RetrogeneDB ID: retro_pabe_2466

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:120853513..120853795(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000009938
• Aliases: None
• Description: None

Sequence

>retro_pabe_2466
TTGCCAGAAGGCCTGGAAGTGGCAGGTCTCCAGCAAGTCGCCGAGGTGCAAAATCTGTTGGATTGCCTGCTCCTCTTGTT
GTGCTGGTGGATCATGCACGTGGACAGGGTGAAGTTGGTGTGTGGCAGGGGTTGAGGGCGCCTTCAGCAGGATCTGGGCA
GTGACCGTGGTCTGAAAAAATGCTGGGTTGAACTCGCAAAGCTTCAGGACAGCCAGGTTGGCTTCTAGATCATAGGCATT
CTCCTTGGCCTGTGTCTCCACTTAGCGCTCCAGGGTGGCCAG

Alignment

ORF - retro_pabe_2466 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.26 %
• Parental protein coverage: 60.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPEGLEVAGLQQVPKVQNLSDWPFFLLMCLVDHALAQGEVCVRQVGEGLQQDLGGDRGLKEGWVELLQLQ
          LPEGLEVAGLQQV..VQNL.D....LL.....H......VC.R..G..LQQDLG.DRGLK..WVEL..LQ
Retrocopy LPEGLEVAGLQQVAEVQNLLDCLLLLLCWWIMHVDRVKLVCGRG*GR-LQQDLGSDRGLKKCWVELAKLQ

Parental  DSQVGFQIIGIFLGLRLYIALQGGQ
          DSQVGF.IIGI.LGL.L..ALQGGQ
Retrocopy DSQVGF*IIGILLGLCLHLALQGGQ

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2466 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2466 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2466 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000021632	2 retrocopies	retro_mmul_1542, retro_mmul_2098,
Pongo abelii	ENSPPYG00000009938	2 retrocopies	retro_pabe_136, retro_pabe_2466 ,