RetrogeneDB ID: retro_sscr_721

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 3:134265091..134265453(+)
• Located in intron of: ENSSSCG00000008629

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP3S2
• Ensembl ID: ENSSSCG00000030174
• Aliases: None
• Description: adaptor-related protein complex 3, sigma 2 subunit [Source:HGNC Symbol;Acc:571]

Sequence

>retro_sscr_721
CTCGTCTTTAATAACCACGGGAAGCCGCGGCTCGCCAAGTTCCACCAGCCCTACAGTGAAGACACCCACAGCAAATCATC
AGGGAGACATCCCATTTGGTGTCTAAGAGAGATGAGCATGTTTGCAACTTCCTAGAAGGAGGATTATTGGAGGATCTGAG
AGCAAAGTGATTTATAGACATTATGGCAACATTGTATTTCGTCTTCTGTGTGGATTCTTCAGAAGGTGAACTTGGCATTT
TAGATCTAATTCAAGTATTTGTGGAAACATTAGACAAGTGTTTTGAAAATGTCTGTGAACTGGATTTAGTTTTCCATGTA
GATAAGGTTCACAATATTCTTGCGGAAATGGTGATGGGAGGG

Alignment

ORF - retro_sscr_721 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.8 %
• Parental protein coverage: 63.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LVFNNHGKPRLVRFYQRFPEEIQ-QQIVRETFHLVLKRDDNICNFLEGGSL-IGGSDYKLIYRHY-ATLY
          LVFNNHGKPRL..F.Q...E....QQI.RET.HLV.KRD...CNFLE.G.L.IGGS..K.IYRHY.ATLY
Retrocopy LVFNNHGKPRLAKFHQPYSEDTH<QQIIRETSHLVSKRDEHVCNFLE-GGL<IGGSESKVIYRHY>ATLY

Parental  FVFCVDSSESELGILDLIQVFVETLDKCFENVCELDLIFHMDKVHYILQEVVMGG
          FVFCVDSSE.ELGILDLIQVFVETLDKCFENVCELDL.FH.DKVH.IL.E.VMGG
Retrocopy FVFCVDSSEGELGILDLIQVFVETLDKCFENVCELDLVFHVDKVHNILAEMVMGG

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	0.93 RPM	24.82 RPM
SRP014902_testis	1.70 RPM	31.40 RPM
SRP018288_heart	2.04 RPM	18.96 RPM
SRP018288_kidney	1.58 RPM	57.53 RPM
SRP018288_liver	1.12 RPM	34.38 RPM
SRP018288_lung	3.77 RPM	31.77 RPM
SRP018856_adipose	1.00 RPM	46.77 RPM
SRP035408_brain	4.10 RPM	30.20 RPM
SRP035408_liver	1.67 RPM	28.62 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_721 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_721 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_721 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001407	1 retrocopy	retro_btau_436,
Choloepus hoffmanni	ENSCHOG00000003359	4 retrocopies	retro_chof_1775, retro_chof_194, retro_chof_434, retro_chof_88,
Dipodomys ordii	ENSDORG00000004247	1 retrocopy	retro_dord_115,
Equus caballus	ENSECAG00000024044	1 retrocopy	retro_ecab_549,
Felis catus	ENSFCAG00000028122	1 retrocopy	retro_fcat_311,
Macropus eugenii	ENSMEUG00000003421	1 retrocopy	retro_meug_2032,
Monodelphis domestica	ENSMODG00000019522	1 retrocopy	retro_mdom_316,
Nomascus leucogenys	ENSNLEG00000011780	2 retrocopies	retro_nleu_1380, retro_nleu_1555,
Otolemur garnettii	ENSOGAG00000030982	1 retrocopy	retro_ogar_1737,
Rattus norvegicus	ENSRNOG00000043141	1 retrocopy	retro_rnor_931,
Sus scrofa	ENSSSCG00000030174	7 retrocopies	retro_sscr_1109, retro_sscr_199, retro_sscr_268, retro_sscr_339, retro_sscr_620, retro_sscr_721 , retro_sscr_753,
Tursiops truncatus	ENSTTRG00000015554	2 retrocopies	retro_ttru_1233, retro_ttru_1361,
Vicugna pacos	ENSVPAG00000008668	1 retrocopy	retro_vpac_54,