RetrogeneDB ID: retro_pabe_119

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:2271688..2272351(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000019910
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000005031
• Aliases: None
• Description: None

Sequence

>retro_pabe_119
ATGTCGGGCTGGGCGGACGAGCGCGGCGGCGAGGGCGACGGGCGCATCTACGTGGGGAACCTTCCGACCGACGTGCGCGA
GAAGGACTTGGAGGACCTGTTCTACAAGTACGGCCGCATCCGCGAGATCGAGCTCAAGAACCGGCACGGCCTCGTGCCCT
TCGCCTTCGTGCGCTTCGAGGACCCCCGAGATGCAGAGGATGCTATTTATGGAAGAAATGGTTATGATTATGGCCAGTGT
CGGCTTCGTGTGGAGTTCCCCAGGACTTACGGAGGTCGGGGTGGGTGGCCCCGTGGTGGGAGGAATGGGCCTCCTACAAG
AAGATCTGATTTCCGAGTTCTTGTTTCAGGACTTCCTCCGTCAGGCAGCTGGCAGGACCTGAAGGATCACATGCGAGAAG
CTGGGGATGTCTGTTATGCTGATGTGCAGAAGGATGGAGTGGGGATGGTTGAGTATCTCAGAAAAGAAGACGTGGAATAT
GCCCTGCGTAAACTGGATGACACCAAATTCCACTCTCATGAGGGTGAAACTTCCTACATCCGAGTTTATCCTGAGAGAAG
CACCAGCTATGGCTACTCACGGTCTCGGTCTGGGTCAAGGGGCCGTGACTCTCCATACCAAAGCAGGGGTTCCCCACACC
ACTTCTCTCCTTTCAGGCCCTAC

Alignment

ORF - retro_pabe_119 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.64 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGWADERGGEGDGRIYVGNLPTDVREKDLEDLFYKYGRIREIELKNRHGLVPFAFVRFEDPRDAEDAIY
          MSGWADERGGEGDGRIYVGNLPTDVREKDLEDLFYKYGRIREIELKNRHGLVPFAFVRFEDPRDAEDAIY
Retrocopy MSGWADERGGEGDGRIYVGNLPTDVREKDLEDLFYKYGRIREIELKNRHGLVPFAFVRFEDPRDAEDAIY

Parental  GRNGYDYGQCRLRVEFPRTYGGRGGWPRGGRNGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYA
          GRNGYDYGQCRLRVEFPRTYGGRGGWPRGGRNGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYA
Retrocopy GRNGYDYGQCRLRVEFPRTYGGRGGWPRGGRNGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYA

Parental  DVQKDGVGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPERSTSYGYSRSRSGSRGRDSPYQSRG
          DVQKDGVGMVEYLRKED.EYALRKLDDTKF.SHEGETSYIRVYPERSTSYGYSRSRSGSRGRDSPYQSRG
Retrocopy DVQKDGVGMVEYLRKEDVEYALRKLDDTKFHSHEGETSYIRVYPERSTSYGYSRSRSGSRGRDSPYQSRG

Parental  SPHYFSPFRPY
          SPH.FSPFRPY
Retrocopy SPHHFSPFRPY

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	25.05 RPM
SRP007412_cerebellum	0.00 RPM	13.50 RPM
SRP007412_heart	0.00 RPM	4.85 RPM
SRP007412_kidney	0.07 RPM	26.52 RPM
SRP007412_liver	0.09 RPM	18.88 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_119 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_119 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_119 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012792	1 retrocopy	retro_btau_837,
Choloepus hoffmanni	ENSCHOG00000009241	1 retrocopy	retro_chof_1119,
Callithrix jacchus	ENSCJAG00000001187	1 retrocopy	retro_cjac_442,
Dasypus novemcinctus	ENSDNOG00000012598	2 retrocopies	retro_dnov_1555, retro_dnov_2648,
Homo sapiens	ENSG00000111786	1 retrocopy	retro_hsap_2530,
Macaca mulatta	ENSMMUG00000016494	1 retrocopy	retro_mmul_2154,
Nomascus leucogenys	ENSNLEG00000015661	1 retrocopy	retro_nleu_1931,
Otolemur garnettii	ENSOGAG00000003852	1 retrocopy	retro_ogar_2328,
Ochotona princeps	ENSOPRG00000004234	1 retrocopy	retro_opri_878,
Pongo abelii	ENSPPYG00000005031	1 retrocopy	retro_pabe_119 ,
Pongo abelii	ENSPPYG00000011019	1 retrocopy	retro_pabe_1483,
Sarcophilus harrisii	ENSSHAG00000005685	1 retrocopy	retro_shar_598,
Sus scrofa	ENSSSCG00000009906	1 retrocopy	retro_sscr_745,
Tupaia belangeri	ENSTBEG00000008499	1 retrocopy	retro_tbel_2602,
Tarsius syrichta	ENSTSYG00000006848	4 retrocopies	retro_tsyr_1432, retro_tsyr_1648, retro_tsyr_585, retro_tsyr_891,