RetrogeneDB ID: retro_sscr_516

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 15:157198652..157198957(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BET1
• Ensembl ID: ENSSSCG00000015325
• Aliases: None
• Description: Bet1 golgi vesicular membrane trafficking protein [Source:HGNC Symbol;Acc:14562]

Sequence

>retro_sscr_516
ATGAGGTGTGCAGGCCTGGATGAAAGAGTAGCTCCTGGGAACTATGGGTATCCTATGGTGGGTATAGTGCCAATGAAGAA
AACAAGAGACTCACAGAAAATCTGAAAAGCAAAGTAACTGCTATAACATTTCTTTCCATTGCAACAGACTATGAGGTTAA
ACATCAAAATAAACTATTAGCTGAAATGGATTCACAATGGATTCACGTTTTACCTGGATTTCTAGGTAAAACTACAAGAA
AACTGAAGATTTTATCTGGAAGGAGCTCTATGCTGCTGTTTTCATTGTCTTTTTTGTCATTTATT

Alignment

ORF - retro_sscr_516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.72 %
• Parental protein coverage: 90.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRRAGLGEGVPPGNYGNYGYPN-SGYSACEEENERLTESLRNKVTAIKSLSIEIGHEVKHQNKLLAEMDS
          MR.AGL.E.V.P...GNYGYP...GYSA..EEN.RLTE.L..KVTAI..LSI....EVKHQNKLLAEMDS
Retrocopy MRCAGLDERVAP---GNYGYPM<GGYSA-NEENKRLTENLKSKVTAITFLSIATDYEVKHQNKLLAEMDS

Parental  QF-DSTTGFLGKTMGKLKILSRGSQTKLLCYMMLFSLFV
          Q......GFLGKT..KLKILS.......L.....F..F.
Retrocopy QWIHVLPGFLGKTTRKLKILS--GRSSMLLFSLSFLSFI

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	4.38 RPM
SRP014902_testis	0.00 RPM	8.35 RPM
SRP018288_heart	0.00 RPM	8.02 RPM
SRP018288_kidney	0.00 RPM	17.34 RPM
SRP018288_liver	0.00 RPM	52.29 RPM
SRP018288_lung	0.00 RPM	14.05 RPM
SRP018856_adipose	0.00 RPM	9.73 RPM
SRP035408_brain	0.00 RPM	6.26 RPM
SRP035408_liver	0.00 RPM	11.77 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_516 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_516 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_516 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003424	1 retrocopy	retro_btau_1054,
Choloepus hoffmanni	ENSCHOG00000001276	1 retrocopy	retro_chof_2211,
Callithrix jacchus	ENSCJAG00000013720	3 retrocopies	retro_cjac_1411, retro_cjac_2019, retro_cjac_3155,
Dasypus novemcinctus	ENSDNOG00000001012	3 retrocopies	retro_dnov_1683, retro_dnov_393, retro_dnov_60,
Homo sapiens	ENSG00000105829	1 retrocopy	retro_hsap_3809,
Gorilla gorilla	ENSGGOG00000002176	1 retrocopy	retro_ggor_2560,
Loxodonta africana	ENSLAFG00000000587	1 retrocopy	retro_lafr_1023,
Macaca mulatta	ENSMMUG00000000007	1 retrocopy	retro_mmul_1656,
Nomascus leucogenys	ENSNLEG00000015441	1 retrocopy	retro_nleu_2151,
Oryctolagus cuniculus	ENSOCUG00000017029	2 retrocopies	retro_ocun_1116, retro_ocun_355,
Ochotona princeps	ENSOPRG00000004536	4 retrocopies	retro_opri_201, retro_opri_249, retro_opri_388, retro_opri_880,
Pan troglodytes	ENSPTRG00000019408	1 retrocopy	retro_ptro_2584,
Rattus norvegicus	ENSRNOG00000011008	2 retrocopies	retro_rnor_2195, retro_rnor_2196,
Sus scrofa	ENSSSCG00000015325	2 retrocopies	retro_sscr_455, retro_sscr_516 ,
Tupaia belangeri	ENSTBEG00000000765	2 retrocopies	retro_tbel_3115, retro_tbel_4272,
Tarsius syrichta	ENSTSYG00000009729	2 retrocopies	retro_tsyr_136, retro_tsyr_1843,