RetrogeneDB ID: retro_sscr_241

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 10:18129163..18129492(-)
• Located in intron of: ENSSSCG00000010872

Retrocopy information

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

Parental gene information

• Parental gene symbol: MPC2
• Ensembl ID: ENSSSCG00000006304
• Aliases: MPC2, BRP44
• Description: mitochondrial pyruvate carrier 2 [Source:HGNC Symbol;Acc:24515]

Sequence

>retro_sscr_241
ATGTTAGCTGCCAGTGCCCAGGGCCTACAGGCCATCTACCAGTGGGCCCTCAATAAAGGGGAGCACCCATTGACTGAGAA
ATTGAGGCACTGTACAACCAACCAGCAGATTCCAGAAGCTTATTTTTCTGGGCTCCAATTATGACATGGGGGTTGGTGTA
TGCTGGACTGGTTGACATGCCTGGACTTTCAGAAAAACTTAAAACATCTCAACTTGCTATTCTGATGGCTTCAGGGTTTA
TCTGGTCAAGACACTTACTTATAATTATTAAAACAAACAAACAAAAAACCTGGATTTTGTTTGCTGTTAATTTATTAGGA
CAGCAGGAA

Alignment

ORF - retro_sscr_241 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.68 %
• Parental protein coverage: 86.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSAAGARGLRATYHRVLDKVELLLPEKLR-PLYNHPAGPRTVFFWAPIMKWGLVCAGLADMARPAEKLST
          M.AA.A.GL.A.Y...L.K.E..L.EKLR..LYN.PA..R..FFWAPIM.WGLV.AGL.DM....EKL.T
Retrocopy MLAASAQGLQAIYQWALNKGEHPLTEKLR<ALYNQPADSRSLFFWAPIMTWGLVYAGLVDMPGLSEKLKT

Parental  AQSAVLMATAGFIWSRYSLVIIPKNWSLFAVNFFVGTAGASQ
          .Q.A.LMA..GFIWSR..L.II..........F.V...G...
Retrocopy SQLAILMA-SGFIWSRHLLIIIXXXXXXXWILFAVNLLGQQE

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	22.96 RPM
SRP014902_testis	0.00 RPM	17.96 RPM
SRP018288_heart	0.00 RPM	162.35 RPM
SRP018288_kidney	0.00 RPM	106.88 RPM
SRP018288_liver	0.00 RPM	57.89 RPM
SRP018288_lung	0.00 RPM	23.62 RPM
SRP018856_adipose	0.00 RPM	160.90 RPM
SRP035408_brain	0.00 RPM	37.00 RPM
SRP035408_liver	0.00 RPM	61.15 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_241 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_241 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_241 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 17 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006273	2 retrocopies	retro_amel_527, retro_amel_987,
Bos taurus	ENSBTAG00000020968	2 retrocopies	retro_btau_1459, retro_btau_557,
Canis familiaris	ENSCAFG00000015358	2 retrocopies	retro_cfam_1350, retro_cfam_1897,
Choloepus hoffmanni	ENSCHOG00000007752	6 retrocopies	retro_chof_1286, retro_chof_1294, retro_chof_2021, retro_chof_23, retro_chof_47, retro_chof_835,
Callithrix jacchus	ENSCJAG00000016985	1 retrocopy	retro_cjac_4207,
Cavia porcellus	ENSCPOG00000003860	1 retrocopy	retro_cpor_494,
Dasypus novemcinctus	ENSDNOG00000011180	1 retrocopy	retro_dnov_475,
Microcebus murinus	ENSMICG00000011691	5 retrocopies	retro_mmur_1158, retro_mmur_1503, retro_mmur_317, retro_mmur_348, retro_mmur_986,
Myotis lucifugus	ENSMLUG00000011873	1 retrocopy	retro_mluc_610,
Macaca mulatta	ENSMMUG00000010387	1 retrocopy	retro_mmul_432,
Mus musculus	ENSMUSG00000026568	3 retrocopies	retro_mmus_1651, retro_mmus_578, retro_mmus_647,
Otolemur garnettii	ENSOGAG00000003130	3 retrocopies	retro_ogar_1494, retro_ogar_1992, retro_ogar_2653,
Sus scrofa	ENSSSCG00000006304	1 retrocopy	retro_sscr_241 ,
Tupaia belangeri	ENSTBEG00000014189	9 retrocopies	retro_tbel_1099, retro_tbel_1446, retro_tbel_1614, retro_tbel_1847, retro_tbel_2174, retro_tbel_3168, retro_tbel_433, retro_tbel_4444, retro_tbel_734,
Tarsius syrichta	ENSTSYG00000010251	3 retrocopies	retro_tsyr_10, retro_tsyr_141, retro_tsyr_1810,
Tursiops truncatus	ENSTTRG00000008566	1 retrocopy	retro_ttru_1743,
Vicugna pacos	ENSVPAG00000010556	1 retrocopy	retro_vpac_51,