RetrogeneDB ID: retro_sscr_268

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 11:60569055..60569451(+)
• Located in intron of: None

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_268
GAGACATTCCATTTTGTCTCAAAGAGAGATGAGAAGGTATGTAATTTCCTAGAATGAGGATTATTAATTGGAGGACCCGA
CAACAAACTGATTTATAGACATTATGCAACATTATATTTCATCTTCTGTATCGATTCTTCAGAAAGTGAACTTGGCATTT
TAGATCTAATTCAAGTATTTGTGGAAACTTTAGATAAGTGTTTTGAAAATATCTGTGAACTGGATTTAATTTTCCATGTA
GATAAGGTTCACAATATTCTTGCAGAAATGACAATGCAAGGAGTGGTACTGGAGACCAACATGAATGAGATTGTTACACA
AATTGATGCACAAAGTAAACTGGAGAAATCTGAGGCTGGCTTAGCAGGGGCTCCAGCCCATGCTGTATCAGTTGTT

Alignment

ORF - retro_sscr_268 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.55 %
• Parental protein coverage: 68.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ETFHLVLKRDDNICNFLEGGSLIGGSDYKLIYRHYATLYFVFCVDSSESELGILDLIQVFVETLDKCFEN
          ETFH.V.KRD...CNFLE.G.LIGG.D.KLIYRHYATLYF.FC.DSSESELGILDLIQVFVETLDKCFEN
Retrocopy ETFHFVSKRDEKVCNFLE*GLLIGGPDNKLIYRHYATLYFIFCIDSSESELGILDLIQVFVETLDKCFEN

Parental  VCELDLIFHMDKVHYILQEVVMGGMVLETNMNEIVAQIEAQNKLEKSEGGLSAAPARAVSAV
          .CELDLIFH.DKVH.IL.E..M.G.VLETNMNEIV.QI.AQ.KLEKSE.GL..APA.AVS.V
Retrocopy ICELDLIFHVDKVHNILAEMTMQGVVLETNMNEIVTQIDAQSKLEKSEAGLAGAPAHAVSVV

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	1.33 RPM	24.82 RPM
SRP014902_testis	0.42 RPM	31.40 RPM
SRP018288_heart	0.58 RPM	18.96 RPM
SRP018288_kidney	0.59 RPM	57.53 RPM
SRP018288_liver	0.00 RPM	34.38 RPM
SRP018288_lung	0.71 RPM	31.77 RPM
SRP018856_adipose	0.75 RPM	46.77 RPM
SRP035408_brain	3.14 RPM	30.20 RPM
SRP035408_liver	1.17 RPM	28.62 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_268 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_268 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_268 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,