RetrogeneDB ID: retro_pabe_2122

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:63686845..63687057(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LY6E
• Ensembl ID: ENSPPYG00000018927
• Aliases: None
• Description: lymphocyte antigen 6 complex, locus E [Source:HGNC Symbol;Acc:6727]

Sequence

>retro_pabe_2122
ATGAAGGTCTTCTTGCCAGCCCTGCTGGCTGCCTTTTTGGGTGTGGGTCGGCCCGCTTGTTGGTGCACTGCTGCTGCACA
AACCAGAACAGCAATCTGTGCTGCCTGAAGCCCACCATCTGCTCCCACGAGGACCGCCCCTACGTGAACATGTCCGCTGT
GGGCATTGGGAGCGTCATGGACATTGGCCACATCCTGAACAAGGGCTGCTCC

Alignment

ORF - retro_pabe_2122 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.53 %
• Parental protein coverage: 54.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKIFLPVLLAALLGVER-ASSLMCFSCLNQKSNLYCLKPTICSDQDNYCVTVSASAGIGNLVTFGHSLSK
          MK.FLP.LLAA.LGV.R.A..L....C.NQ.SNL.CLKPTICS..D...V..SA..GIG.....GH.L.K
Retrocopy MKVFLPALLAAFLGVGR<ARLLVHCCCTNQNSNLCCLKPTICSHEDRPYVNMSA-VGIGSVMDIGHILNK

Parental  TCS
          .CS
Retrocopy GCS

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	35.28 RPM
SRP007412_cerebellum	0.00 RPM	15.32 RPM
SRP007412_heart	0.00 RPM	7.22 RPM
SRP007412_kidney	0.00 RPM	10.74 RPM
SRP007412_liver	0.00 RPM	10.80 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2122 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2122 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2122 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021460	2 retrocopies	retro_cjac_2250, retro_cjac_808,
Mus musculus	ENSMUSG00000022587	1 retrocopy	retro_mmus_724,
Pongo abelii	ENSPPYG00000018927	1 retrocopy	retro_pabe_2122 ,
Tursiops truncatus	ENSTTRG00000001986	2 retrocopies	retro_ttru_1323, retro_ttru_742,