RetrogeneDB ID: retro_ptro_72

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 19:62409654..62410077(+)
• Located in intron of: ENSPTRG00000011551

Retrocopy information

• Ensembl ID: ENSPTRG00000041285
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TRAPPC2
• Ensembl ID: ENSPTRG00000021674
• Aliases: None
• Description: trafficking protein particle complex 2 [Source:HGNC Symbol;Acc:23068]

Sequence

>retro_ptro_72
ATGTCTGGAAGCTTCTACTTTGTAATTGTTGGTCACCATGATAATCCAGTTTTTGAAATGGAGTTTTTGCCAGCTGGGAA
GGCAGAATCCAAAGACGACCATCGTCATCTGAACCAGTTCATAGCTCATGCTGCTCTCGACCTCGTAGATGAGAACATGT
GGCTGTCGAACAACATGTACTTGAAAACTGTGGACAAGTTCAACGAGTGGTTTGTGTCAGCATTTGTCACCGCGGGGCAT
ATGAGGTTTATTATGCTTCATGACATAAGACAAGAAGATGGAATAAAGAACTTCTTTACTGATGTTTATGATTTATATAT
AAAATTTTCAATGAATCCATTTTATGAACCCAATTCTCCTATTCGATCAAGTGCATTTGACAGAAAAGTTCAGTTTCTTG
GGAAGAAACACCTTTTAAGCTGA

Alignment

ORF - retro_ptro_72 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 80.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGSFYFVIVGHHDNPVFEMEFLPAGKAESKDDHRHLNQFIAHAALDLVDENMWLSNNMYLKTVDKFNEW
          MSGSFYFVIVGHHDNPVFEMEFLPAGKAESKDDHRHLNQFIAHAALDLVDENMWLSNNMYLKTVDKFNEW
Retrocopy MSGSFYFVIVGHHDNPVFEMEFLPAGKAESKDDHRHLNQFIAHAALDLVDENMWLSNNMYLKTVDKFNEW

Parental  FVSAFVTAGHMRFIMLHDIRQEDGIKNFFTDVYDLYIKFSMNPFYEPNSPIRSSAFDRKVQFLGKKHLLS
          FVSAFVTAGHMRFIMLHDIRQEDGIKNFFTDVYDLYIKFSMNPFYEPNSPIRSSAFDRKVQFLGKKHLLS
Retrocopy FVSAFVTAGHMRFIMLHDIRQEDGIKNFFTDVYDLYIKFSMNPFYEPNSPIRSSAFDRKVQFLGKKHLLS

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	2.31 RPM	3.57 RPM
SRP007412_cerebellum	2.01 RPM	4.02 RPM
SRP007412_heart	1.22 RPM	0.76 RPM
SRP007412_kidney	2.22 RPM	2.30 RPM
SRP007412_liver	0.56 RPM	1.21 RPM
SRP007412_testis	12.65 RPM	0.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_72 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_72 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_72 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_73
Macaca mulatta	retro_mmul_326

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001719	1 retrocopy	retro_acar_53,
Canis familiaris	ENSCAFG00000011754	2 retrocopies	retro_cfam_1608, retro_cfam_368,
Homo sapiens	ENSG00000196459	1 retrocopy	retro_hsap_73,
Microcebus murinus	ENSMICG00000004690	1 retrocopy	retro_mmur_1022,
Macaca mulatta	ENSMMUG00000022619	1 retrocopy	retro_mmul_326,
Monodelphis domestica	ENSMODG00000017312	2 retrocopies	retro_mdom_1737, retro_mdom_1901,
Mus musculus	ENSMUSG00000079317	2 retrocopies	retro_mmus_198, retro_mmus_2522,
Otolemur garnettii	ENSOGAG00000002870	2 retrocopies	retro_ogar_369, retro_ogar_60,
Pan troglodytes	ENSPTRG00000021674	1 retrocopy	retro_ptro_72 ,
Sorex araneus	ENSSARG00000006353	1 retrocopy	retro_sara_244,
Ictidomys tridecemlineatus	ENSSTOG00000025097	1 retrocopy	retro_itri_1014,