RetrogeneDB ID: retro_hsap_14

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:40235373..40236927(-)
• Located in intron of: ENSG00000116985

Retrocopy information

• Ensembl ID: ENSG00000198754
• Aliases: OXCT2, SCOTT
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: OXCT1
• Ensembl ID: ENSG00000083720
• Aliases: OXCT1, OXCT, SCOT
• Description: 3-oxoacid CoA transferase 1 [Source:HGNC Symbol;Acc:8527]

Sequence

>retro_hsap_14
ATGGCGGCGCTGCGGCTCCTGGCGTCAGTGCTCGGGCGCGGGGTCCCCGCCGGCGGCTCAGGGCTCGCGCTGTCCCAGGG
CTGCGCCCGCTGCTTTGCCACCAGTCCCCGGCTCCGTGCCAAGTTCTACGCGGACCCGGTGGAGATGGTGAAGGACATCT
CTGACGGGGCGACCGTCATGATCGGGGGCTTCGGGCTCTGCGGGATCCCCGAGAACCTGATCGCCGCGCTGCTCAGGACC
CGCGTGAAAGACCTGCAGGTGGTCAGCAGCAACGTGGGCGTGGAGGACTTCGGCCTGGGCCTCCTGCTGGCCGCCAGGCA
GGTCCGTCGCATCGTCTGTTCCTACGTGGGCGAGAACACCCTGTGCGAGAGCCAGTACCTGGCAGGAGAGCTGGAGCTGG
AGCTCACGCCCCAGGGCACCCTGGCCGAGCGCATCCGCGCGGGGGGCGCCGGGGTGCCCGCCTTCTACACCCCCACGGGC
TACGGGACCCTGGTCCAGGAAGGGGGCGCCCCCATCCGCTACACCCCGGACGGCCACCTGGCGCTCATGAGCCAGCCCCG
AGAGGTGAGGGAGTTCAACGGCGACCACTTCCTTTTGGAGCGCGCCATCCGGGCAGACTTCGCCCTGGTGAAAGGGTGGA
AGGCCGACCGGGCAGGAAACGTGGTCTTCAGGAGAAGCGCCCGCAATTTCAACGTGCCCATGTGCAAAGCTGCAGACGTC
ACGGCGGTGGAGGTGGAAGAGATCGTGGAGGTGGGGGCTTTCCCCCCAGAAGACATCCACGTTCCTAACATTTATGTAGA
TCGCGTGATAAAGGGGCAGAAATACGAGAAACGAATTGAGCGCTTAACGATCCTGAAAGAGGAAGATGGAGACGCTGGAA
AGGAAGAGGACGCCAGGACGCGCATCATCAGACGCGCAGCTCTGGAATTTGAGGACGGCATGTACGCCAATCTGGGCATA
GGCATCCCCCTGCTGGCCAGCAACTTCATCAGTCCCAGCATGACTGTCCATCTTCACAGTGAGAACGGGATCCTGGGCCT
GGGCCCGTTTCCCACGGAAGATGAGGTGGATGCCGACCTCATCAATGCAGGCAAGCAGACGGTCACGGTGCTTCCCGGGG
GCTGCTTCTTCGCCAGCGACGACTCCTTCGCCATGATCCGAGGGGGACACATCCAACTAACCATGCTTGGAGCCATGCAG
GTTTCCAAATACGGCGACCTGGCGAACTGGATGATCCCTGGCAAGAAGGTGAAAGGCATGGGCGGTGCCATGGACTTGGT
GTCCAGTCAGAAGACCAGAGTGGTGGTCACCATGCAGCACTGCACAAAGGACAACACCCCCAAGATCATGGAGAAATGCA
CCATGCCGCTGACCGGGAAGCGGTGCGTGGACCGCATCATCACCGAGAAGGCCGTGTTTGACGTGCACAGGAAGAAAGAG
CTGACGCTGAGGGAGCTCTGGGAGGGCCTGACGGTGGACGACATCAAAAAGAGCACGGGGTGTGCCTTTGCTGTGTCCCC
GAACCTCAGGCCCATGCAGCAGGTGGCACCCTGA

