RetrogeneDB ID: retro_pabe_2294

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:18927048..18927777(-)
• Located in intron of: ENSPPYG00000013534

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTDNEP1
• Ensembl ID: ENSPPYG00000007902
• Aliases: None
• Description: CTD nuclear envelope phosphatase 1 [Source:HGNC Symbol;Acc:19085]

Sequence

>retro_pabe_2294
ATGATGCGGACGCAGTCTGCTGGGCTGCGCACGTTCGTGGCCTTCGCCTCCAAGCTCTGGAGCTTCTCCATTTACCTTTT
GCGGGGGCAGATCCGCACGGTAATTCAGTACCAAACTGTTCTATATGATATCCTCCCCTTATCTCCTGTGTCCCGGAATC
GGCTAGCCCAGGTGAAGAGGAAGATCCTGGTGCTGGATCTGGATGAGACACTTATTCACTCCCACCATGATGGGGTCCTG
AGGCCCACAGTCCGGCCTGGTAAGCCTCCTGACTTCATCCTCAAGGTGGTAATAGACAAACATCCTGTCCGGTTTTTTGT
ACGTAAGAGGCCCCATGTGGATTTCTTCCTGGAAGTGGTGAGCCAGTGGTACGAGCTGGTGGTGTTTACAGCAAGCATGG
AGATCTATGGCTCTGCTGTGGCAGGTAAACTGGACAATAGCAGAAGCATTCTTAAGAGGAGATATTACAGACAGCACTGC
ACTTTGGAGTTGAGCAGCTACATCAAGGACCTCTCTGTGGTCCACAGTGACCTCTCCAGCATTGTGATCCTGGATAACTC
CCCAGGGGCTTACAGGAGCCGTCCAGACAATGCCATCCCCATCAAATCCTGGTTCAGTGACCCCAGCGACACAGCCCTTC
TCAACCAGCTCCCGATGCTGGATGCCCTCAGGTTCACCGCTGACGTTCGTTCCGTGCTGAGCCGAAACCTTCACCAACAT
CGGCTCTGG

Alignment

ORF - retro_pabe_2294 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.67 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMRTQCLLGLRTFVAFAAKLWSFFIYLLRRQIRTVIQYQTVRYDILPLSPVSRNRLAQVKRKILVLDLDE
          MMRTQ...GLRTFVAFA.KLWSF.IYLLR.QIRTVIQYQTV.YDILPLSPVSRNRLAQVKRKILVLDLDE
Retrocopy MMRTQSA-GLRTFVAFASKLWSFSIYLLRGQIRTVIQYQTVLYDILPLSPVSRNRLAQVKRKILVLDLDE

Parental  TLIHSHHDGVLRPTVRPGTPPDFILKVVIDKHPVRFFVHKRPHVDFFLEVVSQWYELVVFTASMEIYGSA
          TLIHSHHDGVLRPTVRPG.PPDFILKVVIDKHPVRFFV.KRPHVDFFLEVVSQWYELVVFTASMEIYGSA
Retrocopy TLIHSHHDGVLRPTVRPGKPPDFILKVVIDKHPVRFFVRKRPHVDFFLEVVSQWYELVVFTASMEIYGSA

Parental  VADKLDNSRSILKRRYYRQHCTLELGSYIKDLSVVHSDLSSIVILDNSPGAYRSHPDNAIPIKSWFSDPS
          VA.KLDNSRSILKRRYYRQHCTLEL.SYIKDLSVVHSDLSSIVILDNSPGAYRS.PDNAIPIKSWFSDPS
Retrocopy VAGKLDNSRSILKRRYYRQHCTLELSSYIKDLSVVHSDLSSIVILDNSPGAYRSRPDNAIPIKSWFSDPS

Parental  DTALLNLLPMLDALRFTADVRSVLSRNLHQHRLW
          DTALLN.LPMLDALRFTADVRSVLSRNLHQHRLW
Retrocopy DTALLNQLPMLDALRFTADVRSVLSRNLHQHRLW

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	3.37 RPM	24.83 RPM
SRP007412_cerebellum	4.01 RPM	18.85 RPM
SRP007412_heart	1.26 RPM	8.58 RPM
SRP007412_kidney	3.35 RPM	18.53 RPM
SRP007412_liver	1.07 RPM	8.11 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2294 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2294 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2294 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2687
Pan troglodytes	retro_ptro_1814
Gorilla gorilla	retro_ggor_1874

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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,