RetrogeneDB ID: retro_ptro_1999

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:83017990..83018435(+)
• Located in intron of: ENSPTRG00000016049

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPI1
• Ensembl ID: ENSPTRG00000004595
• Aliases: None
• Description: Pan troglodytes triosephosphate isomerase 1 (TPI1), mRNA. [Source:RefSeq mRNA;Acc:NM_001071782]

Sequence

>retro_ptro_1999
GGGAACTGGAAGATGAATGGGTGGAAGAAGAGTCTTGGGGAGCTCATTGACACTGAACGTGACCAAGGTGCCAGCCGACG
CTGAGGTGGTTTTCTCTCCCCCAACTGCCTATATCGACTTCACCCAGCAGAAGCTAGATCCCAAGATTGCTGTGCCTGTG
CAGAACTGCTACAAAGTGACTAATGGGGCCTTTACTGGGGAGATCAGCCCTGGCATAATCAAAGACTGCGGAGGTACGTG
GGTGGTCCTGGGGCACTCAGAGAGAAGGCATGTCTTTGGGGAGTCAGATGAACTGATTGAGCAGAAAGTGGCCCATGCTC
TGGCAGAGGGACTTGGAGTAATCACCTGCATTGGGAAGAAGCTAGATGCAAGGGAAGCTGGCATCACTGAGAAGGTTGTT
TTCGAGCAGGCAAAGGTCATCACAGATAAGGTGAAGGGACTAAGC

Alignment

ORF - retro_ptro_1999 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.0 %
• Parental protein coverage: 59.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GNWKMNGRKQS-LGELIGTLNAAKVPADTEVVCAPPTAYIDFARQKLDPKIAVAAQNCYKVTNGAFTGEI
          GNWKMNG.K.S.LG....TLN..KVPAD.EVV..PPTAYIDF..QKLDPKIAV..QNCYKVTNGAFTGEI
Retrocopy GNWKMNGWKKS>LGSSL-TLNVTKVPADAEVVFSPPTAYIDFTQQKLDPKIAVPVQNCYKVTNGAFTGEI

Parental  SPGMIKDCGATWVVLGHSERRHVFGESDELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTK
          SPG.IKDCG.TWVVLGHSERRHVFGESDELI.QKVAHALAEGLGVI.CIG.KLD.REAGITEKVVFEQ.K
Retrocopy SPGIIKDCGGTWVVLGHSERRHVFGESDELIEQKVAHALAEGLGVITCIGKKLDAREAGITEKVVFEQAK

Parental  VIADNVKDWS
          VI.D.VK..S
Retrocopy VITDKVKGLS

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	602.46 RPM
SRP007412_cerebellum	0.00 RPM	278.72 RPM
SRP007412_heart	0.00 RPM	265.67 RPM
SRP007412_kidney	0.00 RPM	371.36 RPM
SRP007412_liver	0.00 RPM	210.35 RPM
SRP007412_testis	0.00 RPM	142.16 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1999 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1999 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1999 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3038
Callithrix jacchus	retro_cjac_2190

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007348	2 retrocopies	retro_cjac_2190, retro_cjac_2370,
Homo sapiens	ENSG00000111669	3 retrocopies	retro_hsap_3038, retro_hsap_3510, retro_hsap_3784,
Gorilla gorilla	ENSGGOG00000002623	1 retrocopy	retro_ggor_151,
Macropus eugenii	ENSMEUG00000006977	5 retrocopies	retro_meug_1348, retro_meug_1520, retro_meug_1934, retro_meug_267, retro_meug_512,
Myotis lucifugus	ENSMLUG00000024989	4 retrocopies	retro_mluc_1090, retro_mluc_1311, retro_mluc_1777, retro_mluc_1807,
Macaca mulatta	ENSMMUG00000005194	2 retrocopies	retro_mmul_1864, retro_mmul_250,
Mustela putorius furo	ENSMPUG00000016774	1 retrocopy	retro_mputfur_136,
Mus musculus	ENSMUSG00000023456	4 retrocopies	retro_mmus_1180, retro_mmus_3260, retro_mmus_532, retro_mmus_558,
Nomascus leucogenys	ENSNLEG00000004821	2 retrocopies	retro_nleu_1120, retro_nleu_847,
Otolemur garnettii	ENSOGAG00000031254	1 retrocopy	retro_ogar_109,
Pan troglodytes	ENSPTRG00000004595	4 retrocopies	retro_ptro_160, retro_ptro_1999 , retro_ptro_2382, retro_ptro_2565,
Rattus norvegicus	ENSRNOG00000015290	1 retrocopy	retro_rnor_1304,
Rattus norvegicus	ENSRNOG00000050669	2 retrocopies	retro_rnor_2615, retro_rnor_787,