RetrogeneDB ID: retro_sscr_449

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:115688801..115689142(-)
• Located in intron of: ENSSSCG00000022139

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000001038
• Aliases: None
• Description: None

Sequence

>retro_sscr_449
ATGCAGAAGGACTCTGGCCCACGAGTGCCTTCACACTGGATTGGCTTTGGTTATGTGGCACTGGTTGCTTCTAGTGGGAT
CATTGGCTATGCAAAAGCAGGTAGGGTCCCATCCCTGGCGGCCGGGGTCCTCTTCGGTGGCTTAGAGGGCCTGGGTGCCT
ACCAGCTATCTCAGGATCCAAGGAACATTTGGGTTTTCTCAGTTACATCTGGAACCTTGGCTGGCATTATGGGAATGAGA
TTCTACCACATTGGAAAATTTACGCCTGCAGCTTGACTGAGGATGCCAGTTTGCTGATGGTCGCCAAACTTGAAATTAGT
GTGTTGAGTAAACCCCATCCA

Alignment

ORF - retro_sscr_449 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.09 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQKDSGPLVPLHWIGFGYAALVASGGIIGYAKAGSVPSLAAGLLFGGLAGLGAYQLSQDPRNIWVFLVTS
          MQKDSGP.VP.HWIGFGY.ALVAS.GIIGYAKAG.VPSLAAG.LFGGL.GLGAYQLSQDPRNIWVF.VTS
Retrocopy MQKDSGPRVPSHWIGFGYVALVASSGIIGYAKAGRVPSLAAGVLFGGLEGLGAYQLSQDPRNIWVFSVTS

Parental  GTLAGIMGMRFYHSGKFMPA-GLIAGASLLMVAKLGISVLSKPHP
          GTLAGIMGMRFYH.GKF.PA..L...ASLLMVAKL.ISVLSKPHP
Retrocopy GTLAGIMGMRFYHIGKFTPA<SLTEDASLLMVAKLEISVLSKPHP

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	28.94 RPM
SRP014902_testis	0.00 RPM	35.50 RPM
SRP018288_heart	0.03 RPM	32.19 RPM
SRP018288_kidney	0.10 RPM	130.13 RPM
SRP018288_liver	0.00 RPM	107.30 RPM
SRP018288_lung	0.00 RPM	29.02 RPM
SRP018856_adipose	0.00 RPM	54.33 RPM
SRP035408_brain	0.00 RPM	28.81 RPM
SRP035408_liver	0.00 RPM	57.13 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_449 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_449 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_449 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 58 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002614	3 retrocopies	retro_amel_1256, retro_amel_939, retro_amel_957,
Bos taurus	ENSBTAG00000005808	1 retrocopy	retro_btau_970,
Canis familiaris	ENSCAFG00000009692	2 retrocopies	retro_cfam_115, retro_cfam_1716,
Callithrix jacchus	ENSCJAG00000004957	1 retrocopy	retro_cjac_725,
Dasypus novemcinctus	ENSDNOG00000007732	6 retrocopies	retro_dnov_1220, retro_dnov_1547, retro_dnov_1968, retro_dnov_289, retro_dnov_316, retro_dnov_367,
Equus caballus	ENSECAG00000026994	1 retrocopy	retro_ecab_659,
Erinaceus europaeus	ENSEEUG00000009000	1 retrocopy	retro_eeur_26,
Felis catus	ENSFCAG00000014178	5 retrocopies	retro_fcat_301, retro_fcat_314, retro_fcat_367, retro_fcat_93, retro_fcat_983,
Homo sapiens	ENSG00000111843	2 retrocopies	retro_hsap_1793, retro_hsap_2481,
Homo sapiens	ENSG00000137210	1 retrocopy	retro_hsap_684,
Gorilla gorilla	ENSGGOG00000009702	1 retrocopy	retro_ggor_4,
Loxodonta africana	ENSLAFG00000009795	2 retrocopies	retro_lafr_1233, retro_lafr_1246,
Macropus eugenii	ENSMEUG00000000210	1 retrocopy	retro_meug_1704,
Macaca mulatta	ENSMMUG00000018788	2 retrocopies	retro_mmul_1244, retro_mmul_1597,
Mustela putorius furo	ENSMPUG00000000613	2 retrocopies	retro_mputfur_1322, retro_mputfur_226,
Mus musculus	ENSMUSG00000021361	2 retrocopies	retro_mmus_1634, retro_mmus_2355,
Nomascus leucogenys	ENSNLEG00000000564	3 retrocopies	retro_nleu_269, retro_nleu_2933, retro_nleu_607,
Oryctolagus cuniculus	ENSOCUG00000016368	3 retrocopies	retro_ocun_1129, retro_ocun_1348, retro_ocun_284,
Otolemur garnettii	ENSOGAG00000012165	3 retrocopies	retro_ogar_1155, retro_ogar_2425, retro_ogar_3462,
Ochotona princeps	ENSOPRG00000014366	4 retrocopies	retro_opri_192, retro_opri_29, retro_opri_409, retro_opri_898,
Pongo abelii	ENSPPYG00000016225	1 retrocopy	retro_pabe_1473,
Pan troglodytes	ENSPTRG00000017720	2 retrocopies	retro_ptro_1199, retro_ptro_1435,
Rattus norvegicus	ENSRNOG00000015437	2 retrocopies	retro_rnor_1595, retro_rnor_33,
Sarcophilus harrisii	ENSSHAG00000011456	1 retrocopy	retro_shar_177,
Sus scrofa	ENSSSCG00000001038	3 retrocopies	retro_sscr_438, retro_sscr_449 , retro_sscr_614,
Ictidomys tridecemlineatus	ENSSTOG00000022833	1 retrocopy	retro_itri_47,
Tursiops truncatus	ENSTTRG00000003666	2 retrocopies	retro_ttru_1504, retro_ttru_258,