RetrogeneDB ID: retro_rnor_931

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 13:75174600..75174927(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ap3s2
• Ensembl ID: ENSRNOG00000043141
• Aliases: None
• Description: AP-3 complex subunit sigma-2 [Source:RefSeq peptide;Acc:NP_001108511]

Sequence

>retro_rnor_931
ATTGGAGGATCTGATAACAAACCAATTTGCAGACATTATGCAACACTATATTTTTGTCTTCTGTGTGGATTCCTCAGTAA
GCGAACTTGGCATTTTAGATCTAATTCAAGTATCTGGGGAAACGTTAGACAAATGTTTTGAAGATGTCTCTGAACTGGAT
TTAATATTCCAGGTAGACAAGGATCATAATATTCTTGCAGAAATGGTGGTAGGCGAATGGTATTGGAGACCGACAGGAAT
GAGATTGTCACACAAATTGATACACAAAATAAGCTGGAGAAATCTGAGGCTGGCTTAGCAGGAGCTCCAGCCCGTGCTGT
GTCAGCT

Alignment

ORF - retro_rnor_931 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.68 %
• Parental protein coverage: 64.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IGGSDYKLIYRHYATLYF-VFCVDSSESELGILDLIQVFVETLDKCFENVCELDLIFHMDKVHYILQEVV
          IGGSD.K.I.RHYATLYF.VFCVDSS.SELGILDLIQV..ETLDKCFE.V.ELDLIF..DK.H.IL.E.V
Retrocopy IGGSDNKPICRHYATLYF>VFCVDSSVSELGILDLIQVSGETLDKCFEDVSELDLIFQVDKDHNILAEMV

Parental  MG-GMVLETNMNEIVAQIEAQNRLEKSEGGLSAAPARAVSA
          .G..MVLET..NEIV.QI..QN.LEKSE.GL..APARAVSA
Retrocopy VG<RMVLETDRNEIVTQIDTQNKLEKSEAGLAGAPARAVSA

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
SRP017611_brain	0.00 RPM	26.53 RPM
SRP017611_kidney	0.00 RPM	33.98 RPM
SRP017611_liver	0.00 RPM	15.94 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_931 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_931 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_931 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 25 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	ENSRNOG00000003829	1 retrocopy	retro_rnor_1460,
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,