RetrogeneDB ID: retro_pabe_2459

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:104366832..104367150(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000005032
• Aliases: None
• Description: None

Sequence

>retro_pabe_2459
TTAACCAGATTTGAACAGAAGAATGCCCATTTGGCCCAGGTAGAAGTAGATGAAGTGTTTGGTTTCATGTGTCAGGCAAC
TACCAAAGTTCCTCCCCATGATGCAATGTCAGGTGGGATTGTACTTCTTGTCAAACTGCTTCTTGATATGGGCTGAAATA
GTCTTTTTTATGTTCTCCAATGCCTGCATAGCTCACACCACTAAGTCCTGCTGCATCTCTTCCAACATGACTACATTTTT
TTATCCCAGCCTTTCAATTTCACATGGTTACTGTGGAGCAGAGGCTGGCCAACTGGAGTAGTCTCCTTGGGGAGGTGC

Alignment

ORF - retro_pabe_2459 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.37 %
• Parental protein coverage: 98.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LTRFEQKNGHLAQVEVDEVFGFMCHVTTEVPPHDAMPGGIVLLVKFLLLDMSRNVLLYVVFLQRLSSALH
          LTRFEQKN.HLAQVEVDEVFGFMC..TT.VPPHDAM.GGIVLLVK.LLLDM..N.L.YV..LQ.L.S..H
Retrocopy LTRFEQKNAHLAQVEVDEVFGFMCQATTKVPPHDAMSGGIVLLVK-LLLDMG*NSLFYV--LQCLHSSHH

Parental  RVLLHLFRH-VRIFDHGLSVAHGYRG-EGGWPTATVSWGRC
          .VLLHLF.H....F...LS..HGY.G...GWPT..VS.GRC
Retrocopy *VLLHLFQH>TTFFYPSLSISHGYCG<SRGWPTGVVSLGRC

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	4.70 RPM
SRP007412_cerebellum	0.00 RPM	1.70 RPM
SRP007412_heart	0.00 RPM	1.11 RPM
SRP007412_kidney	0.00 RPM	1.09 RPM
SRP007412_liver	0.00 RPM	1.99 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2459 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2459 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2459 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1897

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000009268	3 retrocopies	retro_etel_1297, retro_etel_390, retro_etel_781,
Gorilla gorilla	ENSGGOG00000008793	4 retrocopies	retro_ggor_1066, retro_ggor_1113, retro_ggor_2055, retro_ggor_3078,
Macaca mulatta	ENSMMUG00000001195	6 retrocopies	retro_mmul_1463, retro_mmul_1723, retro_mmul_1897, retro_mmul_2269, retro_mmul_470, retro_mmul_835,
Pongo abelii	ENSPPYG00000005032	6 retrocopies	retro_pabe_1134, retro_pabe_1198, retro_pabe_1215, retro_pabe_1469, retro_pabe_2371, retro_pabe_2459 ,
Tupaia belangeri	ENSTBEG00000008820	3 retrocopies	retro_tbel_1196, retro_tbel_1765, retro_tbel_695,