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 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]

Sequence

>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

Alignment

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:

Parental  MTANRLAESLLALSQQEELADLPKDYLLSESEDEGDNDGERKHQKLLEAISSLDGKNRRKLAERSEASLK
          M..N..AE.L.ALS.QEEL.DLPK.Y.LSE.EDEGD.DGERKHQKLLEAI.SLDGKNRRKLAERSEASLK
Retrocopy MNVNQVAENL-ALSHQEELVDLPKNYPLSENEDEGDSDGERKHQKLLEAIISLDGKNRRKLAERSEASLK

Parental  VSEFNVSSEGSGEKLVLADLLEPVKTSSSLATVKKQLSRVKSKKTVELPLNKEEIERIHREVAFNKTAQV
          VSEF.VSSEGSGEKL.LADLLEPVKTSSSLATVKKQL.RVKSKK.VELPLNKE.IE.IHREVAF.KT.QV
Retrocopy VSEFSVSSEGSGEKLGLADLLEPVKTSSSLATVKKQLNRVKSKKVVELPLNKEKIEQIHREVAFSKTSQV

Parental  LSKWDPVVLKNRQAEQLVFPLEKEEPAIAPIEHVLSGWKARTPLEQEIFNLLHKNKQPVTDPLLTPVEKA
          LSKWDP..LKN.QAEQLVFPL.KE.PAIAPIEH.LSGWKARTPLEQEIFNLLHKNKQPVTDPLLTP.EKA
Retrocopy LSKWDPIILKNQQAEQLVFPLGKEQPAIAPIEHALSGWKARTPLEQEIFNLLHKNKQPVTDPLLTPMEKA

Parental  SLRAMSLEEAKMRRAELQRARALQSYYEAKARREKKIKSKKYHKVVKKGKAKKALKEFEQLRKVNPAAAL
          SL.AMSLEEAKM.RAELQRARALQSYYEAKAR.EKKIKSKKYHKVVKKGKAKKALKEFEQL.KVNP..AL
Retrocopy SLQAMSLEEAKMHRAELQRARALQSYYEAKARKEKKIKSKKYHKVVKKGKAKKALKEFEQLQKVNPTVAL

Parental  EELEKIEKARMMERMSLKHQNSGKWAKSKAIMAKYDLEARQAMQEQLSKNKELTQKLQVASESEEEEGGT
          EE.EKIE.ARMMERMSLKHQNSGKWAKSKAIMAKYDLEARQAMQEQL.KNKELTQKLQVASESEEEEGGT
Retrocopy EEMEKIENARMMERMSLKHQNSGKWAKSKAIMAKYDLEARQAMQEQLAKNKELTQKLQVASESEEEEGGT

Parental  EDVEELLVPDVVNEVQMNADGPNPWMLRSCTSDTKEAATQEDPEQLPELEAHGVSESEGEERPVAEEEIL
          E.VEELLVP.V.NEVQMN.DGPNPWM.RSCTSDTKEAATQEDPEQ.PEL.AH.VS.SE.EERPVAEEEIL
Retrocopy E-VEELLVPHVANEVQMNVDGPNPWMFRSCTSDTKEAATQEDPEQVPELAAHEVSASEAEERPVAEEEIL

Parental  LREFEERRSLRKRSELSQDAEPAGSQETKDSGSQEVLSELRVLSQKLKENHQSRKQKASSEGTIPQVQRE
          LREFEER.SLRKRSEL.QDAEPA.SQETKDS.SQEVLSELR.LSQKLKE.HQSRKQKASSEGT.PQVQRE
Retrocopy LREFEERQSLRKRSELNQDAEPASSQETKDSSSQEVLSELRALSQKLKEKHQSRKQKASSEGTVPQVQRE

Parental  EPAPEEEEPLLLQRPERVQTLEELEELGKEECFQNKELPRPVLEGQQSERTPNNRPDAPKEKKKKEQMID
          EPAPEE.EPLLLQR.ERVQTLEELEELGKE.CFQNKELPRPVLEGQQSERTPNNRPDAPKEKK.KEQ.I.
Retrocopy EPAPEEAEPLLLQRSERVQTLEELEELGKEDCFQNKELPRPVLEGQQSERTPNNRPDAPKEKKEKEQLIN

Parental  LQNLLTTQSPSVKSLAVPT-IEELEDEEERNHRQMIKEAFAGDDVIRDFLKEKREAVEASKPKDVDLTLP
          LQN.LTTQSPSV.SLAVPT.IEELEDEEER..RQMIKEAFAGDDVIRDFLKEKREAVEASKPKDVDLTLP
Retrocopy LQNFLTTQSPSVRSLAVPTIIEELEDEEERDQRQMIKEAFAGDDVIRDFLKEKREAVEASKPKDVDLTLP

Parental  GWGEWGGVGLKPSAKKRRRFLIKAPEGPPRKDKNLPNVIINEKRNIHAAAHQVRVLPYPFTHHWQFERTI
          GWGEWGGVGLKPSAKKRR.FLIKAPEGPPRKDKNLPNVII.EKRNIHAAAHQV.VLPYPFTHH.QFERTI
Retrocopy GWGEWGGVGLKPSAKKRRQFLIKAPEGPPRKDKNLPNVIISEKRNIHAAAHQVQVLPYPFTHHRQFERTI

Parental  QTPIGSTWNTQRAFQKLTTPKVVTKPGHIINPIKAEDVGYRSSSRSDLSVIQRNPKRITTRHKKQLK
          QTPIGSTWNTQRAFQKLTTPKVVTKPGHII.PIKAEDVGY.SSSRSDL.VIQRNPKRITTRH.K..K
Retrocopy QTPIGSTWNTQRAFQKLTTPKVVTKPGHIIKPIKAEDVGYQSSSRSDLPVIQRNPKRITTRHNKEEK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

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

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

EST

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

No TSS is located nearby retro_hsap_29 retrocopy 5' end.

Lab

retro_hsap_29 was not experimentally validated.

Homology

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

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013671	2 retrocopies	retro_btau_133, retro_btau_1706,
Cavia porcellus	ENSCPOG00000014231	2 retrocopies	retro_cpor_1272, retro_cpor_242,
Dasypus novemcinctus	ENSDNOG00000002180	1 retrocopy	retro_dnov_1479,
Homo sapiens	ENSG00000156697	1 retrocopy	retro_hsap_29 ,
Gorilla gorilla	ENSGGOG00000014930	1 retrocopy	retro_ggor_163,
Loxodonta africana	ENSLAFG00000016653	1 retrocopy	retro_lafr_110,
Myotis lucifugus	ENSMLUG00000001984	2 retrocopies	retro_mluc_1643, retro_mluc_308,
Macaca mulatta	ENSMMUG00000020700	1 retrocopy	retro_mmul_35,
Mus musculus	ENSMUSG00000063785	1 retrocopy	retro_mmus_261,
Nomascus leucogenys	ENSNLEG00000015258	1 retrocopy	retro_nleu_2091,
Procavia capensis	ENSPCAG00000006070	1 retrocopy	retro_pcap_127,
Pan troglodytes	ENSPTRG00000022262	1 retrocopy	retro_ptro_824,
Tarsius syrichta	ENSTSYG00000009415	1 retrocopy	retro_tsyr_2104,
Tursiops truncatus	ENSTTRG00000003794	1 retrocopy	retro_ttru_1687,