RetrogeneDB ID: retro_ptro_2653

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:129396741..129397360(-)
• Located in intron of: ENSPTRG00000023911

Retrocopy information

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

Parental gene information

• Parental gene symbol: CD2BP2
• Ensembl ID: ENSPTRG00000007995
• Aliases: None
• Description: CD2 (cytoplasmic tail) binding protein 2 [Source:HGNC Symbol;Acc:1656]

Sequence

>retro_ptro_2653
CGCCAGGCCTCAGACTTGGAAGAGGAGGACAGCTTGGGCCAGACCCCAGTGAGTGCCCAAGCCTTCTTGGAGGGACTTTT
GGAGCTCCTATTGCCTAGAGAGACAGTGGCTAGGGCACTGAGGCATCTGGGGGCCCGAGGAGGAGGCAAAGGGAGCAGCA
AGGGGCCTGGGTGACCCAGTTCCCTGCAGTGCCCGGACCGGCTCTCCGAATTGGCCGACCAGATGGTGGCCCAGGGAAAC
CTTGGCATGTACCAGGAAACGGAACAGTTGGCCATGCGGCTGAAGGGTTTGGGGTGCCAGGCCCTAGGGACCCCACAATC
CCACACCCCCACACTCCCTAGACATGTTCGCTGAGGAAGTGGCAGAGGGGGAACTGGAGACCCCAACCCCTACCCAGAGA
GGAGAAGCAGAGTTGCCAGGAGATGGTCTGGTGGATGTGATGTGGGAATATAAGTGGGAGAACCCGGGGGATGCCGAGCT
GCATGGGCCCTTCACCAGCGACCAGATGCAGATCTGGGTGAGCGAAGGCTACTTTCCTGATGGTGTTTACTGCCGGAAGC
TGGACCCCCTTCATGGTCAGTTCTACAACTCCAAACGCATTGACTTTGACCTCTACACC

Alignment

ORF - retro_ptro_2653 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.73 %
• Parental protein coverage: 67.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RQASDSEEEDSLGQTSMSAQALLEGLLELLLPRETVAGALRRLGARGGGKGS-KGPGQPSSPQRLDRLSG
          RQASD.EEEDSLGQT..SAQA.LEGLLELLLPRETVA.ALR.LGARGGGKGS.KGPG.PSS.Q..DRLS.
Retrocopy RQASDLEEEDSLGQTPVSAQAFLEGLLELLLPRETVARALRHLGARGGGKGSSKGPG*PSSLQCPDRLSE

Parental  LADQMVARGNLGVYQETRERLAMRLKGLGCQTV-GPHNPTPLPSLDMFAEEVAEEELETPTPTQRGEAES
          LADQMVA.GNLG.YQET.E.LAMRLKGLGCQ...G..........DMFAEEVAE.ELETPTPTQRGEAE.
Retrocopy LADQMVAQGNLGMYQET-EQLAMRLKGLGCQAL>GXXXXXXXXXXDMFAEEVAEGELETPTPTQRGEAEL

Parental  RGDGLVDVMWEYKWENTGDAELYGPFTSTQMQTWVSEGYFPDGVYCRKLDPPGGQFYNSKRIDFDLYT
          .GDGLVDVMWEYKWEN.GDAEL.GPFTS.QMQ.WVSEGYFPDGVYCRKLDP..GQFYNSKRIDFDLYT
Retrocopy PGDGLVDVMWEYKWENPGDAELHGPFTSDQMQIWVSEGYFPDGVYCRKLDPLHGQFYNSKRIDFDLYT

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	0.05 RPM	65.19 RPM
SRP007412_cerebellum	0.04 RPM	66.28 RPM
SRP007412_heart	0.00 RPM	30.69 RPM
SRP007412_kidney	0.03 RPM	67.86 RPM
SRP007412_liver	0.00 RPM	80.46 RPM
SRP007412_testis	0.11 RPM	65.76 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2653 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2653 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2653 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3900
Gorilla gorilla	retro_ggor_2627
Pongo abelii	retro_pabe_3179
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 ,