RetrogeneDB ID: retro_hsap_2191

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:190687019..190687556(+)
• Located in intron of: ENSG00000064933

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: GNPNAT1
• Ensembl ID: ENSG00000100522
• Aliases: GNPNAT1, GNPNAT, Gpnat1
• Description: glucosamine-phosphate N-acetyltransferase 1 [Source:HGNC Symbol;Acc:19980]

Sequence

>retro_hsap_2191
ATGAAACCTGATGAAACTCTTATGTTTGACCCAAGTCTACTCGAAGAAGTGGACTGGAGGCAGAATACAGCTACATTTTC
TCCAGCCATTTCCCCAACACATCCTGGAGAAGGCTTGATTTTGTGGCCTCTTTGTACTGCTGACTTAAATAGAGGGTTTT
TTTTTAAGGTATTGGGTCAGCTGATCGAGACTGGAGTTGTCAGCCCTGAACAGTTTATGAAATCTTTTGAGTATATGAAG
AAATCTGGGGATTATGTTACAGTTGTAGAAGATGTGACTCTAGGACAGATTGTTGCTACAGCAACTCTGATAATAGAACA
TAAATTCATCCATTCCTGTGCTAAGAGAGTAAGAGTAGAAGATGTTGTCGTTAGTGATGAATGCAGAGGAAAGCAGCTCG
GCTAATTGTTAGTATCAACCCTTACTTTGCTAAGCAAGAAACTGAACTGTTACAAGATTACCCTTGAATGTCTACCACAA
AATGTTGGTTTCTATAAAAAGTTTGGATATACTGTATCTGAAGAAAACTACATGTGT

Alignment

ORF - retro_hsap_2191 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.22 %
• Parental protein coverage: 97.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKPDETPMFDPSLLKEVDWSQNTATFSPAISPTHPGEGLVLRPLCTADLNRG-FFKVLGQLTETGVVSPE
          MKPDET.MFDPSLL.EVDW.QNTATFSPAISPTHPGEGL.L.PLCTADLNRG...KVLGQL.ETGVVSPE
Retrocopy MKPDETLMFDPSLLEEVDWRQNTATFSPAISPTHPGEGLILWPLCTADLNRGXXXKVLGQLIETGVVSPE

Parental  QFMKSFEHMKKSGDYYVTVVEDVTLGQIVATATLIIEHKFIHSCAKRGRVEDVVVSDECRGKQLGKLLLS
          QFMKSFE.MKKSGD.YVTVVEDVTLGQIVATATLIIEHKFIHSCAKR.RVEDVVVSDECRGKQLG.LL.S
Retrocopy QFMKSFEYMKKSGD-YVTVVEDVTLGQIVATATLIIEHKFIHSCAKRVRVEDVVVSDECRGKQLG*LLVS

Parental  TLTLLSKKLNCYKITLECLPQNVGFYKKFGYTVSEENYMC
          TLTLLSKKLNCYKITLECLPQNVGFYKKFGYTVSEENYMC
Retrocopy TLTLLSKKLNCYKITLECLPQNVGFYKKFGYTVSEENYMC

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	0.12 RPM	23.08 RPM
bodymap2_adrenal	0.25 RPM	20.51 RPM
bodymap2_brain	0.16 RPM	18.33 RPM
bodymap2_breast	0.14 RPM	25.08 RPM
bodymap2_colon	0.00 RPM	22.76 RPM
bodymap2_heart	0.06 RPM	8.79 RPM
bodymap2_kidney	0.00 RPM	34.08 RPM
bodymap2_liver	0.06 RPM	59.67 RPM
bodymap2_lung	0.00 RPM	11.64 RPM
bodymap2_lymph_node	0.00 RPM	17.49 RPM
bodymap2_ovary	0.04 RPM	33.35 RPM
bodymap2_prostate	0.00 RPM	17.75 RPM
bodymap2_skeletal_muscle	0.00 RPM	16.15 RPM
bodymap2_testis	0.94 RPM	28.41 RPM
bodymap2_thyroid	0.15 RPM	17.49 RPM
bodymap2_white_blood_cells	0.00 RPM	13.74 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2191 was not detected

EST

No EST(s) were mapped for retro_hsap_2191 retrocopy.

TSS

No TSS is located nearby retro_hsap_2191 retrocopy 5' end.

