RetrogeneDB ID: retro_sscr_373

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:74413443..74414200(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000025515
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PGAM1
• Ensembl ID: ENSSSCG00000010517
• Aliases: None
• Description: phosphoglycerate mutase 1 (brain) [Source:HGNC Symbol;Acc:8888]

Sequence

>retro_sscr_373
GCTGCCTACAAGCTGGTGATGAACCAGCACGGTGAGAGCACGTGGAACCAGAGAACCGCTTCAGCAGCTGGTGCCACACG
GACCTGAGCCCAGCGGGGCACAAGGAGGTGAAGCGCAGCAGGCAGGTGCTGTGAGATGCTGGCTATGAGTTTGACATCTG
CTTCACCTCAGTGAGAAGAGAGCAAATCAGACCCTCTGGACAGTGCTGGATGCCATTAACCAAATGTGGCTGCTAGTGGT
GAGGATCTGGCACCTTAATGAGCGACACTATGGGGGTCTGACTGGCCTCAATAAGGCAGAAACTGCTGCCAAGTATGGCA
AGGCCCAGGTAAAGATCTGGAGGCGCTCCTATGATGTCCCACCACCTCCAATGGAGCCCAACCATCCCTTCTACAGCAAC
ATCAGTAAGGATCGCAGATATGCAGACCTCACTGAGGATCAGCTGCCCTCCTATGAGAGTCTGAAGGACACTATTGCCAG
AGCTCTGCCCTTCTGGAATGAGGAAATAGCTCCCCAGATCAAGGAGGGGAAATGGGTACTGATTGCAGCCCATGGCAGTA
GCCTTCAGGGCATCGTCAAGCATCTGGAGGATTTCTCTGAAGAGGCGATCATGGAGCTGAACCTGCCGACTGGCATTCAC
ACTGTTTATGAATTGGACACGAAGTTGAAGCCCATCAAGCCCATGCAGTTCCTGGGCGATGTAGAGACCGTGCATAAAGC
CATGGAGGCTGTGGCTGCCCAGGGCAAGGCCAAGAAA

Alignment

ORF - retro_sscr_373 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.31 %
• Parental protein coverage: 98.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAYKLVLIRHGESAWNL-ENRFSGWYDADLSPAGHEEAKRGGQALRDAGYEFDICFTSV-QKRAIRTLWT
          AAYKLV...HGES.WN..ENRFS.W...DLSPAGH.E.KR..Q.L.DAGYEFDICFTSV..KRA..TLWT
Retrocopy AAYKLVMNQHGESTWNQ<ENRFSSWCHTDLSPAGHKEVKRSRQVL*DAGYEFDICFTSV<EKRANQTLWT

Parental  VLDAIDQMWLPVVRTWRLNERHYGGLTGLNKAETAAKHGEAQVKIWRRSYDVPPPPMEPDHPFYSNISKD
          VLDAI.QMWL.VVR.W.LNERHYGGLTGLNKAETAAK.G.AQVKIWRRSYDVPPPPMEP.HPFYSNISKD
Retrocopy VLDAINQMWLLVVRIWHLNERHYGGLTGLNKAETAAKYGKAQVKIWRRSYDVPPPPMEPNHPFYSNISKD

Parental  RRYADLTEDQLPSCESLKDTIARALPFWNEEIVPQIKEGKRVLIAAHGNSLRGIVKHLEGLSEEAIMELN
          RRYADLTEDQLPS.ESLKDTIARALPFWNEEI.PQIKEGK.VLIAAHG.SL.GIVKHLE..SEEAIMELN
Retrocopy RRYADLTEDQLPSYESLKDTIARALPFWNEEIAPQIKEGKWVLIAAHGSSLQGIVKHLEDFSEEAIMELN

Parental  LPTGIPIVYELDKNLKPIKPMQFLGDEETVRKAMEAVAAQGKAKK
          LPTGI..VYELD..LKPIKPMQFLGD.ETV.KAMEAVAAQGKAKK
Retrocopy LPTGIHTVYELDTKLKPIKPMQFLGDVETVHKAMEAVAAQGKAKK

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	264.93 RPM
SRP014902_testis	0.14 RPM	172.00 RPM
SRP018288_heart	0.03 RPM	206.69 RPM
SRP018288_kidney	0.10 RPM	234.15 RPM
SRP018288_liver	0.00 RPM	107.46 RPM
SRP018288_lung	0.00 RPM	217.09 RPM
SRP018856_adipose	0.11 RPM	160.27 RPM
SRP035408_brain	0.00 RPM	374.87 RPM
SRP035408_liver	0.00 RPM	271.39 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_373 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_373 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_373 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 69 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016575	1 retrocopy	retro_cjac_370,
Cavia porcellus	ENSCPOG00000006844	4 retrocopies	retro_cpor_158, retro_cpor_539, retro_cpor_605, retro_cpor_660,
Echinops telfairi	ENSETEG00000002467	1 retrocopy	retro_etel_1595,
Homo sapiens	ENSG00000171314	12 retrocopies	retro_hsap_1048, retro_hsap_1052, retro_hsap_1142, retro_hsap_2235, retro_hsap_2604, retro_hsap_3083, retro_hsap_3488, retro_hsap_4249, retro_hsap_4686, retro_hsap_4821, retro_hsap_885, retro_hsap_913,
Gorilla gorilla	ENSGGOG00000028602	13 retrocopies	retro_ggor_1220, retro_ggor_1500, retro_ggor_1667, retro_ggor_1824, retro_ggor_2061, retro_ggor_2118, retro_ggor_2353, retro_ggor_2849, retro_ggor_3005, retro_ggor_3034, retro_ggor_716, retro_ggor_738, retro_ggor_827,
Loxodonta africana	ENSLAFG00000015979	1 retrocopy	retro_lafr_886,
Macaca mulatta	ENSMMUG00000020027	1 retrocopy	retro_mmul_119,
Monodelphis domestica	ENSMODG00000004242	4 retrocopies	retro_mdom_1342, retro_mdom_1893, retro_mdom_610, retro_mdom_668,
Mustela putorius furo	ENSMPUG00000017045	1 retrocopy	retro_mputfur_1409,
Pongo abelii	ENSPPYG00000002530	9 retrocopies	retro_pabe_1325, retro_pabe_2309, retro_pabe_2554, retro_pabe_2639, retro_pabe_2881, retro_pabe_3389, retro_pabe_3639, retro_pabe_3749, retro_pabe_671,
Pan troglodytes	ENSPTRG00000002807	12 retrocopies	retro_ptro_1082, retro_ptro_1580, retro_ptro_1645, retro_ptro_1755, retro_ptro_2080, retro_ptro_2361, retro_ptro_2889, retro_ptro_2890, retro_ptro_3114, retro_ptro_3238, retro_ptro_634, retro_ptro_714,
Rattus norvegicus	ENSRNOG00000050585	7 retrocopies	retro_rnor_1669, retro_rnor_2241, retro_rnor_2275, retro_rnor_2361, retro_rnor_2568, retro_rnor_691, retro_rnor_703,
Sus scrofa	ENSSSCG00000010517	1 retrocopy	retro_sscr_373 ,
Ictidomys tridecemlineatus	ENSSTOG00000025955	1 retrocopy	retro_itri_1187,
Drosophila melanogaster	FBgn0014869	1 retrocopy	retro_dmel_57,