RetrogeneDB ID: retro_sscr_643

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:124650602..124651005(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2C
• Ensembl ID: ENSSSCG00000007423
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2C [Source:HGNC Symbol;Acc:15937]

Sequence

>retro_sscr_643
CCACTGGGCAGGAGGCTCCAACGGGAGCTGGTGACCCTGGGGATATCTGGCGACAAGGGAGTTTCTGCCTACCTGGTATA
AGACCATTCCAAATGGGTAGGGACTATCCACGGAGCAGAGGAAACAGGCTGTGAAGACCTGATGTCTCTGGCCCTGCAGT
TCCCAGGGCTTCCATCCCAGCGCCTGCGCAGTGAGGCTCCTCAGCCCTGGACCACCGCCACGTGGACACCGGCGTCACGT
GGCCCTGAATACTTTGGAGGGTAAGTGGGTCGCCCTGCGTGATAGCAGGACCATCCTGCTCTCCTCACAGAGCCTACTAG
AACCGAACATCTACAGCCCTTTGCGCACACATTCGGCTAAGTTCTAGAAACATCTCCAACCTTTAAAGAAGTACCTGCAA
GAA

Alignment

ORF - retro_sscr_643 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.57 %
• Parental protein coverage: 77.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PVGKRLQQELMTLMMSGDKGISAFPESDNLFKWVGTIHGAAGTVYEDLRYKLSLEFPSGYPY-NAPTVKF
          P.G.RLQ.EL.TL..SGDKG.SA....D...KWVGTIHGA..T..EDL...L.L.FP.G.P...A..V..
Retrocopy PLGRRLQRELVTLGISGDKGVSAYLV*DHS-KWVGTIHGAEETGCEDL-MSLALQFP-GLPS>SACAVRL

Parental  LTPCYHPNVDTQGNICLDILKDKWSALYDVRTILLSIQSLLGEPNIDSPLNTHAAELWKNPTAFKKYLQE
          L.P...P.........L..L..KW.AL.D.RTILLS.QSLL.EPNI.SPL.TH.A...K.....KKYLQE
Retrocopy LSPGPPPR-GHRRHVALNTLEGKWVALRDSRTILLSSQSLL-EPNIYSPLRTHSAKF*KHLQPLKKYLQE

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	2.79 RPM
SRP014902_testis	0.00 RPM	16.69 RPM
SRP018288_heart	0.03 RPM	3.06 RPM
SRP018288_kidney	0.00 RPM	4.14 RPM
SRP018288_liver	0.00 RPM	2.40 RPM
SRP018288_lung	0.00 RPM	14.97 RPM
SRP018856_adipose	0.00 RPM	0.54 RPM
SRP035408_brain	0.00 RPM	1.21 RPM
SRP035408_liver	0.06 RPM	4.23 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_643 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_643 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_643 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016746	1 retrocopy	retro_btau_249,
Canis familiaris	ENSCAFG00000009745	6 retrocopies	retro_cfam_1031, retro_cfam_1805, retro_cfam_1878, retro_cfam_2078, retro_cfam_290, retro_cfam_356,
Equus caballus	ENSECAG00000014619	2 retrocopies	retro_ecab_297, retro_ecab_316,
Erinaceus europaeus	ENSEEUG00000010643	14 retrocopies	retro_eeur_113, retro_eeur_177, retro_eeur_249, retro_eeur_253, retro_eeur_266, retro_eeur_272, retro_eeur_294, retro_eeur_346, retro_eeur_375, retro_eeur_518, retro_eeur_592, retro_eeur_604, retro_eeur_641, retro_eeur_80,
Felis catus	ENSFCAG00000001885	4 retrocopies	retro_fcat_1440, retro_fcat_1530, retro_fcat_1667, retro_fcat_1734,
Loxodonta africana	ENSLAFG00000003164	1 retrocopy	retro_lafr_73,
Macropus eugenii	ENSMEUG00000007177	14 retrocopies	retro_meug_1021, retro_meug_1128, retro_meug_1203, retro_meug_1398, retro_meug_1435, retro_meug_145, retro_meug_1476, retro_meug_1504, retro_meug_1575, retro_meug_1773, retro_meug_1808, retro_meug_2034, retro_meug_334, retro_meug_645,
Microcebus murinus	ENSMICG00000011218	2 retrocopies	retro_mmur_332, retro_mmur_988,
Macaca mulatta	ENSMMUG00000021023	4 retrocopies	retro_mmul_1345, retro_mmul_170, retro_mmul_1951, retro_mmul_777,
Monodelphis domestica	ENSMODG00000013661	6 retrocopies	retro_mdom_1549, retro_mdom_1552, retro_mdom_1732, retro_mdom_1970, retro_mdom_2020, retro_mdom_415,
Mustela putorius furo	ENSMPUG00000017619	2 retrocopies	retro_mputfur_103, retro_mputfur_189,
Oryctolagus cuniculus	ENSOCUG00000012176	3 retrocopies	retro_ocun_1005, retro_ocun_1294, retro_ocun_348,
Otolemur garnettii	ENSOGAG00000004989	3 retrocopies	retro_ogar_2347, retro_ogar_249, retro_ogar_3067,
Pan troglodytes	ENSPTRG00000013564	1 retrocopy	retro_ptro_38,
Sus scrofa	ENSSSCG00000007423	1 retrocopy	retro_sscr_643 ,