RetrogeneDB ID: retro_sscr_504

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 15:91166401..91166626(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL42
• Ensembl ID: ENSSSCG00000030478
• Aliases: None
• Description: mitochondrial ribosomal protein L42 [Source:HGNC Symbol;Acc:14493]

Sequence

>retro_sscr_504
ATGGCATTGGCAGCAGTAAAATGGGCCATATCAAGCAGAGCTGTCTTGAAACATTTATTTCCAGTTCAAAGTGGAGCCCC
ATATTTCATTTGTTGTAAACCTACATATTCTTCTCTCCCAGATAACTATAATTGCAAAGGAGAGCTTGCTTTGATGTCTG
ATGGCAGGACAATAGTATGTTGTCACCCTTCTGTGGACATTCCACATGAACACACAAAACCTGTG

Alignment

ORF - retro_sscr_504 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.33 %
• Parental protein coverage: 58.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALAAVKWVISSRTILKHLFPIQNSASYCVCHKSTYSSLPDDYNCKVELALTSDGRTIVCYHPSVDIPYE
          MALAAVKW.ISSR..LKHLFP.Q..A.Y..C.K.TYSSLPD.YNCK.ELAL.SDGRTIVC.HPSVDIP.E
Retrocopy MALAAVKWAISSRAVLKHLFPVQSGAPYFICCKPTYSSLPDNYNCKGELALMSDGRTIVCCHPSVDIPHE

Parental  HTKPI
          HTKP.
Retrocopy HTKPV

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	4.25 RPM
SRP014902_testis	0.00 RPM	6.65 RPM
SRP018288_heart	0.00 RPM	36.33 RPM
SRP018288_kidney	0.00 RPM	16.06 RPM
SRP018288_liver	0.00 RPM	13.59 RPM
SRP018288_lung	0.00 RPM	7.13 RPM
SRP018856_adipose	0.00 RPM	4.85 RPM
SRP035408_brain	0.00 RPM	20.20 RPM
SRP035408_liver	0.00 RPM	23.43 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_504 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_504 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_504 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 74 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009832	1 retrocopy	retro_amel_403,
Bos taurus	ENSBTAG00000002708	3 retrocopies	retro_btau_1395, retro_btau_346, retro_btau_775,
Callithrix jacchus	ENSCJAG00000032825	4 retrocopies	retro_cjac_1541, retro_cjac_3684, retro_cjac_3966, retro_cjac_722,
Homo sapiens	ENSG00000198015	3 retrocopies	retro_hsap_3427, retro_hsap_3528, retro_hsap_3844,
Gorilla gorilla	ENSGGOG00000022760	5 retrocopies	retro_ggor_1983, retro_ggor_2317, retro_ggor_2385, retro_ggor_2483, retro_ggor_2589,
Loxodonta africana	ENSLAFG00000013779	1 retrocopy	retro_lafr_681,
Macaca mulatta	ENSMMUG00000016805	3 retrocopies	retro_mmul_1751, retro_mmul_1850, retro_mmul_2210,
Nomascus leucogenys	ENSNLEG00000005699	5 retrocopies	retro_nleu_1364, retro_nleu_1724, retro_nleu_1979, retro_nleu_493, retro_nleu_606,
Oryctolagus cuniculus	ENSOCUG00000010928	7 retrocopies	retro_ocun_1321, retro_ocun_1378, retro_ocun_1497, retro_ocun_1716, retro_ocun_1717, retro_ocun_622, retro_ocun_686,
Ochotona princeps	ENSOPRG00000010967	5 retrocopies	retro_opri_190, retro_opri_51, retro_opri_653, retro_opri_747, retro_opri_997,
Procavia capensis	ENSPCAG00000003791	1 retrocopy	retro_pcap_179,
Pongo abelii	ENSPPYG00000004833	7 retrocopies	retro_pabe_1286, retro_pabe_2368, retro_pabe_2840, retro_pabe_2914, retro_pabe_3031, retro_pabe_3054, retro_pabe_3552,
Pan troglodytes	ENSPTRG00000022791	3 retrocopies	retro_ptro_1046, retro_ptro_2327, retro_ptro_2396,
Rattus norvegicus	ENSRNOG00000042740	4 retrocopies	retro_rnor_1383, retro_rnor_633, retro_rnor_729, retro_rnor_920,
Sus scrofa	ENSSSCG00000030478	4 retrocopies	retro_sscr_504 , retro_sscr_505, retro_sscr_912, retro_sscr_946,
Ictidomys tridecemlineatus	ENSSTOG00000026544	12 retrocopies	retro_itri_1020, retro_itri_1132, retro_itri_1266, retro_itri_1285, retro_itri_1353, retro_itri_1695, retro_itri_1793, retro_itri_268, retro_itri_284, retro_itri_393, retro_itri_558, retro_itri_899,
Tarsius syrichta	ENSTSYG00000006370	3 retrocopies	retro_tsyr_1296, retro_tsyr_2113, retro_tsyr_276,
Tursiops truncatus	ENSTTRG00000003312	2 retrocopies	retro_ttru_1632, retro_ttru_416,
Vicugna pacos	ENSVPAG00000007658	1 retrocopy	retro_vpac_336,