RetrogeneDB ID: retro_sscr_1121

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: GL895893.2:57576..57762(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DUT
• Ensembl ID: ENSSSCG00000026096
• Aliases: None
• Description: deoxyuridine triphosphatase [Source:HGNC Symbol;Acc:3078]

Sequence

>retro_sscr_1121
GTCCTAGATGAGGATTATAGAGGGGATGTTGGTATTGTAGTGTTTAATTTTGGCAAAGAAATGTCTGATGTCAAAAAGGA
TGTTTGAATGGTACAACTCATTTGTGAACAGATTTCTTATCCAGAAATAGAGGAAGTTCAAGTTTTGGATGATACTGAAA
GGGATTCAAGAAGTTTTGGTTCCACC

Alignment

ORF - retro_sscr_1121 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.97 %
• Parental protein coverage: 83.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VIDEDYRGNVGVVLFNFGKEKFEVKKGDRIAQLICERIFYPEIEEVQVLDDTKRGSGGFGST
          V.DEDYRG.VG.V.FNFGKE...VKK.....QLICE.I.YPEIEEVQVLDDT.R.S..FGST
Retrocopy VLDEDYRGDVGIVVFNFGKEMSDVKKDV*MVQLICEQISYPEIEEVQVLDDTERDSRSFGST

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	1.46 RPM
SRP014902_testis	0.00 RPM	8.49 RPM
SRP018288_heart	0.00 RPM	10.43 RPM
SRP018288_kidney	0.00 RPM	23.35 RPM
SRP018288_liver	0.00 RPM	8.32 RPM
SRP018288_lung	0.00 RPM	7.03 RPM
SRP018856_adipose	0.00 RPM	5.03 RPM
SRP035408_brain	0.00 RPM	44.34 RPM
SRP035408_liver	0.00 RPM	53.93 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1121 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1121 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1121 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 71 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011998	3 retrocopies	retro_btau_1765, retro_btau_510, retro_btau_60,
Callithrix jacchus	ENSCJAG00000001813	2 retrocopies	retro_cjac_1014, retro_cjac_2008,
Dasypus novemcinctus	ENSDNOG00000024791	8 retrocopies	retro_dnov_204, retro_dnov_2096, retro_dnov_2230, retro_dnov_225, retro_dnov_2270, retro_dnov_2608, retro_dnov_528, retro_dnov_639,
Dipodomys ordii	ENSDORG00000010560	1 retrocopy	retro_dord_146,
Equus caballus	ENSECAG00000015971	1 retrocopy	retro_ecab_375,
Felis catus	ENSFCAG00000015350	3 retrocopies	retro_fcat_1158, retro_fcat_33, retro_fcat_937,
Homo sapiens	ENSG00000128951	6 retrocopies	retro_hsap_1698, retro_hsap_256, retro_hsap_2699, retro_hsap_2963, retro_hsap_3624, retro_hsap_4771,
Gorilla gorilla	ENSGGOG00000005658	5 retrocopies	retro_ggor_1272, retro_ggor_1453, retro_ggor_2053, retro_ggor_2974, retro_ggor_306,
Macropus eugenii	ENSMEUG00000006318	3 retrocopies	retro_meug_1739, retro_meug_2104, retro_meug_476,
Myotis lucifugus	ENSMLUG00000006842	2 retrocopies	retro_mluc_1550, retro_mluc_487,
Macaca mulatta	ENSMMUG00000016898	6 retrocopies	retro_mmul_1429, retro_mmul_2645, retro_mmul_449, retro_mmul_707, retro_mmul_720, retro_mmul_910,
Monodelphis domestica	ENSMODG00000002687	3 retrocopies	retro_mdom_1606, retro_mdom_1858, retro_mdom_693,
Nomascus leucogenys	ENSNLEG00000005996	2 retrocopies	retro_nleu_2602, retro_nleu_859,
Oryctolagus cuniculus	ENSOCUG00000003862	1 retrocopy	retro_ocun_798,
Otolemur garnettii	ENSOGAG00000028847	7 retrocopies	retro_ogar_1207, retro_ogar_1422, retro_ogar_1500, retro_ogar_1653, retro_ogar_2348, retro_ogar_2815, retro_ogar_3485,
Pongo abelii	ENSPPYG00000006454	2 retrocopies	retro_pabe_3820, retro_pabe_3831,
Pan troglodytes	ENSPTRG00000007044	2 retrocopies	retro_ptro_216, retro_ptro_3177,
Rattus norvegicus	ENSRNOG00000007221	1 retrocopy	retro_rnor_859,
Sus scrofa	ENSSSCG00000026096	3 retrocopies	retro_sscr_1121 , retro_sscr_122, retro_sscr_175,
Ictidomys tridecemlineatus	ENSSTOG00000007811	1 retrocopy	retro_itri_125,
Tarsius syrichta	ENSTSYG00000012669	9 retrocopies	retro_tsyr_1044, retro_tsyr_1236, retro_tsyr_1251, retro_tsyr_1825, retro_tsyr_1991, retro_tsyr_215, retro_tsyr_616, retro_tsyr_747, retro_tsyr_771,