RetrogeneDB ID: retro_pabe_1844

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 21:37077366..37078207(+)
• Located in intron of: ENSPPYG00000011398

Retrocopy information

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

Parental gene information

• Parental gene symbol: RIMKLB
• Ensembl ID: ENSPPYG00000004244
• Aliases: None
• Description: ribosomal modification protein rimK-like family member B [Source:HGNC Symbol;Acc:29228]

Sequence

>retro_pabe_1844
ATGTGTAGTTCTGTGGCTGCCAAGTTGTGGTTTTTGACAGATCATCACATCAGGGAAGACTATCCTCAAAAAGATTTTAC
TAGCATTGAAGGCCAAATGTTGTGAGGAGGAACTGGACTTTAGGGCTGTGGTGATGGATGAGGTGGTGCTGACAATCGAG
CAAGGAAACCTGGGTCTGCAGATCAATGGAGAGCTAATCACTGCCTACCCACAAGTGGTGGCAGTCAGAGTACCAACCCC
TTGGGTGCAAAGTGATAGTGACATTACTGTTTTGCGCCATCTAGAGAAGATGGGATGCCAGTTAATGAACCGACCTCAAG
CCATCCTGAACTGCGTTAATAAGTTCTGGACATTTCAAGAGTTGGCTGGCCACCGTGTTCCTCTGCCGGATACTTTCTCT
CATGGTGGCCATGAAAATTTTGCTAAAATGATTGATGAAGCTGAAGTACTGGAGTTCCCAATGGTAGTAAAGAATACGCG
GGGTCATAGAGGTAAAGCTGTTTTCTTGGCTTGAGATAAGCACCATTTGGCTGATCTAAGCCATCTTATTTGCCATGAAG
CACCATACTTGTTCCAGAAGTATGTTAAAGAGTCACATGGACGGGATGTACGTGTCATTGTCGTGGGAGGCCGTGTGGTT
GGCACCATGTTACATTGTTCAACAGATGGGAGAATGCAAAGCAACTGCTCATTAGGTGGTGTGGGGATGATGTGCTCACT
GAGTGAACAAGGGAAACAGCTAGTTATCCAGGTGTCTAATATCCTGGGGATGGATGTGTGTGGCATTGACCTGTTGATGA
AAGATGGCGGCTCCTTCTGCGTCTGTGAGGCCAATGCAAAT

Alignment

ORF - retro_pabe_1844 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.84 %
• Parental protein coverage: 91.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MCSSVAAKLWFLTDRRIREDYPQKE-ILRALKAKCCEEELDFRAVVMDEVVLTIEQGNLGLRINGELITA
          MCSSVAAKLWFLTD..IREDYPQK...L......C.EE.LDFRAVVMDEVVLTIEQGNLGL.INGELITA
Retrocopy MCSSVAAKLWFLTDHHIREDYPQKD>LLALKAKCCEEE-LDFRAVVMDEVVLTIEQGNLGLQINGELITA

Parental  YPQVVVVRVPTPWVQSDSDITVLRHLEKMGCRLMNRPQAILNCVNKFWTFQELAGHGVPLPDTFSYGGHE
          YPQVV.VRVPTPWVQSDSDITVLRHLEKMGC.LMNRPQAILNCVNKFWTFQELAGH.VPLPDTFS.GGHE
Retrocopy YPQVVAVRVPTPWVQSDSDITVLRHLEKMGCQLMNRPQAILNCVNKFWTFQELAGHRVPLPDTFSHGGHE

Parental  NFAKMIDEAEVLEFPMVVKNTRGHRGKAVFLARDKHHLADLSHLIRHEAPYLFQKYVKESHGRDVRVIVV
          NFAKMIDEAEVLEFPMVVKNTRGHRGKAVFLA.DKHHLADLSHLI.HEAPYLFQKYVKESHGRDVRVIVV
Retrocopy NFAKMIDEAEVLEFPMVVKNTRGHRGKAVFLA*DKHHLADLSHLICHEAPYLFQKYVKESHGRDVRVIVV

Parental  GGRVVGTMLRCSTDGRMQSNCSLGGVGMMCSLSEQGKQLAIQVSNILGMDVCGIDLLMKDDGSFCVCEAN
          GGRVVGTML.CSTDGRMQSNCSLGGVGMMCSLSEQGKQL.IQVSNILGMDVCGIDLLMKD.GSFCVCEAN
Retrocopy GGRVVGTMLHCSTDGRMQSNCSLGGVGMMCSLSEQGKQLVIQVSNILGMDVCGIDLLMKDGGSFCVCEAN

Parental  AN
          AN
Retrocopy AN

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	0.55 RPM	21.40 RPM
SRP007412_cerebellum	0.97 RPM	21.65 RPM
SRP007412_heart	0.12 RPM	7.41 RPM
SRP007412_kidney	0.36 RPM	9.65 RPM
SRP007412_liver	0.15 RPM	2.11 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1844 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1844 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1844 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2506
Pan troglodytes	retro_ptro_1457
Gorilla gorilla	retro_ggor_31

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000166532	1 retrocopy	retro_hsap_2506,
Gorilla gorilla	ENSGGOG00000000332	1 retrocopy	retro_ggor_31,
Oryctolagus cuniculus	ENSOCUG00000013997	1 retrocopy	retro_ocun_1777,
Otolemur garnettii	ENSOGAG00000011440	2 retrocopies	retro_ogar_1183, retro_ogar_2985,
Pongo abelii	ENSPPYG00000004244	1 retrocopy	retro_pabe_1844 ,
Pan troglodytes	ENSPTRG00000004643	1 retrocopy	retro_ptro_1457,
Rattus norvegicus	ENSRNOG00000023814	1 retrocopy	retro_rnor_255,
Tarsius syrichta	ENSTSYG00000003996	1 retrocopy	retro_tsyr_1977,