 RPM
bodymap2_thyroid 25 .61 RPM 21 .03 RPM
bodymap2_white_blood_cells 21 .38 RPM 20 .20 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_29 was not detected

EST - click to see more details

18 EST(s) were mapped to retro_hsap_29 retrocopy
EST ID Start End Identity Match Mis-match Score
AA824593 52603289 52603793 99.7 502 2 500
AL711178 52604164 52604695 99.5 528 3 525
AU141779 52603788 52604518 99.2 728 1 725
AW291601 52603347 52603624 100 277 0 277
AW501110 52603062 52603483 100 421 0 421
BE762879 52604099 52604422 99.7 322 1 321
BF431420 52603318 52603778 99.6 457 2 454
BF756763 52603118 52603529 98.3 407 2 400
BF805361 52603952 52604393 98.5 439 1 434
BG471872 52604107 52604580 98.4 472 1 468
BM144786 52603273 52603666 98.5 379 5 371
BM993493 52603020 52603666 100 645 0 645
BP193244 52603108 52603689 96.8 565 15 547
BP256572 52603688 52604271 99.9 581 1 579
BP380599 52603291 52603919 97.9 604 8 594
CN387730 52603167 52603869 99.6 702 0 701
CN387731 52602963 52603367 99.8 403 1 402
CV570026 52602864 52603462 99.7 596 2 594

TSS - click to see more details

No TSS is located nearby retro_hsap_29 retrocopy 5' end.

Lab - click to see more details

retro_hsap_29 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_29 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_824
Gorilla gorilla retro_ggor_163
Parental genes homology:
Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000136712 retrocopies
retro_btau_133, retro_btau_1706,
Cavia porcellus ENSCPOG000000142312 retrocopies
retro_cpor_1272, retro_cpor_242,
Dasypus novemcinctus ENSDNOG000000021801 retrocopy
retro_dnov_1479,
Homo sapiens ENSG00000156697 1 retrocopy
retro_hsap_29 ,
Gorilla gorilla ENSGGOG000000149301 retrocopy
retro_ggor_163,
Loxodonta africana ENSLAFG000000166531 retrocopy
retro_lafr_110,
Myotis lucifugus ENSMLUG000000019842 retrocopies
retro_mluc_1643, retro_mluc_308,
Macaca mulatta ENSMMUG000000207001 retrocopy
retro_mmul_35,
Mus musculus ENSMUSG000000637851 retrocopy
retro_mmus_261,
Nomascus leucogenys ENSNLEG000000152581 retrocopy
retro_nleu_2091,
Procavia capensis ENSPCAG000000060701 retrocopy
retro_pcap_127,
Pan troglodytes ENSPTRG000000222621 retrocopy
retro_ptro_824,
Tarsius syrichta ENSTSYG000000094151 retrocopy
retro_tsyr_2104,
Tursiops truncatus ENSTTRG000000037941 retrocopy
retro_ttru_1687,

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 = 18.56 RPM Legend:


Library Retrogene expression
CEU_NA11831 8 .13 RPM
CEU_NA11843 5 .00 RPM
CEU_NA11930 13 .82 RPM
CEU_NA12004 6 .72 RPM
CEU_NA12400 6 .38 RPM
CEU_NA12751 16 .27 RPM
CEU_NA12760 10 .06 RPM
CEU_NA12827 8 .21 RPM
CEU_NA12872 14 .45 RPM
CEU_NA12873 11 .90 RPM
FIN_HG00183 8 .70 RPM
FIN_HG00277 11 .39 RPM
FIN_HG00315 10 .76 RPM
FIN_HG00321 11 .82 RPM
FIN_HG00328 9 .94 RPM
FIN_HG00338 9 .03 RPM
FIN_HG00349 8 .91 RPM
FIN_HG00375 12 .76 RPM
FIN_HG00377 9 .53 RPM
FIN_HG00378 16 .94 RPM
GBR_HG00099 15 .90 RPM
GBR_HG00111 6 .47 RPM
GBR_HG00114 7 .73 RPM
GBR_HG00119 11 .76 RPM
GBR_HG00131 17 .45 RPM
GBR_HG00133 10 .85 RPM
GBR_HG00134 14 .83 RPM
GBR_HG00137 5 .86 RPM
GBR_HG00142 14 .39 RPM
GBR_HG00143 11 .65 RPM
TSI_NA20512 4 .78 RPM
TSI_NA20513 17 .80 RPM
TSI_NA20518 12 .52 RPM
TSI_NA20532 12 .01 RPM
TSI_NA20538 12 .35 RPM
TSI_NA20756 10 .65 RPM
TSI_NA20765 17 .20 RPM
TSI_NA20771 13 .96 RPM
TSI_NA20786 11 .64 RPM
TSI_NA20798 12 .91 RPM
YRI_NA18870 12 .66 RPM
YRI_NA18907 13 .66 RPM
YRI_NA18916 12 .48 RPM
YRI_NA19093 8 .67 RPM
YRI_NA19099 12 .06 RPM
YRI_NA19114 15 .02 RPM
YRI_NA19118 11 .37 RPM
YRI_NA19213 18 .56 RPM
YRI_NA19214 16 .18 RPM
YRI_NA19223 16 .47 RPM

Indel association:

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





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