Alignment

ORF - retro_hsap_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.37 %
• Parental protein coverage: 99.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAALKLLSSGLRLCASARGSGATWYKGCVCSFSTSAHRHTKFYTDPVEAVKDIPDGATVLVGGFGLCGIP
          MAAL.LL.S.L.....A.GSG.....GC...F.TS.....KFY.DPVE.VKDI.DGATV..GGFGLCGIP
Retrocopy MAALRLLASVLGRGVPAGGSGLALSQGCARCFATSPRLRAKFYADPVEMVKDISDGATVMIGGFGLCGIP

Parental  ENLIDALLKTGVKGLTAVSNNAGVDNFGLGLLLRSKQIKRMVSSYVGENAEFERQYLSGELEVELTPQGT
          ENLI.ALL.T.VK.L..VS.N.GV..FGLGLLL...Q..R.V.SYVGEN...E.QYL.GELE.ELTPQGT
Retrocopy ENLIAALLRTRVKDLQVVSSNVGVEDFGLGLLLAARQVRRIVCSYVGENTLCESQYLAGELELELTPQGT

Parental  LAERIRAGGAGVPAFYTPTGYGTLVQEGGSPIKYNKDGSVAIASKPREVREFNGQHFILEEAITGDFALV
          LAERIRAGGAGVPAFYTPTGYGTLVQEGG.PI.Y..DG..A..S.PREVREFNG.HF.LE.AI..DFALV
Retrocopy LAERIRAGGAGVPAFYTPTGYGTLVQEGGAPIRYTPDGHLALMSQPREVREFNGDHFLLERAIRADFALV

Parental  KAWKADRAGNVIFRKSARNFNLPMCKAAETTVVEVEEIVDIGAFAPEDIHIPQIYVHRLIKGEKYEKRIE
          K.WKADRAGNV.FR.SARNFN.PMCKAA..T.VEVEEIV..GAF.PEDIH.P.IYV.R.IKG.KYEKRIE
Retrocopy KGWKADRAGNVVFRRSARNFNVPMCKAADVTAVEVEEIVEVGAFPPEDIHVPNIYVDRVIKGQKYEKRIE

Parental  RLSIRKEGDGEAKSAKPGDDVRERIIKRAALEFEDGMYANLGIGIPLLASNFISPNITVHLQSENGVLGL
          RL.I.KE.DG.A.......D.R.RII.RAALEFEDGMYANLGIGIPLLASNFISP..TVHL.SENG.LGL
Retrocopy RLTILKEEDGDAGKE---EDARTRIIRRAALEFEDGMYANLGIGIPLLASNFISPSMTVHLHSENGILGL

Parental  GPYPRQHEADADLINAGKETVTILPGASFFSSDESFAMIRGGHVDLTMLGAMQVSKYGDLANWMIPGKMV
          GP.P...E.DADLINAGK.TVT.LPG..FF.SD.SFAMIRGGH..LTMLGAMQVSKYGDLANWMIPGK.V
Retrocopy GPFPTEDEVDADLINAGKQTVTVLPGGCFFASDDSFAMIRGGHIQLTMLGAMQVSKYGDLANWMIPGKKV

Parental  KGMGGAMDLVSSAKTKVVVTMEHSAKGNAHKIMEKCTLPLTGKQCVNRIITEKAVFDVDKKKGLTLIELW
          KGMGGAMDLVSS.KT.VVVTM.H..K.N..KIMEKCT.PLTGK.CV.RIITEKAVFDV..KK.LTL.ELW
Retrocopy KGMGGAMDLVSSQKTRVVVTMQHCTKDNTPKIMEKCTMPLTGKRCVDRIITEKAVFDVHRKKELTLRELW

Parental  EGLTVDDVQKSTGCDFAVSPKLMPMQQIA
          EGLTVDD..KSTGC.FAVSP.L.PMQQ.A
Retrocopy EGLTVDDIKKSTGCAFAVSPNLRPMQQVA

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	0.08 RPM	27.17 RPM
bodymap2_adrenal	0.41 RPM	35.96 RPM
bodymap2_brain	0.49 RPM	183.25 RPM
bodymap2_breast	0.00 RPM	110.66 RPM
bodymap2_colon	0.14 RPM	43.95 RPM
bodymap2_heart	0.18 RPM	247.43 RPM
bodymap2_kidney	0.00 RPM	69.49 RPM
bodymap2_liver	0.06 RPM	1.03 RPM
bodymap2_lung	0.05 RPM	12.38 RPM
bodymap2_lymph_node	0.11 RPM	28.80 RPM
bodymap2_ovary	0.33 RPM	29.40 RPM
bodymap2_prostate	0.19 RPM	51.49 RPM
bodymap2_skeletal_muscle	0.00 RPM	29.79 RPM
bodymap2_testis	7.18 RPM	44.17 RPM
bodymap2_thyroid	0.26 RPM	71.75 RPM
bodymap2_white_blood_cells	0.00 RPM	28.59 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_14 was not detected

EST

1 EST(s) were mapped to retro_hsap_14 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
HY047427	40235455	40235865	99.6	405	2	403

TSS

No TSS is located nearby retro_hsap_14 retrocopy 5' end.

