RetrogeneDB ID: retro_ptro_310

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:71287906..71288362(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CASP3
• Ensembl ID: ENSPTRG00000016640
• Aliases: None
• Description: Pan troglodytes caspase 3, apoptosis-related cysteine peptidase (CASP3), mRNA. [Source:RefSeq mRNA;Acc:NM_001012433]

Sequence

>retro_ptro_310
ATAATAATTAATGATAAGAATAAGTGGAATCATAAAAGCACTGGAATGGCATCTTGGTCTGGTACAGATGTCAATGTGGC
AAACCTCAGGGAAACACTCACAACCTTGAAATATGAAGTCAGGAATAAAAATCATCTTACATGTCAAGAAATTGTGGAAT
TGATGCACAGTGTTTCTTAAGAAGATCACAGCAAAAGGAGCAGTTTTGTTTGTGTGCTTTGGAGCCATGGTGAAGAAGGA
ATAATTTTTGGAACAAATGGACCTGTTGACCAGAAAAAGGTAACAAGTTTTTTCAGAGGGGATTGTTGTAGAAGTCTAAC
TGGAAAACCCAAGCTTTTCATTATTCAGGCCTGCCATGGTACAGAACTGGATTCTGGCATTGAGACTGACAGTGGTATTG
ATGATGACATGGCGTGTCATAAAATACCAGTGAAGGCCGAATTTTTGTATGCATAT

Alignment

ORF - retro_ptro_310 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.24 %
• Parental protein coverage: 54.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IIINNKNF--HKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFV
          IIIN.KN...HKSTGM.S.SGTDV..ANLRET...LKYEVRNKN.LT..EIVELM..VS.EDHSKRSSFV
Retrocopy IIINDKNKWNHKSTGMASWSGTDVNVANLRETLTTLKYEVRNKNHLTCQEIVELMHSVS*EDHSKRSSFV

Parental  CVLLSHGEEGIIFGTNGPVDLKKITNFFRGDRCRSLTGKPKLFIIQACRGTELDCGIETDSGVDDDMACH
          CVL.SHGEEGIIFGTNGPVD.KK.T.FFRGD.CRSLTGKPKLFIIQAC.GTELD.GIETDSG.DDDMACH
Retrocopy CVLWSHGEEGIIFGTNGPVDQKKVTSFFRGDCCRSLTGKPKLFIIQACHGTELDSGIETDSGIDDDMACH

Parental  KIPVEADFLYAY
          KIPV.A.FLYAY
Retrocopy KIPVKAEFLYAY

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	0.00 RPM	11.49 RPM
SRP007412_cerebellum	0.00 RPM	17.64 RPM
SRP007412_heart	0.00 RPM	10.55 RPM
SRP007412_kidney	0.00 RPM	10.57 RPM
SRP007412_liver	0.00 RPM	15.48 RPM
SRP007412_testis	0.00 RPM	15.39 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_310 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_310 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_310 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_406
Gorilla gorilla	retro_ggor_402
Pongo abelii	retro_pabe_312

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005740	2 retrocopies	retro_cjac_2678, retro_cjac_3011,
Dasypus novemcinctus	ENSDNOG00000013931	1 retrocopy	retro_dnov_1013,
Dipodomys ordii	ENSDORG00000002554	2 retrocopies	retro_dord_178, retro_dord_620,
Homo sapiens	ENSG00000164305	1 retrocopy	retro_hsap_406,
Gorilla gorilla	ENSGGOG00000025155	1 retrocopy	retro_ggor_402,
Macaca mulatta	ENSMMUG00000012053	1 retrocopy	retro_mmul_114,
Nomascus leucogenys	ENSNLEG00000010895	1 retrocopy	retro_nleu_1005,
Pongo abelii	ENSPPYG00000015236	1 retrocopy	retro_pabe_312,
Pan troglodytes	ENSPTRG00000016640	1 retrocopy	retro_ptro_310 ,
Rattus norvegicus	ENSRNOG00000010475	1 retrocopy	retro_rnor_2747,
Sarcophilus harrisii	ENSSHAG00000009178	1 retrocopy	retro_shar_404,
Ictidomys tridecemlineatus	ENSSTOG00000003865	2 retrocopies	retro_itri_172, retro_itri_586,