RetrogeneDB ID: retro_pabe_174

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:134808674..134809757(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000020748
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000025858
• Aliases: None
• Description: None

Sequence

>retro_pabe_174
ATGGGGAACGTGTTGGCCGCCAGCTCGCCGCCCGCAGGGCCGCCACCGCCGCCTGCGCCGGCCCTCGTGGGGCTGCCGCC
ACCTCCGCCCTCGCCGCCGGGCTTCACGCTGCCGCCGCTGGGAGGCAGCCTGGGCGCCGGCACCAGTACGAGTCGAGGTT
CGGAACGGACCCCCGGGGCTGCAACCGCCAGCGCCTCAGGGGCCGCCGAGGATGGGGCCTGCGGCTGCCTGCCCAACCCG
GGCACATTCGAGGAGTGCCACCGGAAGTGCAAGGAGCTGTTTCCCATTCAGATGGAGGGTATCAAGCTCACAGTCAACAA
AGGGTTGAGTAACCATTTCCAGGTCAACCACACAGTAGCCCTCAGCACAATCGGGGAGTCCAACTACCACTTCGGGGTCA
CGTATGTGGGGACAAAGCAGCTGAGTCCCACAGAGGCGTTCCCTGTACTGGTGGGTGACATGGACAACAGTGGCAGTCTC
AACGCTCAGGTCATTCACCAGCTGGGCCCCGGTCTCAGGTCCAAGATGGCCATCCAGACCCAGCAATCGAAGTTTGTGAA
CTGGCAGGTGGACGGCGAGTATCGGGGCTCTGACTTCACAGCAGCCATCACCCTGGGGAACCCAGACGTCCTCGTGGGTT
CAGGAATCCTCGTAGCCCACTACCTCCAGAGCATCACGCCCTGCCTGGCCCTGGGCGGAGAGCTGGTCTACCACCGGCGG
CCTGGAGAGGAGGGCACTGTCATGTCTCTAGCTGCGAAATACACATTGAACAACTGGTTGGCAACGGTAACGTTGGGCCA
GGCGGGCATGCACACAACATACTACCACAAAGCCAGTGACAAGCTGCAGGTGGGTGTGGAGTTTGAGGCCAGCACAAGGA
TGCAGGACACCAGCGTCTCCTTCGGGTACCAGCTGGACCTGTCCAAGGCCAACCTCCTCTTCAAAGGCTCTGTGGATAGC
AACTGGATCGTGGGTGCCACGCTGGAGAAGAAGCTCCCGCCCCTGCCCCTGACACTGGCCCTTGGGGCCTTCCTGAATCA
CCGCAAGAACAAGTTCCAGTGTGGCTTTGGCCTCACCATCGGC

Alignment

ORF - retro_pabe_174 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGNVLAASSPPAGPPPPPAPALVGLPPPPASPPGFTLPPLGGYRGAGTSTSRGSERTPGAATASTSGAAE
          MGNVLAASSPPAGPPPPPAPALVGLPPPP.SPPGFTLPPLGG..GAGTSTSRGSERTPGAATAS.SGAAE
Retrocopy MGNVLAASSPPAGPPPPPAPALVGLPPPPPSPPGFTLPPLGGSLGAGTSTSRGSERTPGAATASASGAAE

Parental  DGACGCLPNPGTFEECHGKCKELFPIQMEGVKLTVNKGLSNHFQVNHTVALSTIGESNYHFGVTYVGTKQ
          DGACGCLPNPGTFEECH.KCKELFPIQMEG.KLTVNKGLSNHFQVNHTVALSTIGESNYHFGVTYVGTKQ
Retrocopy DGACGCLPNPGTFEECHRKCKELFPIQMEGIKLTVNKGLSNHFQVNHTVALSTIGESNYHFGVTYVGTKQ

Parental  LSPTEAFPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQTQQSKFVNWQVDGEYRGSDFTVAVTLGNPDV
          LSPTEAFPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQTQQSKFVNWQVDGEYRGSDFT.A.TLGNPDV
Retrocopy LSPTEAFPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQTQQSKFVNWQVDGEYRGSDFTAAITLGNPDV

Parental  LVGSGILVAHYLQSITPCLALGGELVYHRRPGEEGTVMSLAGKYTLNNWLATVTLGQAGMHATYYHKASD
          LVGSGILVAHYLQSITPCLALGGELVYHRRPGEEGTVMSLA.KYTLNNWLATVTLGQAGMH.TYYHKASD
Retrocopy LVGSGILVAHYLQSITPCLALGGELVYHRRPGEEGTVMSLAAKYTLNNWLATVTLGQAGMHTTYYHKASD

Parental  QLQVGVEFEASTRMQDTSVSFGYQLDLPKANLLFKGSVDSNWIVGATLEKKLPPLPLTLALGAFLNHRKN
          .LQVGVEFEASTRMQDTSVSFGYQLDL.KANLLFKGSVDSNWIVGATLEKKLPPLPLTLALGAFLNHRKN
Retrocopy KLQVGVEFEASTRMQDTSVSFGYQLDLSKANLLFKGSVDSNWIVGATLEKKLPPLPLTLALGAFLNHRKN

Parental  KFQCGFGLTIG
          KFQCGFGLTIG
Retrocopy KFQCGFGLTIG

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	1.33 RPM	17.08 RPM
SRP007412_cerebellum	1.22 RPM	9.97 RPM
SRP007412_heart	0.54 RPM	3.85 RPM
SRP007412_kidney	1.43 RPM	14.62 RPM
SRP007412_liver	0.70 RPM	9.46 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_174 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_174 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_174 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000023033	1 retrocopy	retro_ggor_1356,
Microcebus murinus	ENSMICG00000014041	1 retrocopy	retro_mmur_420,
Myotis lucifugus	ENSMLUG00000028928	1 retrocopy	retro_mluc_697,
Macaca mulatta	ENSMMUG00000014303	1 retrocopy	retro_mmul_1998,
Nomascus leucogenys	ENSNLEG00000001726	2 retrocopies	retro_nleu_2368, retro_nleu_2542,
Oryctolagus cuniculus	ENSOCUG00000023582	1 retrocopy	retro_ocun_1143,
Pongo abelii	ENSPPYG00000025858	1 retrocopy	retro_pabe_174 ,
Pan troglodytes	ENSPTRG00000011126	1 retrocopy	retro_ptro_39,
Ictidomys tridecemlineatus	ENSSTOG00000009019	1 retrocopy	retro_itri_150,
Drosophila melanogaster	FBgn0016041	1 retrocopy	retro_dmel_74,