RetrogeneDB ID: retro_ptro_3058

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL392652.1:957571..958633(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCD
• Ensembl ID: ENSPTRG00000002847
• Aliases: None
• Description: None

Sequence

>retro_ptro_3058
ATGCCGGCCCACTTGCTGCAGGACCATATCTCTAGCTCCTATACCACCACCACCACCATTACAGCGCCTCCTTCCAGGGT
CCCGCAGAATGGAGGAGATAAGTTGGAGACGACGCCCCTCTACTTGGAAGAAGACATTCGCCCTGATATAAAAGATGATA
TATACAACCCCACCTACAAGGATAAGGAAGGTCCAAGCCCCAAGGTTGAATATGTGTGGAGAAACATCATCCTTATGTCT
CTGCTACACTTGGGCGCCCTGAATGGGATCACTTTGATTCCTACCTGCAACTTATACACCTGGCTTTGGGGGGTATTCTA
CTATTTTATCAGTGCCCTGGGCATAACAGCAGGAGCTCATCGTCTGTGGAGCCACTGATCTGACAAAGCTCGGCTGCCCC
TGTGGCTCTTTCTGGTCATTGCCAACACAATGGCATTCCAGAATGATGTCTATGAATGGGCTCGCGACCACCGTGCCCAC
CACAAGTTTTCAGAAACACATGCTGATCCTCATAATTCCTGACGTGGCTTTTTCTTCTCTCACGTGGGTTGGCTGCTTGT
GCGCAAACACCCAACGGTCAAAGAGAAGGGCAGTGCGCTAGACTTGTCTGACCTAGAAGCCGAGAAACTGGTGATGTTCC
AGAGGAGGTACTACAAACCCGGCTTGCTGTTGATGTGCTTCATCCTGCCCACGCTTGTGCCCTGGTGTTTCTGGGGTGAA
ACTTTTCAAAACAGCGTGTTCGTTGCCACTTTCTTGCGATATGCTGTGGTGCTTAATGCCACCTGGCTGGTGAACAGTGC
TGCCCACCTCTTCGGATATCGTCCTTATGACAAGAACATTAGCCTCCGGGAGAATATCCTGGTTTCACTTGGAGCTGTGG
GTGAAAGTCACTCCTTTCCCTATGACTGCTCTGCCAGTGAGTACCGCTGGCACATCAACTTCACCACATTCTTCATTGAT
TGCATGGCCGCCCTCGGTCTGGCCTACGACCAGAAGAAGGTCTCCAAGGCCGCCATCTTGGCCAGGATTAAAAGAACCGG
AGAGGGAAACTACAAGAGTGGC

Alignment

ORF - retro_ptro_3058 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.64 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPAHLLQDDISSSYTTTTTITAPPSRVLQNGGDKLETTPLYLEDNIRPDIKDDIYDPTYKDKEGPSPKVE
          MPAHLLQD.ISSSYTTTTTITAPPSRV.QNGGDKLETTPLYLE..IRPDIKDDIY.PTYKDKEGPSPKVE
Retrocopy MPAHLLQDHISSSYTTTTTITAPPSRVPQNGGDKLETTPLYLEEDIRPDIKDDIYNPTYKDKEGPSPKVE

Parental  YVWRNIILMSLLHLGALYGITLIPTCKFYTWLWGVFYYFVSALGITAGAHRLWSHRSYKARLPLRLFLII
          YVWRNIILMSLLHLGAL.GITLIPTC..YTWLWGVFYYF.SALGITAGAHRLWSH.S.KARLPL.LFL.I
Retrocopy YVWRNIILMSLLHLGALNGITLIPTCNLYTWLWGVFYYFISALGITAGAHRLWSH*SDKARLPLWLFLVI

Parental  ANTMAFQNDVYEWARDHRAHHKFSETHADPHNSRRGFFFSHVGWLLVRKHPAVKEKGSTLDLSDLEAEKL
          ANTMAFQNDVYEWARDHRAHHKFSETHADPHNS.RGFFFSHVGWLLVRKHP.VKEKGS.LDLSDLEAEKL
Retrocopy ANTMAFQNDVYEWARDHRAHHKFSETHADPHNS*RGFFFSHVGWLLVRKHPTVKEKGSALDLSDLEAEKL

Parental  VMFQRRYYKTGLLLMCFILPTLVPWYFWGETFQNSVFVATFLRYAVVLNATWLVNSAAHLFGYRPYDKNI
          VMFQRRYYK.GLLLMCFILPTLVPW.FWGETFQNSVFVATFLRYAVVLNATWLVNSAAHLFGYRPYDKNI
Retrocopy VMFQRRYYKPGLLLMCFILPTLVPWCFWGETFQNSVFVATFLRYAVVLNATWLVNSAAHLFGYRPYDKNI

Parental  SPRENILVSLGAVGEGFHNYHHSFPYDYSASEYRWHINFTTFFIDCMAALGLAYDRKKVSKAAILARIKR
          S.RENILVSLGAVGE..H......PYD.SASEYRWHINFTTFFIDCMAALGLAYD.KKVSKAAILARIKR
Retrocopy SLRENILVSLGAVGES-HSF----PYDCSASEYRWHINFTTFFIDCMAALGLAYDQKKVSKAAILARIKR

Parental  TGDGNYKSG
          TG.GNYKSG
Retrocopy TGEGNYKSG

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	0.23 RPM	550.76 RPM
SRP007412_cerebellum	0.68 RPM	329.09 RPM
SRP007412_heart	0.06 RPM	9.94 RPM
SRP007412_kidney	0.16 RPM	26.36 RPM
SRP007412_liver	0.46 RPM	1699.46 RPM
SRP007412_testis	0.32 RPM	90.42 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3058 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3058 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3058 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1733

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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,