RetrogeneDB ID: retro_ptro_2724

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:143920776..143921432(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMED10
• Ensembl ID: ENSPTRG00000006552
• Aliases: None
• Description: None

Sequence

>retro_ptro_2724
ATGTCTGGTTTGTCTGGCCCAGCAGCCTGGCATGGCCCTTGTCCGTCGGCGTTGCTGCTTTTGCTCCTGCTGGGCCCCAG
CTTGGTCCTCGCCATCTCCTTCCATCTGCCCATTAATTCTCACAACTGCTTCCATGAGGAGATCCACAAGGACCTACTAG
TGACTGGCACATACGAGATCTCTGAGCAGTCTGGGGGCACTGGTGGCCTGTGCAGCCACCTCAAGATCACAGATTCTGCT
GGCCATATTTTCTACTCCAAAGAGAATACAACCAAGGGGAAATTTGCCTTTACCACTGAAGATTATGACATGTTGGAAGT
GTGTTTTGAGAGCAAGGAAACAGGGCGGATACCTGACCAACTTGTGATCCTAGACATGAAGCATGGAGTGGAGGTGAAAA
ATTACAAAGAGATTGCAAAAGTTGAGAAGCTCAAACCATTAGAGGTGAAGCTGTGACACCTAGAAGACCTTTCAGAATCT
ATTGTTAATGATTTTGCCTACATGAAGAAGAGAGAAGAGGAGATGGTGATACCAGTGAGTCAACAAACACGTGGGTCCTA
CACTTCAGCATCTTTTCAATGTTCTGCCTCACTGGACTAGCCACCTGGCAGGTCTTCTACCTGTGATGCTTCTTCAAGGC
TAAGAAGTTGATTGAG

Alignment

ORF - retro_ptro_2724 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.45 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSGLSGPPARRGPFPLALLLLFLLGPSLVLAISFHLPINSRKCLREEIHKDLLVTGAYEISDQSGGAGGL
          MSGLSGP.A..GP.P.ALLLL.LLGPSLVLAISFHLPINS..C..EEIHKDLLVTG.YEIS.QSGG.GGL
Retrocopy MSGLSGPAAWHGPCPSALLLLLLLGPSLVLAISFHLPINSHNCFHEEIHKDLLVTGTYEISEQSGGTGGL

Parental  RSHLKITDSAGHILYSKEDATKGKFAFTTEDYDMFEVCFESKGTGRIPDQLVILDMKHGVEAKNYEEIAK
          .SHLKITDSAGHI.YSKE..TKGKFAFTTEDYDM.EVCFESK.TGRIPDQLVILDMKHGVE.KNY.EIAK
Retrocopy CSHLKITDSAGHIFYSKENTTKGKFAFTTEDYDMLEVCFESKETGRIPDQLVILDMKHGVEVKNYKEIAK

Parental  VEKLKPLEVELRRLEDLSESIVNDFAYMKKREEEM-RDTNESTNTRVLYFSIFSMFCLIGLATWQVFYLR
          VEKLKPLEV.L..LEDLSESIVNDFAYMKKREEEM..DT.ESTNT.VL.FSIFSMFCL.GLATWQVFYL.
Retrocopy VEKLKPLEVKL*HLEDLSESIVNDFAYMKKREEEM<GDTSESTNTWVLHFSIFSMFCLTGLATWQVFYL*

Parental  RFFKAKKLIE
          .FFKAKKLIE
Retrocopy CFFKAKKLIE

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	0.07 RPM	37.16 RPM
SRP007412_cerebellum	0.39 RPM	39.86 RPM
SRP007412_heart	0.00 RPM	55.41 RPM
SRP007412_kidney	0.05 RPM	109.60 RPM
SRP007412_liver	0.16 RPM	89.89 RPM
SRP007412_testis	0.63 RPM	88.10 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2724 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2724 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2724 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4014
Pongo abelii	retro_pabe_3296
Macaca mulatta	retro_mmul_2316

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016899	1 retrocopy	retro_acar_187,
Callithrix jacchus	ENSCJAG00000020627	2 retrocopies	retro_cjac_1409, retro_cjac_4223,
Dasypus novemcinctus	ENSDNOG00000019851	1 retrocopy	retro_dnov_1225,
Echinops telfairi	ENSETEG00000010607	1 retrocopy	retro_etel_1798,
Homo sapiens	ENSG00000170348	2 retrocopies	retro_hsap_2701, retro_hsap_4014,
Gorilla gorilla	ENSGGOG00000007453	1 retrocopy	retro_ggor_2696,
Myotis lucifugus	ENSMLUG00000017125	2 retrocopies	retro_mluc_2079, retro_mluc_2093,
Macaca mulatta	ENSMMUG00000015168	2 retrocopies	retro_mmul_2316, retro_mmul_885,
Mus musculus	ENSMUSG00000021248	2 retrocopies	retro_mmus_1093, retro_mmus_649,
Nomascus leucogenys	ENSNLEG00000016453	2 retrocopies	retro_nleu_2897, retro_nleu_2963,
Oryctolagus cuniculus	ENSOCUG00000004669	1 retrocopy	retro_ocun_875,
Pongo abelii	ENSPPYG00000029389	1 retrocopy	retro_pabe_3296,
Pan troglodytes	ENSPTRG00000006552	2 retrocopies	retro_ptro_1823, retro_ptro_2724 ,
Rattus norvegicus	ENSRNOG00000007901	2 retrocopies	retro_rnor_1729, retro_rnor_2031,
Ictidomys tridecemlineatus	ENSSTOG00000007392	1 retrocopy	retro_itri_362,
Vicugna pacos	ENSVPAG00000003089	1 retrocopy	retro_vpac_573,