RetrogeneDB ID: retro_sscr_671

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:63747551..63747938(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000028356
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBE2D4
• Ensembl ID: ENSSSCG00000016722
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2D 4 (putative) [Source:HGNC Symbol;Acc:21647]

Sequence

>retro_sscr_671
ATGGCACTGAAGTGGATTCAGGAAGTAATTAAGTGATCTACAAAGTGACCCACCTATTCATTGTTCCACTGGACTTGTGG
GAGATGACTTGTTCTACAGGCAAGAAACTATTATGGCGCCTCCTGATAGCACATATCAAGGCAGAGTCCTTTCCTCACTG
TACATCCACCGACAGACTATTCTTTCAAAGCATCAAAGATTTCTTTCACAACAAAAGTTTACCATCCAAACTCAAAGAGT
AATGGAAGCATTTGCTTAATATCCTGAGGTCACAGAGGTCACCAGCCCCTGGCTGTATCAAAAGTTTCATTGTCTGTGTG
TTCTCTACTTTGTGACCCTAGTCCAGATGATGACCCATTAGTACCAGATATTGCACAAATCTATAAA

Alignment

ORF - retro_sscr_671 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.92 %
• Parental protein coverage: 87.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MALKRIQ-KELTDLQRDPPAQCSAGPVGDDLFHWQATIMGPNDSPYQGGVF-FLTIHFPTDYPFKPPKVA
          MALK.IQ.K.L.DLQ.DPP..CS.G.VGDDLF..Q.TIM.P.DS.YQG.V..FLT.H.PTDY.FK..K..
Retrocopy MALKWIQ>K*LSDLQSDPPIHCSTGLVGDDLFYRQETIMAPPDSTYQGRVL<FLTVHPPTDYSFKASKIS

Parental  FTTKIYHPNINSNGSICL-DILRSQWSPA-LTVSKVLLSICSLLCDPNP-DDPLVPEIAHTYK
          FTTK.YHPN..SNGSICL..ILRSQ.SPA.L.VSKV.LS.CSLLCDP.P.DDPLVP.IA..YK
Retrocopy FTTKVYHPNSKSNGSICL<NILRSQRSPA>LAVSKVSLSVCSLLCDPSPDDDPLVPDIAQIYK

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	9.29 RPM
SRP014902_testis	0.00 RPM	15.98 RPM
SRP018288_heart	0.00 RPM	32.77 RPM
SRP018288_kidney	0.00 RPM	18.81 RPM
SRP018288_liver	0.00 RPM	5.92 RPM
SRP018288_lung	0.00 RPM	25.05 RPM
SRP018856_adipose	0.03 RPM	29.85 RPM
SRP035408_brain	0.00 RPM	31.25 RPM
SRP035408_liver	0.00 RPM	7.52 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_671 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_671 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_671 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 60 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003997	1 retrocopy	retro_btau_1261,
Callithrix jacchus	ENSCJAG00000007875	4 retrocopies	retro_cjac_1660, retro_cjac_3666, retro_cjac_3882, retro_cjac_925,
Dipodomys ordii	ENSDORG00000006888	5 retrocopies	retro_dord_104, retro_dord_345, retro_dord_408, retro_dord_743, retro_dord_760,
Homo sapiens	ENSG00000078967	2 retrocopies	retro_hsap_452, retro_hsap_453,
Gorilla gorilla	ENSGGOG00000003378	3 retrocopies	retro_ggor_1843, retro_ggor_2936, retro_ggor_436,
Myotis lucifugus	ENSMLUG00000011919	3 retrocopies	retro_mluc_1826, retro_mluc_1827, retro_mluc_594,
Macaca mulatta	ENSMMUG00000002410	5 retrocopies	retro_mmul_1067, retro_mmul_1937, retro_mmul_2514, retro_mmul_2515, retro_mmul_531,
Nomascus leucogenys	ENSNLEG00000003364	3 retrocopies	retro_nleu_54, retro_nleu_876, retro_nleu_90,
Oryctolagus cuniculus	ENSOCUG00000008900	1 retrocopy	retro_ocun_1058,
Pongo abelii	ENSPPYG00000029727	1 retrocopy	retro_pabe_3573,
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,
Tupaia belangeri	ENSTBEG00000003691	9 retrocopies	retro_tbel_1273, retro_tbel_2535, retro_tbel_2782, retro_tbel_307, retro_tbel_367, retro_tbel_37, retro_tbel_4118, retro_tbel_4163, retro_tbel_4312,
Tarsius syrichta	ENSTSYG00000000595	14 retrocopies	retro_tsyr_1007, retro_tsyr_1145, retro_tsyr_1162, retro_tsyr_1314, retro_tsyr_1392, retro_tsyr_1415, retro_tsyr_1677, retro_tsyr_1694, retro_tsyr_1859, retro_tsyr_683, retro_tsyr_789, retro_tsyr_836, retro_tsyr_838, retro_tsyr_919,