RetrogeneDB ID: retro_sscr_338

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:131139305..131139755(+)
• Located in intron of: ENSSSCG00000011776

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000000377
• Aliases: None
• Description: None

Sequence

>retro_sscr_338
GAGAGAACTGCCGTTTACAAATGAGACCCTTCTGAGTAGTTAAGATCTAAAAATGAAAACTTCACATGCCTCTTCAGTGA
GGTCAAAAGGTGTTTTGATGCCATGCCCTTTACTTTTAAGACTGAAGATGGGAAGGCCTGCATGGGTGTGGTAGAGTGCG
CCAAACATGAACTTCTACAGCCATTTAATGTTCTCTTTGAAAAGGAGGGTGAATATGTTGCCAGGTTTAACTTTAGTTCT
GCTCATACTCAGTGGCACCACATGGATGACCAGTGATCCCTTTGAGCCTGACCTTTATGAGTCCGAGATGGAGGTCCAGG
ATACAGAGCTGAAGGTCCTCCTCTAGGGTTGTACAAGTTGGAAAACCCAGAAAAAGAAAAAAAGTCAGCCTCTAAGCCTG
CCAAGAATGCCACCAGTGGGGAAACTTTAGAAGAAAATGAGGCTGGGAAC

Alignment

ORF - retro_sscr_338 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.69 %
• Parental protein coverage: 72.86 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QRTTIYKRDPSK-QYGLKMKTSRA-FFSEVERRFDAMPFTLRAFEDEKKARMGVVECAKHELLQPFNVLY
          .RT..YK.DPS.....LKMKTS.A..FSEV.R.FDAMPFT........KA.MGVVECAKHELLQPFNVL.
Retrocopy ERTAVYK*DPSE>S*DLKMKTSHA<LFSEVKRCFDAMPFTFKT--EDGKACMGVVECAKHELLQPFNVLF

Parental  EKEGEFVAQFKFT-VLLMPNGPMRITSGPFEPDLYKSEMEVQDAELKALLQSSASRKTQKKKKKK-ASKT
          EKEGE.VA.F.F...L....G....TS.PFEPDLY.SEMEVQD.ELK.LL....S.KTQ.......ASK.
Retrocopy EKEGEYVARFNFS>LLIL-SGTTWMTSDPFEPDLYESEMEVQDTELKVLL*GCTSWKTQXXXXXQ<ASKP

Parental  AENATSGETLEENEAGD
          A.NATSGETLEENEAG.
Retrocopy AKNATSGETLEENEAGN

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	48.71 RPM
SRP014902_testis	0.00 RPM	57.43 RPM
SRP018288_heart	0.00 RPM	48.43 RPM
SRP018288_kidney	0.00 RPM	68.17 RPM
SRP018288_liver	0.00 RPM	65.72 RPM
SRP018288_lung	0.00 RPM	116.69 RPM
SRP018856_adipose	0.00 RPM	66.34 RPM
SRP035408_brain	0.00 RPM	113.45 RPM
SRP035408_liver	0.06 RPM	56.77 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_338 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_338 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_338 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007181	2 retrocopies	retro_chof_1089, retro_chof_1847,
Homo sapiens	ENSG00000170515	6 retrocopies	retro_hsap_1930, retro_hsap_2413, retro_hsap_2868, retro_hsap_3646, retro_hsap_4191, retro_hsap_4895,
Macaca mulatta	ENSMMUG00000002164	2 retrocopies	retro_mmul_1168, retro_mmul_2631,
Mus musculus	ENSMUSG00000025364	1 retrocopy	retro_mmus_2803,
Nomascus leucogenys	ENSNLEG00000017544	6 retrocopies	retro_nleu_1212, retro_nleu_1260, retro_nleu_163, retro_nleu_3024, retro_nleu_506, retro_nleu_612,
Oryctolagus cuniculus	ENSOCUG00000017342	1 retrocopy	retro_ocun_1733,
Pongo abelii	ENSPPYG00000025851	7 retrocopies	retro_pabe_1595, retro_pabe_1778, retro_pabe_2375, retro_pabe_2869, retro_pabe_2993, retro_pabe_3430, retro_pabe_3807,
Sus scrofa	ENSSSCG00000000377	1 retrocopy	retro_sscr_338 ,
Sus scrofa	ENSSSCG00000022666	2 retrocopies	retro_sscr_1143, retro_sscr_337,
Tarsius syrichta	ENSTSYG00000006777	1 retrocopy	retro_tsyr_746,
Vicugna pacos	ENSVPAG00000009523	1 retrocopy	retro_vpac_2,