RetrogeneDB ID: retro_pabe_173

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:46921226..46921871(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000005783
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPL10
• Ensembl ID: ENSPPYG00000020874
• Aliases: None
• Description: 60S ribosomal protein L10 [Source:RefSeq peptide;Acc:NP_001126004]

Sequence

>retro_pabe_173
ATGGGCCGCCGTCCAGCTTGTTGTTACCGGTATTGTAAGAACAAGCCGTACCCAAAATCTCGTTTCTGCCGAGGGGTTCC
TGATGCCAAGATCCGCATCTTTGACCTGGGTCGAAAGAAGGCAAAAGTGGATGAGTTCCCACTCTGTGGCCACATGGTGT
CTGATGAATATGAGCAGCTGTCTTCTGAAGCCCTGGAGGCCGCCCGTATTTGTGCCAACAAATACATGGTGAAAAGTTGT
GGCAGAGATGGCTTTCACATGCGAGTGCGGCTCCATCCCTTCCATGTCATCCGCATCAACAAGATGTTGTCCTGTGCTGG
GGCTGACAGGCTCCAGACAGGTATGCGAGGTGCCTTTGGAAAACCCCAGGGTACTGTGGCCCGGGTCCACGTTGGTCAAG
TCATCATGTCCATCCGCACCAAGCTTCAGAACAAGGAGCATGTGATTGAAGCCTTGCGCAGGGCCAAGTTCAAGTTCCCT
GGATGCCAGAAGATTCATATCTCCAAGAAGTGGGGCTTCACGAAGTTTAATGCTGACGAATTTGAAGATATGGTGGCCAA
GAAGCGCCTCATTCCTGACGGTTGTGGAGTCAAGTACGTTCCCAGTCACGGCCCCTTGGACAAGTGGCGGGTTCTGCACT
CATGA

Alignment

ORF - retro_pabe_173 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARI
          MGRRPA.CYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARI
Retrocopy MGRRPACCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARI

Parental  CANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSIRT
          CANKYMVKSCG.DGFH.RVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVH.GQVIMSIRT
Retrocopy CANKYMVKSCGRDGFHMRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHVGQVIMSIRT

Parental  KLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPNRGPLDKWR
          KLQNKEHVIEALRRAKFKFPG.QKIHISKKWGFTKFNADEFEDMVA.KRLIPDGCGVKY.P..GPLDKWR
Retrocopy KLQNKEHVIEALRRAKFKFPGCQKIHISKKWGFTKFNADEFEDMVAKKRLIPDGCGVKYVPSHGPLDKWR

Parental  ALHS
          .LHS
Retrocopy VLHS

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	173.12 RPM
SRP007412_cerebellum	0.12 RPM	94.12 RPM
SRP007412_heart	0.03 RPM	266.99 RPM
SRP007412_kidney	0.00 RPM	425.70 RPM
SRP007412_liver	0.03 RPM	442.93 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_173 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_173 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_173 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_93
Gorilla gorilla	retro_ggor_61
Macaca mulatta	retro_mmul_335
Oryctolagus cuniculus	retro_ocun_147
Bos taurus	retro_btau_99

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007454	2 retrocopies	retro_btau_140, retro_btau_99,
Homo sapiens	ENSG00000147403	3 retrocopies	retro_hsap_2030, retro_hsap_3265, retro_hsap_3437,
Macropus eugenii	ENSMEUG00000013163	3 retrocopies	retro_meug_1839, retro_meug_5, retro_meug_547,
Myotis lucifugus	ENSMLUG00000014337	3 retrocopies	retro_mluc_1592, retro_mluc_191, retro_mluc_275,
Monodelphis domestica	ENSMODG00000008731	2 retrocopies	retro_mdom_177, retro_mdom_829,
Mus musculus	ENSMUSG00000008682	1 retrocopy	retro_mmus_71,
Pongo abelii	ENSPPYG00000020874	5 retrocopies	retro_pabe_173 , retro_pabe_1854, retro_pabe_2036, retro_pabe_2843, retro_pabe_2955,