Lab

retro_hsap_2191 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2191 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1667
Pongo abelii	retro_pabe_2069

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003459	1 retrocopy	retro_chof_2153,
Callithrix jacchus	ENSCJAG00000007154	3 retrocopies	retro_cjac_1479, retro_cjac_1510, retro_cjac_2749,
Dasypus novemcinctus	ENSDNOG00000018802	2 retrocopies	retro_dnov_1564, retro_dnov_548,
Dipodomys ordii	ENSDORG00000016414	1 retrocopy	retro_dord_393,
Homo sapiens	ENSG00000100522	3 retrocopies	retro_hsap_2191 , retro_hsap_4085, retro_hsap_4116,
Gorilla gorilla	ENSGGOG00000025060	2 retrocopies	retro_ggor_2740, retro_ggor_2762,
Macropus eugenii	ENSMEUG00000003086	1 retrocopy	retro_meug_930,
Microcebus murinus	ENSMICG00000014347	1 retrocopy	retro_mmur_528,
Macaca mulatta	ENSMMUG00000011571	2 retrocopies	retro_mmul_2355, retro_mmul_2371,
Monodelphis domestica	ENSMODG00000014505	1 retrocopy	retro_mdom_1609,
Mus musculus	ENSMUSG00000037722	1 retrocopy	retro_mmus_1799,
Nomascus leucogenys	ENSNLEG00000012510	2 retrocopies	retro_nleu_321, retro_nleu_583,
Oryctolagus cuniculus	ENSOCUG00000007858	1 retrocopy	retro_ocun_194,
Otolemur garnettii	ENSOGAG00000010015	1 retrocopy	retro_ogar_1704,
Ochotona princeps	ENSOPRG00000016136	9 retrocopies	retro_opri_1142, retro_opri_1221, retro_opri_278, retro_opri_312, retro_opri_544, retro_opri_634, retro_opri_831, retro_opri_940, retro_opri_962,
Pongo abelii	ENSPPYG00000005822	1 retrocopy	retro_pabe_2069,
Pan troglodytes	ENSPTRG00000006354	3 retrocopies	retro_ptro_1667, retro_ptro_2770, retro_ptro_2795,
Rattus norvegicus	ENSRNOG00000008641	1 retrocopy	retro_rnor_2051,
Sarcophilus harrisii	ENSSHAG00000005482	1 retrocopy	retro_shar_379,
Sus scrofa	ENSSSCG00000005040	1 retrocopy	retro_sscr_480,
Tupaia belangeri	ENSTBEG00000005538	2 retrocopies	retro_tbel_4657, retro_tbel_593,
Tursiops truncatus	ENSTTRG00000003898	1 retrocopy	retro_ttru_655,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.11 RPM
CEU_NA11843	0.17 RPM
CEU_NA11930	0.16 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.12 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.19 RPM
CEU_NA12872	0.08 RPM
CEU_NA12873	0.10 RPM
FIN_HG00183	0.19 RPM
FIN_HG00277	0.18 RPM
FIN_HG00315	0.11 RPM
FIN_HG00321	0.03 RPM
FIN_HG00328	0.09 RPM
FIN_HG00338	0.04 RPM
FIN_HG00349	0.06 RPM
FIN_HG00375	0.05 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.06 RPM
GBR_HG00099	0.09 RPM
GBR_HG00111	0.04 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.12 RPM
GBR_HG00131	0.17 RPM
GBR_HG00133	0.12 RPM
GBR_HG00134	0.17 RPM
GBR_HG00137	0.08 RPM
GBR_HG00142	0.17 RPM
GBR_HG00143	0.10 RPM
TSI_NA20512	0.08 RPM
TSI_NA20513	0.10 RPM
TSI_NA20518	0.06 RPM
TSI_NA20532	0.51 RPM
TSI_NA20538	0.14 RPM
TSI_NA20756	0.09 RPM
TSI_NA20765	0.19 RPM
TSI_NA20771	0.09 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.06 RPM
YRI_NA18870	0.24 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.11 RPM
YRI_NA19093	0.08 RPM
YRI_NA19099	0.05 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.10 RPM
YRI_NA19213	0.17 RPM
YRI_NA19214	0.07 RPM
YRI_NA19223	0.12 RPM

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Indel association:

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