RetrogeneDB ID: retro_sscr_1104

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: GL894759.2:859..1195(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL26L1
• Ensembl ID: ENSSSCG00000016989
• Aliases: None
• Description: ribosomal protein L26-like 1 [Source:HGNC Symbol;Acc:17050]

Sequence

>retro_sscr_1104
AAGTTTAATCCCTTTGTGACTGTCCACCCAAGCACGAACCGTGAAAGGCAACCCAGTGCACCCTCCCGCGTGTGCGGAAA
GATTATGTCTCCCCCTCTTTCCGAAAAGCTGAGACAGGACTATGTTCTCTCCATGCCCATCTGAAAGGATGATGAAGTTC
AGGTTATGCAAGGGCACGACCAAGGGCAGCACATTGGCAAAGTCGTCCAGGTTCACAGGAAGACATATGTCCTCTACATG
GAATGAGGGCAGCGGGAGAAGGCTAAAGGCACGACCGTCCATGTGGGCATTCACCCCAGCGAGGTGGTTATCACTAGACT
GAAACTGGATAATGAC

Alignment

ORF - retro_sscr_1104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.68 %
• Parental protein coverage: 77.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KFNPFVTSDRSKNRKRHFNAPSHVRRKIMSSPLSKELRQKYNVRSMPIRKDDEVQVVRGHYKGQQIGKVV
          KFNPFVT...S.NR.R...APS.V..KIMS.PLS..LRQ.Y.V.SMPI.KDDEVQV..GH..GQ.IGKVV
Retrocopy KFNPFVTVHPSTNRERQPSAPSRVCGKIMSPPLSEKLRQDY-VLSMPI*KDDEVQVMQGHDQGQHIGKVV

Parental  QVYRKKYVIYIERVQREKANGTTVHVGIHPSKVVITRLKLDKD
          QV.RK.YV.Y.E..QREKA.GTTVHVGIHPS.VVITRLKLD.D
Retrocopy QVHRKTYVLYME*GQREKAKGTTVHVGIHPSEVVITRLKLDND

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	22.56 RPM
SRP014902_testis	0.00 RPM	34.51 RPM
SRP018288_heart	0.00 RPM	13.57 RPM
SRP018288_kidney	0.00 RPM	37.92 RPM
SRP018288_liver	0.00 RPM	25.27 RPM
SRP018288_lung	0.00 RPM	19.55 RPM
SRP018856_adipose	0.00 RPM	37.28 RPM
SRP035408_brain	0.00 RPM	53.36 RPM
SRP035408_liver	0.00 RPM	23.37 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1104 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1104 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1104 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 94 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002289	35 retrocopies	retro_dnov_1106, retro_dnov_1147, retro_dnov_1171, retro_dnov_1258, retro_dnov_1304, retro_dnov_1319, retro_dnov_1344, retro_dnov_1381, retro_dnov_1501, retro_dnov_1676, retro_dnov_1819, retro_dnov_1959, retro_dnov_2039, retro_dnov_2041, retro_dnov_2061, retro_dnov_2078, retro_dnov_2103, retro_dnov_2116, retro_dnov_2121, retro_dnov_2287, retro_dnov_2297, retro_dnov_2438, retro_dnov_2545, retro_dnov_2580, retro_dnov_2632, retro_dnov_300, retro_dnov_306, retro_dnov_467, retro_dnov_646, retro_dnov_666, retro_dnov_681, retro_dnov_760, retro_dnov_850, retro_dnov_970, retro_dnov_985,
Felis catus	ENSFCAG00000026949	1 retrocopy	retro_fcat_524,
Homo sapiens	ENSG00000037241	2 retrocopies	retro_hsap_586, retro_hsap_837,
Latimeria chalumnae	ENSLACG00000007599	2 retrocopies	retro_lcha_5, retro_lcha_8,
Microcebus murinus	ENSMICG00000011312	10 retrocopies	retro_mmur_1020, retro_mmur_1144, retro_mmur_313, retro_mmur_327, retro_mmur_346, retro_mmur_412, retro_mmur_471, retro_mmur_623, retro_mmur_72, retro_mmur_75,
Macaca mulatta	ENSMMUG00000003070	1 retrocopy	retro_mmul_676,
Oryctolagus cuniculus	ENSOCUG00000006172	4 retrocopies	retro_ocun_1015, retro_ocun_1224, retro_ocun_354, retro_ocun_845,
Procavia capensis	ENSPCAG00000002246	10 retrocopies	retro_pcap_137, retro_pcap_157, retro_pcap_188, retro_pcap_204, retro_pcap_337, retro_pcap_404, retro_pcap_419, retro_pcap_42, retro_pcap_422, retro_pcap_448,
Pteropus vampyrus	ENSPVAG00000003253	8 retrocopies	retro_pvam_1062, retro_pvam_1208, retro_pvam_122, retro_pvam_353, retro_pvam_688, retro_pvam_71, retro_pvam_769, retro_pvam_877,
Sus scrofa	ENSSSCG00000016989	3 retrocopies	retro_sscr_1104 , retro_sscr_462, retro_sscr_685,
Sus scrofa	ENSSSCG00000028850	9 retrocopies	retro_sscr_261, retro_sscr_363, retro_sscr_426, retro_sscr_427, retro_sscr_471, retro_sscr_485, retro_sscr_508, retro_sscr_609, retro_sscr_736,
Ictidomys tridecemlineatus	ENSSTOG00000026876	1 retrocopy	retro_itri_1141,
Tursiops truncatus	ENSTTRG00000010624	8 retrocopies	retro_ttru_1070, retro_ttru_1124, retro_ttru_1694, retro_ttru_1818, retro_ttru_364, retro_ttru_386, retro_ttru_474, retro_ttru_646,