RetrogeneDB ID: retro_ptro_2394

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:144806573..144807203(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PARL
• Ensembl ID: ENSPTRG00000015673
• Aliases: None
• Description: None

Sequence

>retro_ptro_2394
TCAGGTATCATAGCTGCAAACGTCCTTGTATTCTGTTTGTGGAGAGTACCTTCTCTGCAGTGGACAGTGATCTGATATTT
CAAATCTAATCCAGCCTCAAAAGTCCGTTGTTCTCCAATGTTGCTGTCAACATTCAATCATTTCTCCTTATTTCACATGG
CAGCAAATATGTATGTTTTGTGGAGCTTCTCCTTCAGTATAGTGAACATTCTGGGTCAAGAGCAGTTCATGGCAGTGTAC
CTATCTGCAGGTGTTATTTCCAATTTTGTCAGTTATGTGTGTAAAGTTGCCACACGAAGATATGGACCATCACTTGGTGC
ATCTCGCGCCATCATGATGATCCTCGCAGCTGTCCGCACTAAGATCCCAGAAGGGAGGCTTGCCATTATTTACTTCCAAT
GTTCACATTCACAGCAGGAAATGCCCTACAATCCATTAACGCCATGGATATGGCAGGAATGATCCTGGGACGGAAATTTT
TTGATTATGCAGCACATCTTGGGGGAGCTCTCTTTGGAATATGGTATGTTACTCACACTCATGAACTGATTTGGAAGAAC
AGGGAGCCTCTAGTGAAAATCTGGCATGAAATGAAGACTAATGACCCCCCAAAAAAGAGGTGGCTCTAAG

Alignment

ORF - retro_ptro_2394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.85 %
• Parental protein coverage: 55.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TGIIAANVLVFCLWRVPSLQRTMIRYFTSNPASKVLCSPMLLSTFSHFSLFHMAANMYVLWSFSSSIVNI
          .GIIAANVLVFCLWRVPSLQ.T.I.YF.SNPASKV.CSPMLLSTF.HFSLFHMAANMYVLWSFS.SIVNI
Retrocopy SGIIAANVLVFCLWRVPSLQWTVI*YFKSNPASKVRCSPMLLSTFNHFSLFHMAANMYVLWSFSFSIVNI

Parental  LGQEQFMAVYLSAGVISNFVSYVGKVATGRYGPSLGASGAIMTVLAAVCTKIPEGRLAIIF-LPMFTFTA
          LGQEQFMAVYLSAGVISNFVSYV.KVAT.RYGPSLGAS.AIM..LAAV.TKIPEGRLAII..LPMFTFTA
Retrocopy LGQEQFMAVYLSAGVISNFVSYVCKVATRRYGPSLGASRAIMMILAAVRTKIPEGRLAIIY<LPMFTFTA

Parental  GNALKAIIAMDTAGMILGWKFFDHAAHLGGALFGIWYVTYGHELIWKNREPLVKIWHEIRTNG-PKKGGG
          GNAL..I.AMD.AGMILG.KFFD.AAHLGGALFGIWYVT..HELIWKNREPLVKIWHE..TN..P.K.GG
Retrocopy GNALQSINAMDMAGMILGRKFFDYAAHLGGALFGIWYVTHTHELIWKNREPLVKIWHEMKTND>PQKRGG

Parental  SK
          SK
Retrocopy SK

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	0.48 RPM	26.99 RPM
SRP007412_cerebellum	0.72 RPM	32.37 RPM
SRP007412_heart	0.12 RPM	30.31 RPM
SRP007412_kidney	0.78 RPM	43.83 RPM
SRP007412_liver	0.26 RPM	37.68 RPM
SRP007412_testis	0.00 RPM	32.14 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2394 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2394 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2394 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3526
Pongo abelii	retro_pabe_2912

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021241	2 retrocopies	retro_cjac_1415, retro_cjac_2384,
Dipodomys ordii	ENSDORG00000014935	1 retrocopy	retro_dord_315,
Homo sapiens	ENSG00000175193	1 retrocopy	retro_hsap_3526,
Gorilla gorilla	ENSGGOG00000000416	1 retrocopy	retro_ggor_2384,
Mus musculus	ENSMUSG00000033918	2 retrocopies	retro_mmus_1882, retro_mmus_3526,
Nomascus leucogenys	ENSNLEG00000006072	1 retrocopy	retro_nleu_491,
Otolemur garnettii	ENSOGAG00000006126	1 retrocopy	retro_ogar_648,
Pan troglodytes	ENSPTRG00000015673	1 retrocopy	retro_ptro_2394 ,
Ictidomys tridecemlineatus	ENSSTOG00000023222	1 retrocopy	retro_itri_380,