RetrogeneDB ID: retro_ptro_3004

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL391092.1:4693..5017(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK2AP2
• Ensembl ID: ENSPTRG00000003966
• Aliases: None
• Description: None

Sequence

>retro_ptro_3004
ATGTCCTACTAACCTACCACCCCTGCCCCCAGCAGCACCCCCGGCTCCAGCACCCCTGGGCCAGGCACTCCGGTCCCTAC
AGGAAGCGTCCCGTTGCCGTCGGGCTCAGGGCCAGGAGCCACTGCCCCTTGCAGACCGCTGTTTAAAGACTTTGGACCGC
CTACCGTCGGTTGTGTGCAGGCCATGAAACCACCTGGTGCTCAGGGCTCCCAGAGCACCTACACGGAACTGCTGTTGGTC
ACAGGGGAGATGGGCAAAGGGATCCGGCCCACCTATGCTGGCAGCAAGAGCGCCGCGGAGCGCCTGAAGAGAGGTATCAT
CCAT

Alignment

ORF - retro_ptro_3004 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.26 %
• Parental protein coverage: 85.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSYKPIAPAPSSTPGSSTPGPGTPVPTGSVPSPSGSVPGAGAPFRPLFNDFGPPSMGYVQAMKPPGAQGS
          MSY.P..PAPSSTPGSSTPGPGTPVPTGSVP.PSGS.PGA.AP.RPLF.DFGPP..G.VQAMKPPGAQGS
Retrocopy MSY*PTTPAPSSTPGSSTPGPGTPVPTGSVPLPSGSGPGATAPCRPLFKDFGPPTVGCVQAMKPPGAQGS

Parental  QSTYTDLLSVIEEMGKEIRPTYAGSKSAMERLKRGIIH
          QSTYT.LL.V..EMGK.IRPTYAGSKSA.ERLKRGIIH
Retrocopy QSTYTELLLVTGEMGKGIRPTYAGSKSAAERLKRGIIH

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	0.43 RPM	22.84 RPM
SRP007412_cerebellum	0.50 RPM	9.57 RPM
SRP007412_heart	0.29 RPM	5.65 RPM
SRP007412_kidney	0.34 RPM	31.23 RPM
SRP007412_liver	0.00 RPM	45.01 RPM
SRP007412_testis	0.11 RPM	1.26 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3004 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3004 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3004 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011370	1 retrocopy	retro_cfam_55,
Equus caballus	ENSECAG00000020079	2 retrocopies	retro_ecab_180, retro_ecab_579,
Echinops telfairi	ENSETEG00000006428	3 retrocopies	retro_etel_257, retro_etel_334, retro_etel_437,
Homo sapiens	ENSG00000167797	4 retrocopies	retro_hsap_3699, retro_hsap_4172, retro_hsap_4176, retro_hsap_4268,
Gorilla gorilla	ENSGGOG00000010159	3 retrocopies	retro_ggor_2502, retro_ggor_2799, retro_ggor_2800,
Macaca mulatta	ENSMMUG00000011827	5 retrocopies	retro_mmul_1712, retro_mmul_640, retro_mmul_728, retro_mmul_730, retro_mmul_763,
Nomascus leucogenys	ENSNLEG00000006438	1 retrocopy	retro_nleu_176,
Otolemur garnettii	ENSOGAG00000008275	1 retrocopy	retro_ogar_1584,
Pan troglodytes	ENSPTRG00000003966	9 retrocopies	retro_ptro_2508, retro_ptro_2973, retro_ptro_2976, retro_ptro_3002, retro_ptro_3003, retro_ptro_3004 , retro_ptro_3005, retro_ptro_3008, retro_ptro_3009,
Pan troglodytes	ENSPTRG00000005596	3 retrocopies	retro_ptro_1574, retro_ptro_1921, retro_ptro_2929,
Tupaia belangeri	ENSTBEG00000005476	2 retrocopies	retro_tbel_439, retro_tbel_612,