RetrogeneDB ID: retro_ptro_1814

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:117213831..117214562(+)
• Located in intron of: ENSPTRG00000015236

Retrocopy information

• Ensembl ID: ENSPTRG00000039338
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CTDNEP1
• Ensembl ID: ENSPTRG00000008668
• Aliases: CTDNEP1, DULLARD
• Description: None

Sequence

>retro_ptro_1814
ATGGTGCGGACGCAGTGTCTGCTGGGGCTGCGCACGTTCGTGGCCTTCGCTGCCAAGCTCTGGAGCTTCTTCATTTACCT
TTTGCGGGGGCAGATCCACACGGTAATTCAGTACCAAACTGTTCGATATGATATCCTCCCCTTATCTCCTGTGTCCCGGA
ATCGGCTAGCCCAGGTGAAGAGGAAGATCCTGGTGCTGGATCTGGATGAGACACTTATTCACTCCCACCATGATGGGGTC
CTGAGGCCGCAGTCCGGCCTGGTACGCCTCCTGACTTAATCCTCAAGGTGGTAATAGACAAACATCCTGTCCGGTTTTTT
GTACGTAAGAGGCCCCATGTGGATTTCTTCCTGGAAGTGGTGAGCCAGTGGTACGAGCTGGTGGTGTTTACAGAAAGCAT
GGAGATCTATGGCTCTGCTGTGGCAGGTAAACTGGACAATAGCAGAAGCATCCTTAAGAGGAGATATTACAGACAGCACT
GCACTTTGGAGTTGAGCAGCTACATCAAGGACCTCTCTGTGGTCCACAGTGACCTCTCCAGCATTGTGATCCTGGATAAC
TCCCCAGGGGCTTACAGGAGCCATCCAGACAATGCCATCCCCATCAAATCCTGGTTCAGTGACCCCAGCGACACAGCCCT
TCTCAACCTGCTCCCGATGCTGGATGCCCTCAGGTTCACCGCTGACGTTCGTTCCGTGCTGAGCCGAAGCCTTCACCAAC
ATCGGCTCTGG

Alignment

ORF - retro_ptro_1814 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.51 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MMRTQCLLGLRTFVAFAAKLWSFFIYLLRRQIRTVIQYQTVRYDILPLSPVSRNRLAQVKRKILVLDLDE
          M.RTQCLLGLRTFVAFAAKLWSFFIYLLR.QI.TVIQYQTVRYDILPLSPVSRNRLAQVKRKILVLDLDE
Retrocopy MVRTQCLLGLRTFVAFAAKLWSFFIYLLRGQIHTVIQYQTVRYDILPLSPVSRNRLAQVKRKILVLDLDE

Parental  TLIHSHHDGVLRP-TVRPGTPPDFILKVVIDKHPVRFFVHKRPHVDFFLEVVSQWYELVVFTASMEIYGS
          TLIHSHHDGVLRP..VRPGTPPD.ILKVVIDKHPVRFFV.KRPHVDFFLEVVSQWYELVVFT.SMEIYGS
Retrocopy TLIHSHHDGVLRP<AVRPGTPPDLILKVVIDKHPVRFFVRKRPHVDFFLEVVSQWYELVVFTESMEIYGS

Parental  AVADKLDNSRSILKRRYYRQHCTLELGSYIKDLSVVHSDLSSIVILDNSPGAYRSHPDNAIPIKSWFSDP
          AVA.KLDNSRSILKRRYYRQHCTLEL.SYIKDLSVVHSDLSSIVILDNSPGAYRSHPDNAIPIKSWFSDP
Retrocopy AVAGKLDNSRSILKRRYYRQHCTLELSSYIKDLSVVHSDLSSIVILDNSPGAYRSHPDNAIPIKSWFSDP

Parental  SDTALLNLLPMLDALRFTADVRSVLSRNLHQHRLW
          SDTALLNLLPMLDALRFTADVRSVLSR.LHQHRLW
Retrocopy SDTALLNLLPMLDALRFTADVRSVLSRSLHQHRLW

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	0.36 RPM	59.97 RPM
SRP007412_cerebellum	0.04 RPM	37.10 RPM
SRP007412_heart	0.03 RPM	22.85 RPM
SRP007412_kidney	0.21 RPM	44.33 RPM
SRP007412_liver	0.36 RPM	17.81 RPM
SRP007412_testis	0.11 RPM	24.24 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1814 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1814 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1814 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2687
Gorilla gorilla	retro_ggor_1874
Pongo abelii	retro_pabe_2294

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019443	1 retrocopy	retro_btau_915,
Dasypus novemcinctus	ENSDNOG00000013673	2 retrocopies	retro_dnov_1802, retro_dnov_2494,
Echinops telfairi	ENSETEG00000004654	1 retrocopy	retro_etel_125,
Homo sapiens	ENSG00000175826	2 retrocopies	retro_hsap_2687, retro_hsap_3188,
Gorilla gorilla	ENSGGOG00000013777	2 retrocopies	retro_ggor_1338, retro_ggor_1874,
Macaca mulatta	ENSMMUG00000010547	1 retrocopy	retro_mmul_2011,
Mus musculus	ENSMUSG00000018559	1 retrocopy	retro_mmus_1023,
Otolemur garnettii	ENSOGAG00000004389	1 retrocopy	retro_ogar_1001,
Pongo abelii	ENSPPYG00000007902	2 retrocopies	retro_pabe_2294, retro_pabe_2645,
Pan troglodytes	ENSPTRG00000008668	2 retrocopies	retro_ptro_1814 , retro_ptro_2256,
Drosophila melanogaster	FBgn0029067	1 retrocopy	retro_dmel_18,