RetrogeneDB ID: retro_pabe_1545

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17_random:8342722..8343760(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCD
• Ensembl ID: ENSPPYG00000002566
• Aliases: None
• Description: acyl-CoA desaturase [Source:RefSeq peptide;Acc:NP_001125731]

Sequence

>retro_pabe_1545
ATGCCGGCCCACTTGCTGCAGGACGATATCTCTAGCTCCTATACCACCACCACCACCATTACAGCGCCTCCCTCCAGGGT
CCTGCAGAATGGAGGAGATAAGTTGGAGACGACGCTCCTCTACTTGGAAGAAGACATTCGCCCTGATATAAAAGATGATA
TATATGACCCCACCTACAAGGATAAGGAAGGCCCAAGCCCCAAGGTTGAATATGTCTGGAGAAACATCACCCTTATGTCT
CTGCTACACTTGGGCGCCCTGTATAGGATCACTTTGATTCCTACCTGCAAGTTCTACACCTGGCTTTGGGGGGTATTCTA
CTATTTTGTCAGTGCCCTGGGCATAACAGCAGGAGCTCATCGTCTGTGGAGCCACCGATCTTACAAAGCTCGGCTGCCCC
TGCGGCTCCTTCTGATCATTGCCAACACAATGGCATTCCAGAATGATGTCTATGAATGGGCTCACGACCACCGTGCCCAC
CACAAGTTTTCAGAAACACATACTGATCCTCATAATTCCCGACGTGGCTTTTTCTTCTCTCACGTGGGTCGGCTGCTTGT
GCGCAAACACCCAGCTGTCAAAGAGAAGGGCAGTACGCTAGACTTGTCTGACCTAGAAGCCGAGAAACTGGTGATGTTCC
AGAGGAGGTACTACAAACACGGCTTGCTGTTGATGTGCTTCATCCTGCCCACGCTTGTGCCCTGGTGTTTCTGGGGTGAA
ACTTTTCAAAACAGCGTGTTTGTTGCCACTTTCTTGCGATATGCTGTGGTGCTTAATGCCACCCGGCTGGTGAACAGTGC
TGCCCACCTCTTCGGATATCGTCCTTATGACAAGAACATTAGCCCCCGGGAGAATATCCTGGTTTCACTTGGAGCTGTGG
GTGAGGGCTTCCACAACTACCACCACTCCTTTCCCTATGACTGCGCTGCCAGTGAGTACCGCTGGCACATCAACTTCACC
ACATTCTTCATTGATTGCATGGCCGCCCTCGGTCTGGCCTATGACCGGAAGAAAGTCTCCAAGGCCGCCATCTTGGCC

Alignment

ORF - retro_pabe_1545 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.95 %
• Parental protein coverage: 96.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPAHLLQDDISSSYTTTTTITAPPSRVLQKGGDKLETTPLYLEDDIRPDIKDDIYDPTYKDKEGPSPKVE
          MPAHLLQDDISSSYTTTTTITAPPSRVLQ.GGDKLETT.LYLE.DIRPDIKDDIYDPTYKDKEGPSPKVE
Retrocopy MPAHLLQDDISSSYTTTTTITAPPSRVLQNGGDKLETTLLYLEEDIRPDIKDDIYDPTYKDKEGPSPKVE

Parental  YVWRNIILMSLLHLGALYGITLIPTCKFYTWLWGVFYYFVSALGITAGAHRLWSHRSYKARLPLRLFLII
          YVWRNI.LMSLLHLGALY.ITLIPTCKFYTWLWGVFYYFVSALGITAGAHRLWSHRSYKARLPLRL.LII
Retrocopy YVWRNITLMSLLHLGALYRITLIPTCKFYTWLWGVFYYFVSALGITAGAHRLWSHRSYKARLPLRLLLII

Parental  ANTMAFQNDVYEWARDHRAHHKFSETHADPHNSRRGFFFSHVGWLLVRKHPAVKEKGSTLDLSDLEAEKL
          ANTMAFQNDVYEWA.DHRAHHKFSETH.DPHNSRRGFFFSHVG.LLVRKHPAVKEKGSTLDLSDLEAEKL
Retrocopy ANTMAFQNDVYEWAHDHRAHHKFSETHTDPHNSRRGFFFSHVGRLLVRKHPAVKEKGSTLDLSDLEAEKL

Parental  VMFQRRYYKPGLLLMCFILPTLVPWYFWGETFQNSVFVATFLRYAVVLNATWLVNSAAHLFGYRPYDKNI
          VMFQRRYYK.GLLLMCFILPTLVPW.FWGETFQNSVFVATFLRYAVVLNAT.LVNSAAHLFGYRPYDKNI
Retrocopy VMFQRRYYKHGLLLMCFILPTLVPWCFWGETFQNSVFVATFLRYAVVLNATRLVNSAAHLFGYRPYDKNI

Parental  SPRENILVSLGAVGEGFHNYHHSFPYDYSASEYRWHINFTTFFIDCMAALGLAYDRKKVSKAAILA
          SPRENILVSLGAVGEGFHNYHHSFPYD..ASEYRWHINFTTFFIDCMAALGLAYDRKKVSKAAILA
Retrocopy SPRENILVSLGAVGEGFHNYHHSFPYDCAASEYRWHINFTTFFIDCMAALGLAYDRKKVSKAAILA

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	0.06 RPM	133.69 RPM
SRP007412_cerebellum	0.00 RPM	215.72 RPM
SRP007412_heart	0.00 RPM	2.98 RPM
SRP007412_kidney	0.00 RPM	13.19 RPM
SRP007412_liver	0.00 RPM	56.40 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1545 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1545 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1545 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017338	2 retrocopies	retro_cjac_1077, retro_cjac_2348,
Homo sapiens	ENSG00000099194	1 retrocopy	retro_hsap_1733,
Macaca mulatta	ENSMMUG00000010817	1 retrocopy	retro_mmul_1636,
Pongo abelii	ENSPPYG00000002566	1 retrocopy	retro_pabe_1545 ,
Pan troglodytes	ENSPTRG00000002847	1 retrocopy	retro_ptro_3058,
Drosophila melanogaster	FBgn0086687	1 retrocopy	retro_dmel_78,