RetrogeneDB ID: retro_sscr_329

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:113389343..113389630(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PMM2
• Ensembl ID: ENSSSCG00000021236
• Aliases: None
• Description: phosphomannomutase 2 [Source:HGNC Symbol;Acc:9115]

Sequence

>retro_sscr_329
AAAAAAGAAAATATAAGACAGAAATGTGTAGCAGACCTGTTGAATGAGTTTTCTGATAAAGGCCTCATGTTTTCTATAGG
AGGCAAGATCAGGTTGATGTCTTTCCTAATGGCTAGAACAAGAGGTATTTCCTGGGACATGTGTAAAATTATGGTTATAA
GACCATTTCTTTCTTTGGAGACCAAACCATGGCAGGTGGGAATGGCCATGATATCATCTCAGACCTGAGAACTATAGACT
ACACTGAGTCTGGGCCTGCAGACACACACAAGATCTGTGAAGAGATC

Alignment

ORF - retro_sscr_329 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.89 %
• Parental protein coverage: 71.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKENIRQKFVEDLRQEFAGKGLTFSIGGQISF-DVFPDGWDKRYCLGHVEKDGYKTIYFFGDKTMPGGND
          KKENIRQK.V.DL..EF..KGL.FSIGG.I...DVFP.G..KRY.LGHV...GYKTI.FFGD.TM.GGN.
Retrocopy KKENIRQKCVADLLNEFSDKGLMFSIGGKIRL<DVFPNG*NKRYFLGHV*NYGYKTISFFGDQTMAGGNG

Parental  HEIFEDPRTVSYTVTAPEDTRRICQEL
          H.I..D.RT..YT...P.DT..IC.E.
Retrocopy HDIISDLRTIDYTESGPADTHKICEEI

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	39.16 RPM
SRP014902_testis	0.00 RPM	36.07 RPM
SRP018288_heart	0.00 RPM	10.58 RPM
SRP018288_kidney	0.00 RPM	70.33 RPM
SRP018288_liver	0.00 RPM	42.06 RPM
SRP018288_lung	0.00 RPM	46.33 RPM
SRP018856_adipose	0.00 RPM	22.79 RPM
SRP035408_brain	0.00 RPM	16.80 RPM
SRP035408_liver	0.00 RPM	60.71 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_329 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_329 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_329 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_307

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001440	2 retrocopies	retro_btau_1188, retro_btau_307,
Cavia porcellus	ENSCPOG00000000235	1 retrocopy	retro_cpor_810,
Homo sapiens	ENSG00000140650	2 retrocopies	retro_hsap_1869, retro_hsap_1913,
Gorilla gorilla	ENSGGOG00000010124	1 retrocopy	retro_ggor_1399,
Monodelphis domestica	ENSMODG00000005737	1 retrocopy	retro_mdom_285,
Nomascus leucogenys	ENSNLEG00000010062	1 retrocopy	retro_nleu_3062,
Otolemur garnettii	ENSOGAG00000016560	1 retrocopy	retro_ogar_1095,
Pongo abelii	ENSPPYG00000007084	2 retrocopies	retro_pabe_1583, retro_pabe_1584,
Pan troglodytes	ENSPTRG00000007748	2 retrocopies	retro_ptro_1249, retro_ptro_1279,
Sus scrofa	ENSSSCG00000000061	1 retrocopy	retro_sscr_869,
Sus scrofa	ENSSSCG00000021236	1 retrocopy	retro_sscr_329 ,
Tursiops truncatus	ENSTTRG00000014827	2 retrocopies	retro_ttru_1894, retro_ttru_977,