RetrogeneDB ID: retro_pabe_1954

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:52499918..52500967(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IK
• Ensembl ID: ENSPPYG00000015861
• Aliases: None
• Description: protein Red [Source:RefSeq peptide;Acc:NP_001126465]

Sequence

>retro_pabe_1954
ATGCCGGAGCGAGATAGTGAGCCGTTCTCCAACCCTTTGGCCCCCGATGGTCACGATGTGGATGATCCTCACTCCTTCCA
CCAATCAAAACTCACCAATGAAGACTTCAGGAAACTTCTCATGACCCCCAGGGCTGCACCTACCTCTGCACCACCTTCTA
AGTCACGTCACCATGAGATGCCAAGGGAGTACAATGAGGATGAAGACCCAGCTGCACGAAGGAGGAAAAACAAGTTATTA
TGCTAAGCTACGCCAACAAGAAATTGAGAGAGACAGAGAGCTAGCAGAGAAGTACCGGGGTCGTGCCAAGGAACGGAGAG
ATGGAGTGAACAAAGATTATGAAGAAACCGAGCTTATCAGCACCACAGCTAACTACAGGGCTGTTGGCCCCACTGCTAAG
GCGGACAAATCAGCTGCAGAGAAGAGAAGACAGTTGATCCAGGAGTCCAAATTCTTCGATGGTGACATGGAACACACCCA
TTTGGTGAAAGGCTTGGATTTTGCTCTGCTTCAAAAGGTACGAGCTGAGATTGCCAGCAAAGAGAAAGAGGAAGAGGAAC
TGATGGGAAACCCCCGGAAAGAAACCAAGAAAGACGAGGATCCTGAAAGTAAAATTGAATTTAAAACACGTCTGGGCCGC
AATGTTTACCAAGTGCTTTTTAAGAACAGGCATATGAGCGGAATGAGTTGTTCCTGCCGGGCCGCATGGCCTATGTGGTA
GACCTGGATGATGAGTAAGCTGACACAGATATCCCCACCACTCTTATCCGCAGCAAGGTTGATTGCCCCACCATGGAGGC
CCAGGCCACACTGACCACAAATGATATTGTCATTAGCAAGCTTACCCAGATCCTTTCACACCTGAGGCAGGGAACCCGTA
ACAAGAAGCTTAAGAAGAAGGATAAAGGGAAGCTGGAAGAGAAGAAACCTCCTGAGGCTGACAGGAGTATTTTTGAAGAC
ATTGGGGATTACATACCCTCCACAACCAAGACACCTTGGGACAAGGAGCGGGAGAGATATCGGGACGGGAGCATGATAGG
GAGACAGAG

Alignment

ORF - retro_pabe_1954 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.24 %
• Parental protein coverage: 63.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPERDSEPFSNPLAPDGHDVDDPHSFHQSKLTNEDFRKLLMTPRAAPTSAPPSKSRHHEMPREYNEDEDP
          MPERDSEPFSNPLAPDGHDVDDPHSFHQSKLTNEDFRKLLMTPRAAPTSAPPSKSRHHEMPREYNEDEDP
Retrocopy MPERDSEPFSNPLAPDGHDVDDPHSFHQSKLTNEDFRKLLMTPRAAPTSAPPSKSRHHEMPREYNEDEDP

Parental  AARRRKKK-SYYAKLRQQEIERERELAEKYRDRAKERRDGVNKDYEETELISTTANYRAVGPTAEADKSA
          AAR.R.K..SYYAKLRQQEIER.RELAEKYR.RAKERRDGVNKDYEETELISTTANYRAVGPTA.ADKSA
Retrocopy AAR-RRKN>SYYAKLRQQEIERDRELAEKYRGRAKERRDGVNKDYEETELISTTANYRAVGPTAKADKSA

Parental  AEKRRQLIQESKFLGGDMEHTHLVKGLDFALLQKVRAEIASKEKEEEELMEKPQKETKKDEDPENKIEFK
          AEKRRQLIQESKF..GDMEHTHLVKGLDFALLQKVRAEIASKEKEEEELM..P.KETKKDEDPE.KIEFK
Retrocopy AEKRRQLIQESKFFDGDMEHTHLVKGLDFALLQKVRAEIASKEKEEEELMGNPRKETKKDEDPESKIEFK

Parental  TRLGRNVYRMLFKSK-AYERNELFLPGRMAYVVDLDDEYADTDIPTTLIRSKADCPTMEAQTTLTTNDIV
          TRLGRNVY..LFK...AYERNELFLPGRMAYVVDLDDE.ADTDIPTTLIRSK.DCPTMEAQ.TLTTNDIV
Retrocopy TRLGRNVYQVLFKNR<AYERNELFLPGRMAYVVDLDDE*ADTDIPTTLIRSKVDCPTMEAQATLTTNDIV

Parental  ISKLTQILSYLRQGTRNKKLKKKDKGKLEEKKPPEADMNIFEDIGDYVPSTTKTPRDKERERYRE-RERD
          ISKLTQILS.LRQGTRNKKLKKKDKGKLEEKKPPEAD..IFEDIGDY.PSTTKTP.DKERERYR..RE.D
Retrocopy ISKLTQILSHLRQGTRNKKLKKKDKGKLEEKKPPEADRSIFEDIGDYIPSTTKTPWDKERERYRD<REHD

Parental  RERD
          RE..
Retrocopy RETE

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	0.11 RPM	107.98 RPM
SRP007412_cerebellum	0.12 RPM	121.24 RPM
SRP007412_heart	0.06 RPM	53.86 RPM
SRP007412_kidney	0.10 RPM	89.66 RPM
SRP007412_liver	0.00 RPM	63.56 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1954 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1954 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1954 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2262
Gorilla gorilla	retro_ggor_1685

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009727	3 retrocopies	retro_dnov_618, retro_dnov_714, retro_dnov_960,
Dipodomys ordii	ENSDORG00000006584	4 retrocopies	retro_dord_128, retro_dord_130, retro_dord_134, retro_dord_139,
Homo sapiens	ENSG00000113141	1 retrocopy	retro_hsap_2262,
Gorilla gorilla	ENSGGOG00000013374	1 retrocopy	retro_ggor_1685,
Loxodonta africana	ENSLAFG00000008152	1 retrocopy	retro_lafr_362,
Otolemur garnettii	ENSOGAG00000014281	1 retrocopy	retro_ogar_1402,
Pongo abelii	ENSPPYG00000015861	1 retrocopy	retro_pabe_1954 ,
Sorex araneus	ENSSARG00000007388	3 retrocopies	retro_sara_416, retro_sara_419, retro_sara_558,