RetrogeneDB ID: retro_ptro_1091

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 16:23605526..23606030(+)
• Located in intron of: ENSPTRG00000007886

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000008072
• Aliases: None
• Description: None

Sequence

>retro_ptro_1091
AGATATGCAAATAGATCTCTGGCTATTTTTGACAAGCCAATACACCCACTTTCACAAGAGAAGGTTCCAGGGAAATCCTT
CGAGCATGATCCCAAACGCAGCTGTACTTTCAGATATTTCTGTACTCTTTTTCAAGTCATAAAACTAACAGCTCCATGTG
CAATCGTAGCTTTGGTGTACATCGAACGACTTTTAACTAATGGTAGCATCGCTCTTTGTCCTACTAATTGGAAAGAGATT
GTCCTTGGAGCCATGCTTCTTGCCTCCAAGGTTTGGAGAAATCATGGTCTGTGGAGTGTGGATGACAGCCAGAATCCCAA
GGACATTGCAGTTGAGAACATGAGCAAGATGGAGAAGTGTTTTTTGGAGCTACTTGAGTTTAATATTCATGTGTCTGCCA
GTGTTTATGCAAGATATTACTTCGACCTGTGTGCCTTGGCAAATGACCGTGACCTGTATTTTCTATTTAGTTTTCTTCAC
AAAGATAAAGCACAGAAACTGGAG

Alignment

ORF - retro_ptro_1091 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.29 %
• Parental protein coverage: 70.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RYANRSLAIFEEPIHPLSQEKLPGKSFKHDPKRNCIFRYFCTLFQVIKVTAPCAIIALVYIERLLTSANI
          RYANRSLAIF..PIHPLSQEK.PGKSF.HDPKR.C.FRYFCTLFQVIK.TAPCAI.ALVYIERLLT...I
Retrocopy RYANRSLAIFDKPIHPLSQEKVPGKSFEHDPKRSCTFRYFCTLFQVIKLTAPCAIVALVYIERLLTNGSI

Parental  DLCPTNWKKIVLGTMLLASKVWRNHGLWSVDDSQNPKDTAVENMSKMEKCFLELLEFNIHVSASVYAKYY
          .LCPTNWK.IVLG.MLLASKVWRNHGLWSVDDSQNPKD.AVENMSKMEKCFLELLEFNIHVSASVYA.YY
Retrocopy ALCPTNWKEIVLGAMLLASKVWRNHGLWSVDDSQNPKDIAVENMSKMEKCFLELLEFNIHVSASVYARYY

Parental  FDLRALANDHDLYFLFSFLHKDKAQKLE
          FDL.ALAND.DLYFLFSFLHKDKAQKLE
Retrocopy FDLCALANDRDLYFLFSFLHKDKAQKLE

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	0.21 RPM	0.00 RPM
SRP007412_cerebellum	1.61 RPM	0.04 RPM
SRP007412_heart	0.09 RPM	0.00 RPM
SRP007412_kidney	0.26 RPM	0.00 RPM
SRP007412_liver	0.07 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	2.74 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1091 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1091 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1091 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011445	1 retrocopy	retro_cjac_1164,
Homo sapiens	ENSG00000163249	3 retrocopies	retro_hsap_1629, retro_hsap_1984, retro_hsap_4845,
Gorilla gorilla	ENSGGOG00000008136	1 retrocopy	retro_ggor_1229,
Mus musculus	ENSMUSG00000070871	1 retrocopy	retro_mmus_3072,
Pan troglodytes	ENSPTRG00000002421	2 retrocopies	retro_ptro_1322, retro_ptro_3228,
Pan troglodytes	ENSPTRG00000008072	1 retrocopy	retro_ptro_1091 ,