RetrogeneDB ID: retro_sscr_101

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:29179675..29180131(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000004151
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBE2N
• Ensembl ID: ENSSSCG00000000908
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2N [Source:HGNC Symbol;Acc:12492]

Sequence

>retro_sscr_101
ATGGCCCGTTTGCCCTTCAGGATTAAGAAGGAAACCCAGTGGTTGCTGAAAGAACCAATTCCTGGCATTAAAGCAGAACC
AGATGAGACCAACGCCCATTATTTTCATGTGGTCATTGATGGCCCCCAGGATTCCCCTTTTGAGGGAGGGACTTTTAAAC
TTGAACTCTTTGTGCCAGAAGAGTACCCAATAAAACCTCCTAAAGCACGTTTCGTGACCAAAATTTATCATCCTAATATA
GACAAGTTGGGAAGAATATGTTTAGATATTTTGAAAGAAAACTGGTCCCCAGCACTGCAGATCCGCACAGTTCTGCTATC
CATCCAGGCTTTGTTAGGTGATCCCAATCCAGATGATCCACTAGCATATGATGTAGCGAAGCAGTGGAAGACCAACAAAG
CCCAAGCCATAGAAACAGCTAGAGCATGGACTAGACTATATGCCATGAATAATGTT

Alignment

ORF - retro_sscr_101 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVR
          MA.LP.RI.KETQ.LL.EP.PGIKAEPDE.NA.YFHVVI.GPQDSPFEGGTFKLELF.PEEYP...PK.R
Retrocopy MARLPFRIKKETQWLLKEPIPGIKAEPDETNAHYFHVVIDGPQDSPFEGGTFKLELFVPEEYPIKPPKAR

Parental  FMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETA
          F.TKIYHPN.DKLGRICLDILK..WSPALQIRTVLLSIQALL..PNPDDPLA.DVA.QWKTN.AQAIETA
Retrocopy FVTKIYHPNIDKLGRICLDILKENWSPALQIRTVLLSIQALLGDPNPDDPLAYDVAKQWKTNKAQAIETA

Parental  RAWTRLYAMNNI
          RAWTRLYAMNN.
Retrocopy RAWTRLYAMNNV

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	29.47 RPM
SRP014902_testis	0.14 RPM	51.06 RPM
SRP018288_heart	0.00 RPM	54.64 RPM
SRP018288_kidney	0.00 RPM	81.27 RPM
SRP018288_liver	0.00 RPM	34.70 RPM
SRP018288_lung	0.00 RPM	64.46 RPM
SRP018856_adipose	0.00 RPM	32.17 RPM
SRP035408_brain	0.03 RPM	61.58 RPM
SRP035408_liver	0.00 RPM	33.88 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_101 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_101 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_101 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021767	2 retrocopies	retro_btau_1173, retro_btau_1614,
Canis familiaris	ENSCAFG00000006177	1 retrocopy	retro_cfam_196,
Callithrix jacchus	ENSCJAG00000002979	8 retrocopies	retro_cjac_141, retro_cjac_2121, retro_cjac_3142, retro_cjac_3148, retro_cjac_3216, retro_cjac_3241, retro_cjac_3329, retro_cjac_425,
Cavia porcellus	ENSCPOG00000008581	5 retrocopies	retro_cpor_1548, retro_cpor_230, retro_cpor_24, retro_cpor_655, retro_cpor_750,
Echinops telfairi	ENSETEG00000001882	5 retrocopies	retro_etel_1008, retro_etel_1417, retro_etel_1593, retro_etel_1661, retro_etel_2136,
Homo sapiens	ENSG00000177889	3 retrocopies	retro_hsap_1392, retro_hsap_17, retro_hsap_3124,
Loxodonta africana	ENSLAFG00000028985	1 retrocopy	retro_lafr_57,
Macropus eugenii	ENSMEUG00000002944	7 retrocopies	retro_meug_1236, retro_meug_1287, retro_meug_1453, retro_meug_1473, retro_meug_162, retro_meug_2009, retro_meug_31,
Macaca mulatta	ENSMMUG00000020634	3 retrocopies	retro_mmul_1587, retro_mmul_234, retro_mmul_72,
Monodelphis domestica	ENSMODG00000009451	2 retrocopies	retro_mdom_133, retro_mdom_1485,
Mus musculus	ENSMUSG00000074781	6 retrocopies	retro_mmus_1031, retro_mmus_2656, retro_mmus_3031, retro_mmus_3294, retro_mmus_3510, retro_mmus_524,
Nomascus leucogenys	ENSNLEG00000005695	2 retrocopies	retro_nleu_1078, retro_nleu_2279,
Oryctolagus cuniculus	ENSOCUG00000011287	1 retrocopy	retro_ocun_100,
Pongo abelii	ENSPPYG00000004832	4 retrocopies	retro_pabe_113, retro_pabe_1152, retro_pabe_2580, retro_pabe_3326,
Pan troglodytes	ENSPTRG00000005297	3 retrocopies	retro_ptro_2112, retro_ptro_3253, retro_ptro_956,
Sarcophilus harrisii	ENSSHAG00000007776	1 retrocopy	retro_shar_105,
Sus scrofa	ENSSSCG00000000908	4 retrocopies	retro_sscr_101 , retro_sscr_369, retro_sscr_698, retro_sscr_699,
Tarsius syrichta	ENSTSYG00000008800	5 retrocopies	retro_tsyr_1476, retro_tsyr_1754, retro_tsyr_207, retro_tsyr_348, retro_tsyr_5,