RetrogeneDB ID: retro_sscr_106

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:50667822..50668120(+)
• Located in intron of: ENSSSCG00000023510

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPE1
• Ensembl ID: ENSSSCG00000016078
• Aliases: None
• Description: heat shock 10kDa protein 1 (chaperonin 10) [Source:HGNC Symbol;Acc:5269]

Sequence

>retro_sscr_106
TCAGGACAGACATTTAGTTACAGTCCTCGTCATTACGACCGAGTATTTATTGAAAGGCGCACAGCCCAAACTTCAACCAA
AGAGGCATTATGCGTCCAGAAAATTCTCAGGGAAAAGTACTGCATGTGACCTGAGTAGCTTCTGAATTGGGCTCTAAAAG
AGAGGGTGAAGAGATATTTAACCAGTTAGCATGAAAGTTGGAAATAAACGTTCTTCTTCCAGAATACCAAGGCAACACAG
TAGTTCTAGATGACAAGGGTTCTTTCTTTTTTGAGCTGGTGACATTCATGGTAAGTAT

Alignment

ORF - retro_sscr_106 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.92 %
• Parental protein coverage: 97.06 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AGQAFRKFLPLFDRVLVERSAAETVTKG-GIMLPEKSQGKVLQATVVAVGSGSKGKGGEI-QPVSVKVGD
          .GQ.F.......DRV..ER..A.T.TK..GIM.PE.SQGKVL..T.VA...GSK..G.EI......K...
Retrocopy SGQTFSYSPRHYDRVFIERRTAQTSTKE<GIMRPENSQGKVLHVT*VASELGSKREGEEIFNQLA*KLEI

Parental  KVLLPEYGGTRVVLDDK-DYFLFRDGDILGKY
          .VLLPEY.G..VVLDDK...FLF..GDI.GKY
Retrocopy NVLLPEYQGNTVVLDDK<GFFLF*AGDIHGKY

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	15.13 RPM
SRP014902_testis	0.00 RPM	131.26 RPM
SRP018288_heart	0.00 RPM	147.37 RPM
SRP018288_kidney	0.00 RPM	329.99 RPM
SRP018288_liver	0.00 RPM	397.54 RPM
SRP018288_lung	0.00 RPM	18.94 RPM
SRP018856_adipose	0.00 RPM	93.50 RPM
SRP035408_brain	0.00 RPM	75.65 RPM
SRP035408_liver	0.00 RPM	187.41 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_106 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_106 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_106 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3664
Pan troglodytes	retro_ptro_2485
Gorilla gorilla	retro_ggor_2476
Sus scrofa	retro_sscr_103

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 90 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004008	1 retrocopy	retro_cjac_254,
Dasypus novemcinctus	ENSDNOG00000013246	27 retrocopies	retro_dnov_1088, retro_dnov_1117, retro_dnov_1214, retro_dnov_1375, retro_dnov_1391, retro_dnov_1405, retro_dnov_1412, retro_dnov_1428, retro_dnov_1445, retro_dnov_1546, retro_dnov_1647, retro_dnov_1652, retro_dnov_1686, retro_dnov_1821, retro_dnov_2176, retro_dnov_2291, retro_dnov_2413, retro_dnov_2569, retro_dnov_2625, retro_dnov_2652, retro_dnov_418, retro_dnov_481, retro_dnov_483, retro_dnov_490, retro_dnov_524, retro_dnov_554, retro_dnov_966,
Homo sapiens	ENSG00000115541	18 retrocopies	retro_hsap_1066, retro_hsap_1152, retro_hsap_1351, retro_hsap_1524, retro_hsap_1646, retro_hsap_1703, retro_hsap_2248, retro_hsap_2402, retro_hsap_2480, retro_hsap_2812, retro_hsap_2813, retro_hsap_3455, retro_hsap_3540, retro_hsap_366, retro_hsap_3664, retro_hsap_4194, retro_hsap_495, retro_hsap_963,
Gorilla gorilla	ENSGGOG00000027944	17 retrocopies	retro_ggor_1051, retro_ggor_117, retro_ggor_1243, retro_ggor_1545, retro_ggor_157, retro_ggor_1676, retro_ggor_1821, retro_ggor_1956, retro_ggor_1957, retro_ggor_1958, retro_ggor_2331, retro_ggor_2391, retro_ggor_2476, retro_ggor_2492, retro_ggor_775, retro_ggor_841, retro_ggor_897,
Macaca mulatta	ENSMMUG00000010491	1 retrocopy	retro_mmul_344,
Procavia capensis	ENSPCAG00000009541	1 retrocopy	retro_pcap_330,
Pongo abelii	ENSPPYG00000025876	1 retrocopy	retro_pabe_179,
Pan troglodytes	ENSPTRG00000012774	17 retrocopies	retro_ptro_1033, retro_ptro_1117, retro_ptro_1152, retro_ptro_1591, retro_ptro_1752, retro_ptro_1907, retro_ptro_1908, retro_ptro_2343, retro_ptro_2406, retro_ptro_2485, retro_ptro_2847, retro_ptro_287, retro_ptro_374, retro_ptro_667, retro_ptro_726, retro_ptro_786, retro_ptro_926,
Sus scrofa	ENSSSCG00000016078	7 retrocopies	retro_sscr_103, retro_sscr_1059, retro_sscr_106 , retro_sscr_1088, retro_sscr_294, retro_sscr_298, retro_sscr_401,