RetrogeneDB ID: retro_sscr_988

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 8:3017654..3018033(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBA52
• Ensembl ID: ENSSSCG00000013907
• Aliases: UBA52, UBCEP2
• Description: Sus scrofa ubiquitin A-52 residue ribosomal protein fusion product 1 (UBA52), mRNA. [Source:RefSeq mRNA;Acc:NM_214211]

Sequence

>retro_sscr_988
GTGCAGGTCTTGGTGAAGACCCCGCCAGGTGAGACCCTCACCCTGGAGGTGGAGCCTAGTGATGCCACTGAGAATGCCAG
AGCTAAAATCCAGGCTAAGGAGGGCATCCCGCCTGACCAGCAGCGTCTGAATTTGCCGGCAAACAGCTGGAGGATGGCTG
ACGCTCTCAGACCACACCGTCCAGAAAGAGTCCACCCTGCCCTTGATGCTTCGTCTGCGAGGTGGCATCATTGAGCCCTC
CCTCCGCCGGCTCGCTCAGAAATAGAACTGTGACAAGATAATGTGCAGCAAGTACTACGCTCGCCGGCACCCCTGCGCTG
TGACCTGCGGCAAGAAGTGTGACCACACCAACAAGCTGCACCCCCAAGATCAAATAAGA

Alignment

ORF - retro_sscr_988 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.23 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI-FAGKQLEDG-RTLSDYNIQKESTLH
          .Q..VKT..G.T.TLEVEPSD..EN..AKIQ.KEGIPPDQQRL..FAGKQLEDG..TLSD...QKESTL.
Retrocopy VQVLVKTPPGETLTLEVEPSDATENARAKIQAKEGIPPDQQRLN<FAGKQLEDG<LTLSDHTVQKESTLP

Parental  LVLRLRGGIIEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNNLRPKKKVK
          L.LRLRGGIIEPSLR.LAQK.NCDK..C.K.YAR.HP.AV.C..KKC.HTN.L.P.....
Retrocopy LMLRLRGGIIEPSLRRLAQK*NCDKIMCSKYYARRHPCAVTC-GKKCDHTNKLHPQDQIR

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	930.18 RPM
SRP014902_testis	0.00 RPM	633.68 RPM
SRP018288_heart	0.03 RPM	281.06 RPM
SRP018288_kidney	0.00 RPM	338.07 RPM
SRP018288_liver	0.00 RPM	281.76 RPM
SRP018288_lung	0.00 RPM	463.82 RPM
SRP018856_adipose	0.00 RPM	1056.76 RPM
SRP035408_brain	0.00 RPM	282.03 RPM
SRP035408_liver	0.03 RPM	174.64 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_988 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_988 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_988 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014723	8 retrocopies	retro_cfam_1671, retro_cfam_1725, retro_cfam_1879, retro_cfam_1933, retro_cfam_2205, retro_cfam_600, retro_cfam_654, retro_cfam_873,
Latimeria chalumnae	ENSLACG00000008132	1 retrocopy	retro_lcha_11,
Microcebus murinus	ENSMICG00000017583	5 retrocopies	retro_mmur_143, retro_mmur_1486, retro_mmur_150, retro_mmur_633, retro_mmur_708,
Myotis lucifugus	ENSMLUG00000029594	5 retrocopies	retro_mluc_1995, retro_mluc_2057, retro_mluc_2203, retro_mluc_44, retro_mluc_829,
Macaca mulatta	ENSMMUG00000016085	7 retrocopies	retro_mmul_1184, retro_mmul_1580, retro_mmul_1625, retro_mmul_2183, retro_mmul_2311, retro_mmul_232, retro_mmul_896,
Monodelphis domestica	ENSMODG00000003499	1 retrocopy	retro_mdom_867,
Mustela putorius furo	ENSMPUG00000015527	8 retrocopies	retro_mputfur_1059, retro_mputfur_1119, retro_mputfur_1126, retro_mputfur_382, retro_mputfur_516, retro_mputfur_713, retro_mputfur_78, retro_mputfur_945,
Mus musculus	ENSMUSG00000090137	3 retrocopies	retro_mmus_101, retro_mmus_129, retro_mmus_31,
Otolemur garnettii	ENSOGAG00000028000	10 retrocopies	retro_ogar_1345, retro_ogar_1419, retro_ogar_1583, retro_ogar_1604, retro_ogar_1792, retro_ogar_2026, retro_ogar_2370, retro_ogar_2485, retro_ogar_2544, retro_ogar_3337,
Pongo abelii	ENSPPYG00000009746	2 retrocopies	retro_pabe_111, retro_pabe_3291,
Sus scrofa	ENSSSCG00000013907	1 retrocopy	retro_sscr_988 ,
Ictidomys tridecemlineatus	ENSSTOG00000004678	1 retrocopy	retro_itri_49,
Tursiops truncatus	ENSTTRG00000021461	1 retrocopy	retro_ttru_1582,
Xiphophorus maculatus	ENSXMAG00000003911	1 retrocopy	retro_xmac_6,