RetrogeneDB ID: retro_pabe_3179

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:124916392..124917014(-)
• Located in intron of: ENSPPYG00000017972

Retrocopy information

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

Parental gene information

• Parental gene symbol: CD2BP2
• Ensembl ID: ENSPPYG00000007267
• Aliases: None
• Description: CD2 antigen cytoplasmic tail-binding protein 2 [Source:RefSeq peptide;Acc:NP_001125729]

Sequence

>retro_pabe_3179
CGCCAGGCCTCAGACTTGGAAGAGGAGGACAGCTTGGGCCAGACCCCAGTGAGTGCCCAAGCCCTCTTGGAGGGACTTTT
GGAGCTCCTATTGCCTAGAGAGACAGTGGCTACGGCACTGAGGTGTCTGGGGGCCCGACGAGGAGGCAAAGGGAGCAGCA
AGGGGCCTGGGTGACCCAGTTCCCCGCAGCGCCCGGACCGGCTCTCCGAACTGGCCGACCAGATGGTGGCCCAGGGAAAC
CTTGGCATGTACCAGGAAACAAGGGAACAGTTGGCCATGTGGCTGAAGGGTTTGGGGTGCCAGGCCCTAGGGACCCCACA
ATCCTACACCCCCACACTCCCTGGACATGTTTGCTGAGGAAGTGGCGGAGGGGGAACTGGTGACCCCAACCCCTACCCAG
AGAGGAGAAGCAGAGTTGCCAGGAGATGGTCTGGTGGATGTGATGTGGGAATATAAGTGGGAGAACCCGGGGGATGCTGA
GCTGCATGGGCCCTTCAACAGCACCCAGATGCAGATCTGGGTGAGTGAAGGCTACTTTCCTGATGGTGTTTATTGCTGGA
AGCTGGACCCCCTTAGTGGTCAGTTCTACAACTCCAAACGCATTGACTTTGACCTCTACACC

Alignment

ORF - retro_pabe_3179 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.33 %
• Parental protein coverage: 59.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RQASDSEEEDSLGQTPMSAQALLEGLLELLLPRETVAGALRRLGARGGGRG-SKGPGRPSSPQRLDRLSG
          RQASD.EEEDSLGQTP.SAQALLEGLLELLLPRETVA.ALR.LGAR.GG.G.SKGPG.PSSPQR.DRLS.
Retrocopy RQASDLEEEDSLGQTPVSAQALLEGLLELLLPRETVATALRCLGARRGGKGSSKGPG*PSSPQRPDRLSE

Parental  LADQMVARGNLGVYQETRERLAMRL--LGCQTL--PHNPTPP-SLDMSLRRLAEEELETPTIKKRGEAES
          LADQMVA.GNLG.YQETRE.LAM.L..LGCQ.L..P...TP..SLDM.....AE.EL.TPT...RGEAE.
Retrocopy LADQMVAQGNLGMYQETREQLAMWLKGLGCQALGTPQSYTPT>SLDMFAEEVAEGELVTPTPTQRGEAEL

Parental  PGDGLVDVMWEYKWENTGDAELYGPFTSAQMQTWVSEGYFPDGVYCRKLDPPGGQFYNSKRIDFDLYT
          PGDGLVDVMWEYKWEN.GDAEL.GPF.S.QMQ.WVSEGYFPDGVYC.KLDP..GQFYNSKRIDFDLYT
Retrocopy PGDGLVDVMWEYKWENPGDAELHGPFNSTQMQIWVSEGYFPDGVYCWKLDPLSGQFYNSKRIDFDLYT

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	0.06 RPM	86.14 RPM
SRP007412_cerebellum	0.12 RPM	53.75 RPM
SRP007412_heart	0.18 RPM	35.16 RPM
SRP007412_kidney	0.17 RPM	89.26 RPM
SRP007412_liver	0.18 RPM	37.70 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3179 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3179 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3179 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3900
Pan troglodytes	retro_ptro_2653
Gorilla gorilla	retro_ggor_2627
Macaca mulatta	retro_mmul_1735

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000169217	1 retrocopy	retro_hsap_3900,
Gorilla gorilla	ENSGGOG00000014271	1 retrocopy	retro_ggor_2627,
Macaca mulatta	ENSMMUG00000021844	1 retrocopy	retro_mmul_1735,
Nomascus leucogenys	ENSNLEG00000015767	1 retrocopy	retro_nleu_1139,
Pongo abelii	ENSPPYG00000007267	1 retrocopy	retro_pabe_3179 ,
Pan troglodytes	ENSPTRG00000007995	1 retrocopy	retro_ptro_2653,