RetrogeneDB ID: retro_sscr_1016

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 8:141303561..141303926(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBCH5B
• Ensembl ID: ENSSSCG00000029822
• Aliases: None
• Description: Sus scrofa ubiquitin-conjugating enzyme E2D 2 (UBE2D2), mRNA. [Source:RefSeq mRNA;Acc:NM_001078673]

Sequence

>retro_sscr_1016
ATTAATAAGGAATTCAGTGATTTGGCCAGTGACCCTCGAGAGCAGAGCTCTGCAGGTTCAGCTGCAGATGACATGTTTCA
TTGGCAAGCCACAACTACAGCACCAAGCGACAGCCCATATCGAGGCGGTGTATTCTTTTTGAGAGTTCACTTTCCTGCCG
ATGACCCCCTCAAACCACCTAAGCCTGCATATGCCACCTGAACTTATCATCCAAATATTAACAGTAATGGCAGCACATGC
CGCTACATTCTGAGATTGCAGTGTCTCCGGCTTTAACGATTTCTGAAGTTCTTTTATCCATTTGTTCACTATGTGATCCA
AACCCAGATAACCCCCTAGTGCCAGAGACTGCACAGATTATAAAA

Alignment

ORF - retro_sscr_1016 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.97 %
• Parental protein coverage: 83.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IDKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYH
          I.KE.SDLA.DP..Q.SAG...DDMFHWQAT...P.DSPY.GGVFFL..HFP.D.P.KPPK.A..T..YH
Retrocopy INKEFSDLASDPREQSSAGSAADDMFHWQATTTAPSDSPYRGGVFFLRVHFPADDPLKPPKPAYAT*TYH

Parental  PNINSNGSICLDILRSQW-SPALTISKVLLSICSLLCDPNPDDPLVPEIARIYK
          PNINSNGS.C..ILR.Q..SPALTIS.VLLSICS.LCDPNPD.PLVPE.A.I.K
Retrocopy PNINSNGSTCRYILRLQC<SPALTISEVLLSICS-LCDPNPDNPLVPETAQIIK

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	0.00 RPM
SRP014902_testis	0.00 RPM	0.00 RPM
SRP018288_heart	0.00 RPM	0.71 RPM
SRP018288_kidney	0.00 RPM	0.20 RPM
SRP018288_liver	0.00 RPM	0.16 RPM
SRP018288_lung	0.00 RPM	0.61 RPM
SRP018856_adipose	0.00 RPM	0.06 RPM
SRP035408_brain	0.00 RPM	0.00 RPM
SRP035408_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1016 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1016 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1016 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 117 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004649	2 retrocopies	retro_chof_2549, retro_chof_439,
Ciona intestinalis	ENSCING00000018711	2 retrocopies	retro_cint_19, retro_cint_29,
Callithrix jacchus	ENSCJAG00000015492	3 retrocopies	retro_cjac_512, retro_cjac_657, retro_cjac_791,
Ciona savignyi	ENSCSAVG00000006136	1 retrocopy	retro_csav_18,
Dasypus novemcinctus	ENSDNOG00000009320	30 retrocopies	retro_dnov_1061, retro_dnov_1125, retro_dnov_113, retro_dnov_114, retro_dnov_1167, retro_dnov_1193, retro_dnov_1198, retro_dnov_1257, retro_dnov_141, retro_dnov_1544, retro_dnov_1752, retro_dnov_1761, retro_dnov_1831, retro_dnov_1862, retro_dnov_1912, retro_dnov_1934, retro_dnov_1995, retro_dnov_2084, retro_dnov_2135, retro_dnov_2289, retro_dnov_2362, retro_dnov_2457, retro_dnov_2622, retro_dnov_436, retro_dnov_574, retro_dnov_750, retro_dnov_795, retro_dnov_83, retro_dnov_889, retro_dnov_917,
Dipodomys ordii	ENSDORG00000006762	2 retrocopies	retro_dord_172, retro_dord_323,
Equus caballus	ENSECAG00000020678	1 retrocopy	retro_ecab_859,
Erinaceus europaeus	ENSEEUG00000010820	1 retrocopy	retro_eeur_84,
Erinaceus europaeus	ENSEEUG00000014658	3 retrocopies	retro_eeur_263, retro_eeur_566, retro_eeur_591,
Echinops telfairi	ENSETEG00000001291	3 retrocopies	retro_etel_1218, retro_etel_1998, retro_etel_36,
Felis catus	ENSFCAG00000024918	2 retrocopies	retro_fcat_1106, retro_fcat_785,
Gorilla gorilla	ENSGGOG00000001368	2 retrocopies	retro_ggor_1156, retro_ggor_2321,
Gorilla gorilla	ENSGGOG00000010832	1 retrocopy	retro_ggor_953,
Macropus eugenii	ENSMEUG00000004256	6 retrocopies	retro_meug_1034, retro_meug_1503, retro_meug_2138, retro_meug_564, retro_meug_787, retro_meug_89,
Mus musculus	ENSMUSG00000078578	11 retrocopies	retro_mmus_1818, retro_mmus_1895, retro_mmus_1913, retro_mmus_2293, retro_mmus_2635, retro_mmus_2643, retro_mmus_3119, retro_mmus_3636, retro_mmus_850, retro_mmus_875, retro_mmus_923,
Ornithorhynchus anatinus	ENSOANG00000005415	1 retrocopy	retro_oana_51,
Otolemur garnettii	ENSOGAG00000012860	6 retrocopies	retro_ogar_1124, retro_ogar_3047, retro_ogar_3048, retro_ogar_3110, retro_ogar_544, retro_ogar_599,
Ochotona princeps	ENSOPRG00000011695	9 retrocopies	retro_opri_1042, retro_opri_1189, retro_opri_206, retro_opri_310, retro_opri_447, retro_opri_457, retro_opri_627, retro_opri_77, retro_opri_838,
Pongo abelii	ENSPPYG00000014967	1 retrocopy	retro_pabe_91,
Pteropus vampyrus	ENSPVAG00000015438	1 retrocopy	retro_pvam_234,
Rattus norvegicus	ENSRNOG00000013741	9 retrocopies	retro_rnor_2777, retro_rnor_342, retro_rnor_345, retro_rnor_539, retro_rnor_650, retro_rnor_724, retro_rnor_725, retro_rnor_772, retro_rnor_784,
Sus scrofa	ENSSSCG00000011209	2 retrocopies	retro_sscr_759, retro_sscr_961,
Sus scrofa	ENSSSCG00000016722	2 retrocopies	retro_sscr_671, retro_sscr_79,
Sus scrofa	ENSSSCG00000024306	1 retrocopy	retro_sscr_783,
Sus scrofa	ENSSSCG00000029822	4 retrocopies	retro_sscr_1016 , retro_sscr_672, retro_sscr_673, retro_sscr_918,
Ictidomys tridecemlineatus	ENSSTOG00000013481	6 retrocopies	retro_itri_1222, retro_itri_1474, retro_itri_1628, retro_itri_463, retro_itri_672, retro_itri_998,
Tupaia belangeri	ENSTBEG00000000270	5 retrocopies	retro_tbel_1336, retro_tbel_145, retro_tbel_1837, retro_tbel_262, retro_tbel_3134,