RetrogeneDB ID: retro_ptro_2299

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:127288354..127288671(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BOLA3
• Ensembl ID: ENSPTRG00000012078
• Aliases: None
• Description: None

Sequence

>retro_ptro_2299
ATGGCGGCATGGAGCCTGGCCGCAGCAGCGCCTCTGCTCCGCGGGATCTGCGGGCTTCCACTTCACCATGGGATGTTTGA
CACCCAGACTGAGGGGGAGCTCAGAGTGACCCAAATTCTCAAAGAAAAGTTTCCACGAGCTACAGCTATCAAAGTCACTG
ACATTTCTGGAGTTGTGGGACGATGTATGAAATTAAAATTGAATCAGAAGAATTTAAGGAGAAGAGAACTGTCCAGCAGC
ACCAGATGGTTTATCAGGCACTAAAAGAAGAAATCAAAGAGATGCATGGATTGCGGATATCTACCTCTGTCCCCAAA

Alignment

ORF - retro_ptro_2299 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.59 %
• Parental protein coverage: 99.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAWSPAAAAPLLRGIRGLPLHHRMFATQTEGELRVTQILKEKFPRATAIKVTDISG-GCGAMYEIKIES
          MAAWS.AAAAPLLRGI.GLPLHH.MF.TQTEGELRVTQILKEKFPRATAIKVTDISG..CG.MYEIKIES
Retrocopy MAAWSLAAAAPLLRGICGLPLHHGMFDTQTEGELRVTQILKEKFPRATAIKVTDISG<SCGTMYEIKIES

Parental  EEFKEKRTVQQHQMVNQALKEEIKEMHGLRIFTSVPK
          EEFKEKRTVQQHQMV.QALKEEIKEMHGLRI.TSVPK
Retrocopy EEFKEKRTVQQHQMVYQALKEEIKEMHGLRISTSVPK

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	9.69 RPM
SRP007412_cerebellum	0.04 RPM	6.95 RPM
SRP007412_heart	0.03 RPM	17.75 RPM
SRP007412_kidney	0.00 RPM	11.04 RPM
SRP007412_liver	0.00 RPM	5.89 RPM
SRP007412_testis	0.00 RPM	8.01 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2299 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2299 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2299 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3383
Gorilla gorilla	retro_ggor_2290
Macaca mulatta	retro_mmul_2109

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017844	1 retrocopy	retro_cjac_1112,
Homo sapiens	ENSG00000163170	3 retrocopies	retro_hsap_1959, retro_hsap_3383, retro_hsap_4148,
Gorilla gorilla	ENSGGOG00000024505	4 retrocopies	retro_ggor_1423, retro_ggor_1424, retro_ggor_2290, retro_ggor_2786,
Macaca mulatta	ENSMMUG00000015207	2 retrocopies	retro_mmul_1181, retro_mmul_2109,
Mus musculus	ENSMUSG00000045160	1 retrocopy	retro_mmus_1648,
Nomascus leucogenys	ENSNLEG00000000320	4 retrocopies	retro_nleu_1391, retro_nleu_1567, retro_nleu_2604, retro_nleu_971,
Oryctolagus cuniculus	ENSOCUG00000016658	1 retrocopy	retro_ocun_51,
Pongo abelii	ENSPPYG00000012285	2 retrocopies	retro_pabe_1618, retro_pabe_3461,
Pan troglodytes	ENSPTRG00000012078	3 retrocopies	retro_ptro_1309, retro_ptro_2299 , retro_ptro_2820,
Sorex araneus	ENSSARG00000001754	1 retrocopy	retro_sara_83,