RetrogeneDB ID: retro_pabe_2903

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:120900919..120901485(+)
• Located in intron of: ENSPPYG00000016967

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000020365
• Aliases: None
• Description: None

Sequence

>retro_pabe_2903
ATGAACGGAGACAGCACCTTTGCAAAGAGACCCAGGGATGATGCTCAGATATCAGAGAAGAGACACAAGACCTTCAATGA
TATTGCCAGATACTTATCTAATAAAGAATGGGGAAAGCTGAAAAACTCAGAGAAAATCACCTATGTGTATATGAAGAGAA
ACTATGAGACCATGACTAAACTAGGTCTCTAGGCCATCCTCCCAACTTTCATGTACAATAAATGGGCTGCAGAATTCCAG
GGGAATGATTCTGATGTAGACTAAAACTGCAGGAATCAGGATGAATATCCTCAGATGGCTTTCGGCATGCTACAAGGGAA
CTTTCCAAAGATGATGCCCAAGAAGCCAGCAGAGGAAGGAAATGATTTGAAGGGAGTGCCAGAAGCATCTGGCTCACAAA
ACAATGGGAAACAGCTGTGTCCCCCAGGAAAAGAAAGTACCTCTGAGAAGACTAACAAGACATCTGGACCCAAGAAAAGG
GGGAACATGTCTGGACCCACGGACTGCGAGAGAGAAAGTATCTAGTGATTTATGAAGAGATCAGCGACCCTAAGGAAGAT
GACAAA

Alignment

ORF - retro_pabe_2903 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.16 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNGDDAFARRPTVGAQIPEKMQKAFDDIAKYFSKEEWEKMKASEKIIYVYMKRNYEAMTKLGFKATLPPF
          MNGD..FA.RP...AQI.EK..K.F.DIA.Y.S..EW.K.K.SEKI.YVYMKRNYE.MTKLG..A.LP.F
Retrocopy MNGDSTFAKRPRDDAQISEKRHKTFNDIARYLSNKEWGKLKNSEKITYVYMKRNYETMTKLGL*AILPTF

Parental  MRNKRAEDFQGNDSDNDPNRGNQVERPQMTFGRLQRIFPKIMPKKPAEEGNDSKGVPEASGSQNNGKQLC
          M.NK.A..FQGNDSD.D.N..NQ.E.PQM.FG.LQ..FPK.MPKKPAEEGND.KGVPEASGSQNNGKQLC
Retrocopy MYNKWAAEFQGNDSDVD*NCRNQDEYPQMAFGMLQGNFPKMMPKKPAEEGNDLKGVPEASGSQNNGKQLC

Parental  PPGKPSTSEKINKTSGP-KRG-KHAWTHRLHERKQLVIYEEISDPEEDDE
          PPGK.STSEK.NKTSGP.KRG..H.WTH.L.ERK.LVIYEEISDP.EDD.
Retrocopy PPGKESTSEKTNKTSGPKKRG<EHVWTHGLRERKYLVIYEEISDPKEDDK

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	0.00 RPM
SRP007412_cerebellum	0.36 RPM	0.00 RPM
SRP007412_heart	4.46 RPM	0.00 RPM
SRP007412_kidney	11.40 RPM	0.00 RPM
SRP007412_liver	0.03 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2903 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2903 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2903 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3512
Pan troglodytes	retro_ptro_2385
Gorilla gorilla	retro_ggor_2374
Macaca mulatta	retro_mmul_1862
Callithrix jacchus	retro_cjac_2373

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014776	1 retrocopy	retro_cjac_2373,
Macaca mulatta	ENSMMUG00000019164	1 retrocopy	retro_mmul_1862,
Pongo abelii	ENSPPYG00000020365	1 retrocopy	retro_pabe_2903 ,
Ictidomys tridecemlineatus	ENSSTOG00000015375	3 retrocopies	retro_itri_1394, retro_itri_1855, retro_itri_746,