RetrogeneDB ID: retro_ptro_1148

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 16:63455901..63456237(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EBPL
• Ensembl ID: ENSPTRG00000005877
• Aliases: None
• Description: None

Sequence

>retro_ptro_1148
GAAGGCCCTTTTGTCTACTTGTCTTTAGTAGGAAACGTTGCAAATTCCGATGGCTTGATTGCTTCTTTATGGAAAGAATA
TGGCAAAGCTGATGCAAGATGGGTTTATTTTGATCCAACCATTGTGTCTGTGGAAATTCTGACCGTCGCCCTAGATGTGT
CTCTGGCATTGTTCCTCATTTATGCCATAGTCAAGGAAAAATATTACCGGCATTTCCTGCAGATCACCCTGTGCGTGTGC
GAGATGTATGGCTGCTGGATGACCTTCCTCCCAGAGTGGCTCACCAGAAGCCCCAACCTCAACACCAGCAACTGGCTGTA
CTGTTGGCTTTACCTG

Alignment

ORF - retro_ptro_1148 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.21 %
• Parental protein coverage: 54.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EGPFVYLSLVGNVANSDGLIASLWKEYGKADARWVYFDPTIVSVEILTVALDGSLALFLIYAIVKEKYYR
          EGPFVYLSLVGNVANSDGLIASLWKEYGKADARWVYFDPTIVSVEILTVALD.SLALFLIYAIVKEKYYR
Retrocopy EGPFVYLSLVGNVANSDGLIASLWKEYGKADARWVYFDPTIVSVEILTVALDVSLALFLIYAIVKEKYYR

Parental  HFLQITLCVCELYGCWMTFLPEWLTRSPNLNTSNWLYCWLYL
          HFLQITLCVCE.YGCWMTFLPEWLTRSPNLNTSNWLYCWLYL
Retrocopy HFLQITLCVCEMYGCWMTFLPEWLTRSPNLNTSNWLYCWLYL

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	0.95 RPM
SRP007412_cerebellum	0.00 RPM	1.79 RPM
SRP007412_heart	0.00 RPM	0.93 RPM
SRP007412_kidney	0.00 RPM	2.72 RPM
SRP007412_liver	0.00 RPM	8.48 RPM
SRP007412_testis	0.00 RPM	1.16 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1148 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1148 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1148 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1696

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000123179	1 retrocopy	retro_hsap_1696,
Oryctolagus cuniculus	ENSOCUG00000006778	1 retrocopy	retro_ocun_901,
Pan troglodytes	ENSPTRG00000005877	1 retrocopy	retro_ptro_1148 ,