Lab

retro_hsap_14 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_14 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_336

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033186	2 retrocopies	retro_btau_1243, retro_btau_1302,
Dipodomys ordii	ENSDORG00000016318	1 retrocopy	retro_dord_282,
Equus caballus	ENSECAG00000018312	1 retrocopy	retro_ecab_511,
Homo sapiens	ENSG00000083720	1 retrocopy	retro_hsap_14 ,
Gorilla gorilla	ENSGGOG00000025087	1 retrocopy	retro_ggor_378,
Myotis lucifugus	ENSMLUG00000009431	1 retrocopy	retro_mluc_194,
Nomascus leucogenys	ENSNLEG00000016656	1 retrocopy	retro_nleu_2438,
Oryctolagus cuniculus	ENSOCUG00000009231	1 retrocopy	retro_ocun_672,
Otolemur garnettii	ENSOGAG00000009909	2 retrocopies	retro_ogar_2773, retro_ogar_2781,
Pongo abelii	ENSPPYG00000015428	2 retrocopies	retro_pabe_336, retro_pabe_478,
Pan troglodytes	ENSPTRG00000016829	1 retrocopy	retro_ptro_140,
Rattus norvegicus	ENSRNOG00000043094	2 retrocopies	retro_rnor_2177, retro_rnor_2256,
Ictidomys tridecemlineatus	ENSSTOG00000008271	1 retrocopy	retro_itri_747,
Tarsius syrichta	ENSTSYG00000013641	1 retrocopy	retro_tsyr_1455,
Tursiops truncatus	ENSTTRG00000004331	1 retrocopy	retro_ttru_875,
Vicugna pacos	ENSVPAG00000002550	1 retrocopy	retro_vpac_556,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.79 RPM
CEU_NA11843	0.91 RPM
CEU_NA11930	1.21 RPM
CEU_NA12004	2.85 RPM
CEU_NA12400	0.39 RPM
CEU_NA12751	1.60 RPM
CEU_NA12760	0.81 RPM
CEU_NA12827	0.28 RPM
CEU_NA12872	1.85 RPM
CEU_NA12873	1.24 RPM
FIN_HG00183	0.88 RPM
FIN_HG00277	0.59 RPM
FIN_HG00315	0.83 RPM
FIN_HG00321	1.63 RPM
FIN_HG00328	1.66 RPM
FIN_HG00338	1.34 RPM
FIN_HG00349	1.14 RPM
FIN_HG00375	2.40 RPM
FIN_HG00377	2.27 RPM
FIN_HG00378	0.57 RPM
GBR_HG00099	0.46 RPM
GBR_HG00111	1.20 RPM
GBR_HG00114	2.50 RPM
GBR_HG00119	1.20 RPM
GBR_HG00131	0.75 RPM
GBR_HG00133	0.46 RPM
GBR_HG00134	0.44 RPM
GBR_HG00137	1.59 RPM
GBR_HG00142	0.89 RPM
GBR_HG00143	0.73 RPM
TSI_NA20512	2.03 RPM
TSI_NA20513	0.99 RPM
TSI_NA20518	2.08 RPM
TSI_NA20532	0.51 RPM
TSI_NA20538	2.12 RPM
TSI_NA20756	1.37 RPM
TSI_NA20765	0.95 RPM
TSI_NA20771	0.48 RPM
TSI_NA20786	0.84 RPM
TSI_NA20798	1.34 RPM
YRI_NA18870	0.44 RPM
YRI_NA18907	1.35 RPM
YRI_NA18916	1.18 RPM
YRI_NA19093	1.04 RPM
YRI_NA19099	1.01 RPM
YRI_NA19114	1.21 RPM
YRI_NA19118	1.24 RPM
YRI_NA19213	1.15 RPM
YRI_NA19214	0.81 RPM
YRI_NA19223	0.16 RPM

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Indel association:

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