RetrogeneDB ID: retro_sscr_480

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 15:144882560..144883108(+)
• Located in intron of: ENSSSCG00000016261

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNPNAT1
• Ensembl ID: ENSSSCG00000005040
• Aliases: None
• Description: glucosamine-phosphate N-acetyltransferase 1 [Source:HGNC Symbol;Acc:19980]

Sequence

>retro_sscr_480
ATGAAACCTGATGAAAGGCCCCTCTTTGGCCCAAGTCTGCTCAAAGAAGTGGACTGGAGTCAGAATACAGCTACATTTTC
TCCAGCCACTTCCCCCACACATCCTGGAGAAGGTCTGGTTTTGAGGCTTCTTTGTACTGCTGATTTCAATAGAGGTTTTT
TTAAGGTACTAGGTCAGCCGACAGGGACCGGAGTTGTTAACCCGGAACAATTTATGAAATCTTTGGAGCACATGGAGAGA
TCTGGGGACTCTGATGCTACTGTCGTAGAAGATGTGACTCCAGGACAGAGCGTTGCTACAGCAGCTCTGATGACAGAGCA
TAAATCATCCATTCTTGTGCGAAGAGCGGAAGAGTAGATGTTGCTATTAGTGATGAATGCAGAGGAAAGCAGCTTGGCAA
ATTGTTATTATCCCCCCTTACTTTGCTAAGCAAGAACCTGGACTGTTATAAGATTACCCTTGAATGCCTACCACAGAGTG
TTGGCTTCTACAGAAAGTTTGGATAGACAGTATCTGAAGAAAACTACACATGGAGGCAGTTTCTAAAG

Alignment

ORF - retro_sscr_480 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.16 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKPDETPLFDPSLLKEVDWSQNTATFSPAISPTHPGEGLVLRPLCTADLNRGFFKVLGQLTETGVVNPEQ
          MKPDE.PLF.PSLLKEVDWSQNTATFSPA.SPTHPGEGLVLR.LCTAD.NRGFFKVLGQ.T.TGVVNPEQ
Retrocopy MKPDERPLFGPSLLKEVDWSQNTATFSPATSPTHPGEGLVLRLLCTADFNRGFFKVLGQPTGTGVVNPEQ

Parental  FMKSFEHMKKSGDYYVTVVEDVTLGQIVATATLIIEHK-FIHSCAKRGRVEDVVVSDECRGKQLGKLLLS
          FMKS.EHM..SGD...TVVEDVT.GQ.VATA.L..EHK..IHSCAK.GRV.DV..SDECRGKQLGKLLLS
Retrocopy FMKSLEHMERSGDSDATVVEDVTPGQSVATAALMTEHK<IIHSCAKSGRV-DVAISDECRGKQLGKLLLS

Parental  TLTLLSKKLNCYKITLECLPQNVGFYKKFGYTVSEENYMCRRFLK
          .LTLLSK.L.CYKITLECLPQ.VGFY.KFG.TVSEENY..R.FLK
Retrocopy PLTLLSKNLDCYKITLECLPQSVGFYRKFG*TVSEENYTWRQFLK

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
SRP014902_placenta	0.00 RPM	3.45 RPM
SRP014902_testis	0.00 RPM	16.83 RPM
SRP018288_heart	0.05 RPM	11.16 RPM
SRP018288_kidney	0.20 RPM	23.44 RPM
SRP018288_liver	0.16 RPM	72.44 RPM
SRP018288_lung	0.20 RPM	10.69 RPM
SRP018856_adipose	0.00 RPM	19.06 RPM
SRP035408_brain	0.00 RPM	6.86 RPM
SRP035408_liver	0.00 RPM	52.14 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_480 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_480 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_480 has 0 orthologous retrocopies within eutheria group .

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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,