RetrogeneDB ID: retro_pabe_2147

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:97936385..97937210(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACER2
• Ensembl ID: ENSPPYG00000019192
• Aliases: None
• Description: alkaline ceramidase 2 [Source:HGNC Symbol;Acc:23675]

Sequence

>retro_pabe_2147
ATGGGCGCCCTGCAGTGGTGGGACCAGCTGCAGGCTGGCAGCTCGGAGGTGGACTGGTGCAAGGACAACTACACCATTGT
GCCTGCTATCGCCGAGTTCTACAACACGACCAGCAATGTCTTATTTTTCATTTTACCGCCCATCTGCATGTGCTTGTTTC
GTCAGTATGCAACATGCTCCAACAGCGGCATCTACTTAATCTGGACTCTTTTGGTTGTAGTGGGAATTGGATCCGTCTAC
TTCCATGCAACCCTTAGTTTCCTGGGTCAGATGCTTGATGAACTTGCAGTCCTTTGGGTTCTGATGTGTGCTTTGGCCAT
GTGGTTCCCCAGAAGGTATCTACCAAAGATCTTTCGGAATGACTGGGGTAGGTTCAAGGTGGTGGTCTGTGTCCTGTCTG
CGGTTACGACGTGCCTGGCATTTGTCAAGCCTGCCATCAACAACATCTCTCTGATGACCCTGGGAGTTCCTTGCACTGCA
CTGCTCATCGCAGAGCTAAAGAGGTGTGACAACATGCGTGTGTTTAAGCTGGGCCTCTTCTCAGGCCCCTGGTGGACCCT
GGCCCTGTTCTGCTGGATCAGTGACCGAGCTTTCTGCGAGCTGCTGTCATCCTTCAACTTCCCCTACCTGCACTGCATGT
GGCACATCCGCATCTGACTTGCTGCCTACCTGGGCTGTGTATGCTTTGCCTACTTTGATGCTGCCTCAGAGATTCCTGAG
CAAGGCCCTGTCATCAAGTTCTGGCCCAGCGAGAAATGGGCCTTCATTGGTGTCCCCTATGTGTCCCTCCTGTGTGCCAA
CAAGAAACCATCAGTCAAGATCACA

Alignment

ORF - retro_pabe_2147 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.64 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGAPHWWDQLQAGSSEVDWCEDNYTIVPAIAEFYNTISNVLFFILPPICMCLFRQYATCFNSGIYLIWTL
          MGA..WWDQLQAGSSEVDWC.DNYTIVPAIAEFYNT.SNVLFFILPPICMCLFRQYATC.NSGIYLIWTL
Retrocopy MGALQWWDQLQAGSSEVDWCKDNYTIVPAIAEFYNTTSNVLFFILPPICMCLFRQYATCSNSGIYLIWTL

Parental  LVVVGIGSVYFHATLSFLGQMLDELAVLWVLMCALAMWFPRRYLPKIFRND-GRFKVVVCVLSAVTTCLA
          LVVVGIGSVYFHATLSFLGQMLDELAVLWVLMCALAMWFPRRYLPKIFRND.GRFKVVVCVLSAVTTCLA
Retrocopy LVVVGIGSVYFHATLSFLGQMLDELAVLWVLMCALAMWFPRRYLPKIFRNDWGRFKVVVCVLSAVTTCLA

Parental  FVKPAINNISLMTLGLPCTALLIAELKRCDNMRVFKLGLFSGLWWTLALFCWISDRAFCELLSSFNFPYL
          FVKPAINNISLMTLG.PCTALLIAELKRCDNMRVFKLGLFSG.WWTLALFCWISDRAFCELLSSFNFPYL
Retrocopy FVKPAINNISLMTLGVPCTALLIAELKRCDNMRVFKLGLFSGPWWTLALFCWISDRAFCELLSSFNFPYL

Parental  HCMWHILICLAAYLGCVCFAYFDAASEIPEQGPVIKFWPSEKWAFIGVPYVSLLCANRKSSVKIT
          HCMWHI.I.LAAYLGCVCFAYFDAASEIPEQGPVIKFWPSEKWAFIGVPYVSLLCAN.K.SVKIT
Retrocopy HCMWHIRI*LAAYLGCVCFAYFDAASEIPEQGPVIKFWPSEKWAFIGVPYVSLLCANKKPSVKIT

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	0.44 RPM	2.10 RPM
SRP007412_cerebellum	0.12 RPM	1.58 RPM
SRP007412_heart	0.12 RPM	0.81 RPM
SRP007412_kidney	0.10 RPM	0.99 RPM
SRP007412_liver	0.12 RPM	1.56 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2147 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2147 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2147 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2378
Gorilla gorilla	retro_ggor_1804

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000177076	1 retrocopy	retro_hsap_2378,
Gorilla gorilla	ENSGGOG00000003851	1 retrocopy	retro_ggor_1804,
Myotis lucifugus	ENSMLUG00000007595	1 retrocopy	retro_mluc_727,
Pongo abelii	ENSPPYG00000019192	1 retrocopy	retro_pabe_2147 ,