RetrogeneDB ID: retro_sscr_281

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 11:37257612..37258294(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDHA1
• Ensembl ID: ENSSSCG00000023643
• Aliases: None
• Description: pyruvate dehydrogenase (lipoamide) alpha 1 [Source:HGNC Symbol;Acc:8806]

Sequence

>retro_sscr_281
CATGGTTTTCACTTTACTCATGGACTTTCTGTGAAAGAAATTCTTGCAGAGTTTATAAGATGAATAGGAGGTTGTGCTAA
AGGAAAAGAAAGATCCATACACATATACGCCAAGAATTTCTATGGGAGCAATGGCATCTTGGGAGCTCAGGTGACTCTGG
GGGCTGGGCTTGCTTTGGCCTGTAAGTATAATGGAAAAAATGAGGTCTGTTTGACTTCGTATGGCAATGGCACTGCTAAT
GAGGATCAGGTATACAAAGCTGACAATATGGCAGCTTTGTGGAAATTACCTTGTGTTTTCAACTTTGAGAATAACCACTG
TGGGATGGAAACATCTGTGGAGAGAGCAGCAGCCATCACTGACTACTACAAGAGAGACAACTTCATTCTGGGCTGAGAGT
AGATGGAATGGATATCCTGAGTGTCTGGGAGGCCACAGGGTTTGCAGCTTCCTATTGTAGATCAGGAAAGGGGAACATAC
TGACGGAGCTGCAGACTTACCATTACCATGGGCATATGAGTGATCCTGGTGTCAGTTATGGTACCTGAGAAGAAATTCAG
GAAATAGGAAGAGGGACCCTATCATTGTTCTCAAGGATAGGATGGTGAACAGCAGTCTTATCAGTGTTGAAGAATTAAAC
AAAATTGATGTTGAAGTGAGGAAAGAAATTGAGGATGCTGCG

Alignment

ORF - retro_sscr_281 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.14 %
• Parental protein coverage: 58.97 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HGFTFTRGLSVREILAELTGRRGGCGKGKGGSMHMYAKNFYGGNGIVGAQVPLGAGIALACKYNGKDEVC
          HGF.FT.GLSV.EILAE.....GGC.KGK..S.H.YAKNFYG.NGI.GAQV.LGAG.ALACKYNGK.EVC
Retrocopy HGFHFTHGLSVKEILAEFIR*IGGCAKGKERSIHIYAKNFYGSNGILGAQVTLGAGLALACKYNGKNEVC

Parental  LTLYGDGAANQGQIFEAYNMAALWKLPCVFICENNRYGMGTSVERAAASTDYYKRGDFI-PGLRVDGMDI
          LT.YG.G.AN..Q...A.NMAALWKLPCVF..ENN..GM.TSVERAAA.TDYYKR..FI..GLRVDGMDI
Retrocopy LTSYGNGTANEDQVYKADNMAALWKLPCVFNFENNHCGMETSVERAAAITDYYKRDNFI<SGLRVDGMDI

Parental  LCVREATRFAAAYCRSGKGPILMELQTYRYHGHSMSDPGVSYRTREEIQEV-RSKSDPIMLLKDRMVNSN
          L.V.EAT.FAA.YCRSGKG.IL.ELQTY.YHGH.MSDPGVSY.T.EEIQE..R.....I..LKDRMVNS.
Retrocopy LSVWEATGFAASYCRSGKGNILTELQTYHYHGH-MSDPGVSYGT*EEIQEI<RKRDPIIV-LKDRMVNSS

Parental  LASVEELKEIDVEVRKEIEDAA
          L.SVEEL..IDVEVRKEIEDAA
Retrocopy LISVEELNKIDVEVRKEIEDAA

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	28.67 RPM
SRP014902_testis	0.00 RPM	69.87 RPM
SRP018288_heart	0.00 RPM	888.93 RPM
SRP018288_kidney	0.00 RPM	1343.52 RPM
SRP018288_liver	0.00 RPM	173.34 RPM
SRP018288_lung	0.00 RPM	86.35 RPM
SRP018856_adipose	0.00 RPM	671.62 RPM
SRP035408_brain	0.00 RPM	105.06 RPM
SRP035408_liver	0.00 RPM	161.16 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_281 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_281 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_281 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016730	1 retrocopy	retro_amel_400,
Bos taurus	ENSBTAG00000019852	2 retrocopies	retro_btau_100, retro_btau_1807,
Callithrix jacchus	ENSCJAG00000005496	2 retrocopies	retro_cjac_2414, retro_cjac_27,
Dipodomys ordii	ENSDORG00000011848	1 retrocopy	retro_dord_35,
Equus caballus	ENSECAG00000001964	1 retrocopy	retro_ecab_21,
Erinaceus europaeus	ENSEEUG00000005485	1 retrocopy	retro_eeur_580,
Homo sapiens	ENSG00000131828	1 retrocopy	retro_hsap_41,
Gorilla gorilla	ENSGGOG00000013574	1 retrocopy	retro_ggor_59,
Myotis lucifugus	ENSMLUG00000012932	2 retrocopies	retro_mluc_2363, retro_mluc_323,
Macaca mulatta	ENSMMUG00000017336	1 retrocopy	retro_mmul_123,
Mustela putorius furo	ENSMPUG00000003269	1 retrocopy	retro_mputfur_812,
Mus musculus	ENSMUSG00000031299	2 retrocopies	retro_mmus_63, retro_mmus_631,
Nomascus leucogenys	ENSNLEG00000009805	1 retrocopy	retro_nleu_74,
Oryctolagus cuniculus	ENSOCUG00000014748	1 retrocopy	retro_ocun_264,
Pongo abelii	ENSPPYG00000020171	1 retrocopy	retro_pabe_129,
Pan troglodytes	ENSPTRG00000021717	1 retrocopy	retro_ptro_79,
Pteropus vampyrus	ENSPVAG00000005420	1 retrocopy	retro_pvam_1306,
Sarcophilus harrisii	ENSSHAG00000015375	1 retrocopy	retro_shar_84,
Sus scrofa	ENSSSCG00000023643	2 retrocopies	retro_sscr_1015, retro_sscr_281 ,
Ictidomys tridecemlineatus	ENSSTOG00000015433	1 retrocopy	retro_itri_1529,
Tupaia belangeri	ENSTBEG00000014313	1 retrocopy	retro_tbel_3327,
Tursiops truncatus	ENSTTRG00000000660	1 retrocopy	retro_ttru_1427,