RetrogeneDB ID: retro_sscr_147

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:293663415..293663961(+)
• Located in intron of: ENSSSCG00000005518

Retrocopy information

• Ensembl ID: ENSSSCG00000005519
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GALM
• Ensembl ID: ENSSSCG00000008486
• Aliases: GALM, MUT
• Description: Sus scrofa galactose mutarotase (aldose 1-epimerase) (GALM), mRNA. [Source:RefSeq mRNA;Acc:NM_214406]

Sequence

>retro_sscr_147
GGTGAGTTAAAAGTCTGGGTGACATACACGCTAGATGGCAGGGAGCTCATGGTCAACTCTCAAGCACAGGCCAGTCGGAC
CGCCCCAGTCAATCTGACCAGCCATTCTTATTTCAACCTCGTGGGCCAGGGTTCCCCGAATATATATGACCATGAAGTCA
CTATAGAAGCTGATGCTTTTTTGCCTGCAGATGAAAACCTAATCCCTACAGGAGAAGTTGCTCCAATGCAAGGAGCTGCA
TTTGATCTGAGGAAACCAGCAGAGCTTGGAAAACACCTGCAGGAGTTCCACATCAATGGCTTTGACCACACGTTCCGTCT
GAAGGGATCTAAAGAAAAGCAATTTCGTGTACGGGTCCATCATGCTGGAAGCGGGAGGGTACTGGAAGTGTATACCACCC
AGCCTGGGATCCAGTTTTACACGGGCAACTTCCTGGGTGGCACGCTGAAAGGCCAGACTGGAGCAGTCTGTCCCAAGCAC
TCTGGTTTCTGCCTCGAGACCCAGAACTGGCCCGATACAGTCAATCAGCCCCACTTCCCGTCTGTG

Alignment

ORF - retro_sscr_147 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.26 %
• Parental protein coverage: 53.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GELKVWVTYTLDGGELVVNYRAQASQTTPVNLTNHSYFNLAGQGSPNIYDHEVTIEADAFLPVDETLIPT
          GELKVWVTYTLDG.EL.VN..AQAS.T.PVNLT.HSYFNL.GQGSPNIYDHEVTIEADAFLP.DE.LIPT
Retrocopy GELKVWVTYTLDGRELMVNSQAQASRTAPVNLTSHSYFNLVGQGSPNIYDHEVTIEADAFLPADENLIPT

Parental  GEIAPVQGTAFDLRKPVELGKHLQEFHINGFDHNFCLKRSKEKQFCARVHHAGSGRVLEVYTTQPGIQFY
          GE.AP.QG.AFDLRKP.ELGKHLQEFHINGFDH.F.LK.SKEKQF..RVHHAGSGRVLEVYTTQPGIQFY
Retrocopy GEVAPMQGAAFDLRKPAELGKHLQEFHINGFDHTFRLKGSKEKQFRVRVHHAGSGRVLEVYTTQPGIQFY

Parental  TGNFLDGTLKGKTGAVYPKHSGFCLETQNWPNAVNQPHFPPV
          TGNFL.GTLKG.TGAV.PKHSGFCLETQNWP..VNQPHFP.V
Retrocopy TGNFLGGTLKGQTGAVCPKHSGFCLETQNWPDTVNQPHFPSV

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	14.47 RPM
SRP014902_testis	0.42 RPM	49.22 RPM
SRP018288_heart	0.05 RPM	22.50 RPM
SRP018288_kidney	0.00 RPM	448.89 RPM
SRP018288_liver	0.00 RPM	166.15 RPM
SRP018288_lung	0.20 RPM	65.78 RPM
SRP018856_adipose	0.23 RPM	50.28 RPM
SRP035408_brain	0.06 RPM	25.47 RPM
SRP035408_liver	0.00 RPM	81.67 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_147 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_147 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_147 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000015006	1 retrocopy	retro_meug_2094,
Myotis lucifugus	ENSMLUG00000015685	1 retrocopy	retro_mluc_1049,
Macaca mulatta	ENSMMUG00000008248	1 retrocopy	retro_mmul_761,
Oryctolagus cuniculus	ENSOCUG00000006325	1 retrocopy	retro_ocun_1151,
Sus scrofa	ENSSSCG00000008486	1 retrocopy	retro_sscr_147 ,
Tupaia belangeri	ENSTBEG00000003695	2 retrocopies	retro_tbel_2040, retro_tbel_2771,