RetrogeneDB ID: retro_ptro_2382

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:117167338..117168075(+)
• Located in intron of: ENSPTRG00000018521

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_2382
ATGGCGACCTCCAGGAAGTTCGTTGGGGGGAACTGGAAGATGAACCGACGGAAGAAGAGCCTGGGGGAGCTCATCCGCAC
TCTGAACGCGGCCAAGGTGCCGGCCAACACTGAGGTGGTTTGCACTCTCCCCACTGCCTATATCGACTTTGCCCCAGAAG
CTAGAGCCCAAGATTGCTGTGGCTGCGCAGAACTGCTACAAAGCAACTAACGGGGCCTTTACTTGGGAGATCAGCCCTGG
CATGATCAAAGACTGCAAAGCCAATCGAGGGTCCTGGGGCACTCAGAGAGTAGGCATGTCTTTGGGGAGTCAGATAAGCT
GATTGGGCAGAAAGTGGCCCATGCTCTGGCACAGGGACTCAGAGTAATCGCTTGTACTGGGGAGAAGCTAGCTGAAAGGG
AAGTGGCATCACTGAGAAGTTTGTTTTCGAGAAGAAAGAGGTCATCGCAGATAACGTGAAGGACTGGAGCAAGGTCGTCC
TGGCCTGCGAGCCTGTGTGGGCCATTGGTACCAGCAAGACTGCAACACCCCAGAAGGCCCAGGAAGTACACGAGAAGTTC
TGAGAATGGTGTCCAACATCTCTGATGTGGTGGCTCAGAGCACCCGTATCCATTTATGGAGGCTCTGTGACGGGGGCAAC
CTGCAAGGAGCTGGCCAGCCAGCCTGAAGTGGATGGCTTCCTCGTGGGTGATGCTTCCCTCAAGCCCGAATTCGTGAACA
TCATCAATGCCAAACAA

Alignment

ORF - retro_ptro_2382 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.75 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAPSRKFFVGGNWKMNGRKQSLGELIGTLNAAKVPADTEVVCAPPTAYIDFARQKL-DPKIAVAAQNCYK
          MA.SRK.FVGGNWKMN.RK.SLGELI.TLNAAKVPA.TEVVC..PTAYIDFA......P..........K
Retrocopy MATSRK-FVGGNWKMNRRKKSLGELIRTLNAAKVPANTEVVCTLPTAYIDFAPEAR<SPRLLWLRRTATK

Parental  VTNGAFTG-EISPGMIKDCGATWVVLG-HSERRHVFGESDELIGQKVAHALAEGLGVIACIGEKLDERE-
          ...G...G.EISPGMIKDC.A.....G.HSE.RHVFGESD.LIGQKVAHALA.GL.VIAC.GEKL.ERE.
Retrocopy QLTGPLLG<EISPGMIKDCKANRGSWG<HSESRHVFGESDKLIGQKVAHALAQGLRVIACTGEKLAERE<

Parental  AGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSNVSDAVAQSTR
          .GITEK.VFE...VIADNVKDWSKVVLA.EPVWAIGT.KTATPQ.AQEVHEK...W..............
Retrocopy SGITEKFVFEKKEVIADNVKDWSKVVLACEPVWAIGTSKTATPQKAQEVHEKF*EWCPTSLMWWLRAPVS

Parental  IIYGGSVTGATCKELASQPDVDGFLVGGASLKPEFVDIINAKQ
          I.YGGSVTGATCKELASQP.VDGFLVG.ASLKPEFV.IINAKQ
Retrocopy I-YGGSVTGATCKELASQPEVDGFLVGDASLKPEFVNIINAKQ

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	0.03 RPM	371.36 RPM
SRP007412_liver	0.00 RPM	210.35 RPM
SRP007412_testis	2.85 RPM	142.16 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2382 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2382 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2382 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3510
Pongo abelii	retro_pabe_2902
Macaca mulatta	retro_mmul_1864
Callithrix jacchus	retro_cjac_2370

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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,