RetrogeneDB ID: retro_mmul_1636

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:134748801..134749754(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCD
• Ensembl ID: ENSMMUG00000010817
• Aliases: None
• Description: None

Sequence

>retro_mmul_1636
ATCTCTAGCTCCCGTACCACCACCACCACCATCACAGCGCCTCCCTCCAGGGTCCTGCAGAATGGGGGAGATAAGTTGGA
GACGATGCCCCTCTACTTGGAAGAAGACATTCGCCCTGGTATAAAAGATGATATATATGACCCCACCTATAATGATAAGG
AAGGCCCAAGCCCCAAGGTTAATTATGTCTGGAGAAACGTCATCCTTATGTCTCTGCTACACTTGGGTGCCCTGTTTGGG
ATCACTTTGATTCCTACCTGCAAGTTCTACTCCTGGCTTTGGGGGTTATTCTACTATTTTGTCAGGGCCCTGGACATAAC
AGCAGGAGCTCATCCTCTGTGGAGCCACCCCTCTTACAAAGCTCGGCTGCCCCTGCGGCTCTTTCTGATCATTGCCAACA
CAATGGCATTCCAGAATGGTATCTATGAATGGGCTCACGACCACCATGCCCATCACAAGTTTTCAGAAACACATGCTGAT
CTCGTAATTCCAGACATGGCTTTGTCTTCTCTCACGTGGGTTGGCTGTGCAAACACTCAGCTGTCAAAGAGAAGGGTGGT
ACGCTAGACTTGTCTGATCTAGAAGCCGAGAAACTGGTGATGTTCCAGAGGGGGTACTACAAACCCCGGTTTGCTGCTGA
TATGTGCTTCACCCTGCCCACGCTTGTGCCCTGGTGTTTCTGGGGTGAAACTTTTCAACACAGCTTGTTCATTGCCACCT
TCTTGCGGTATGCTGTAGTGCTTCATGCCACCTGGCTGGTGAACAGTGCTGCTCACCTCTTCGGATATCGTCCTTATGAC
AAGAACATTAGTCCCCGGGAGAATGTCCTGGTTTCACCTGGAGCTGTTGGTGAGGGCTTCCACGAGTACCACCACTCCTT
TCCCTATGACTACTGTGCCAGTGAGTACTGCTGGCACATCAGCTTCACCACATTCTTCATTGATTGCATGGCC

Alignment

ORF - retro_mmul_1636 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.74 %
• Parental protein coverage: 97.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ISSSYTTTTTITAPPSRVLQNGRDKLETTPLYLEEDVRPDIKDDIYDPTYKDKEGPSPKVEYVWRNIILM
          ISSS.TTTTTITAPPSRVLQNG.DKLET.PLYLEED.RP.IKDDIYDPTY.DKEGPSPKV.YVWRN.ILM
Retrocopy ISSSRTTTTTITAPPSRVLQNGGDKLETMPLYLEEDIRPGIKDDIYDPTYNDKEGPSPKVNYVWRNVILM

Parental  SLLHLGALYGITLIPTCKLYTCLWGLFYYVVSALGITAGAHRLWSHRSYKARLPLRLFLIIANTMAFQND
          SLLHLGAL.GITLIPTCK.Y..LWGLFYY.V.AL.ITAGAH.LWSH.SYKARLPLRLFLIIANTMAFQN.
Retrocopy SLLHLGALFGITLIPTCKFYSWLWGLFYYFVRALDITAGAHPLWSHPSYKARLPLRLFLIIANTMAFQNG

Parental  VYEWARDHRAHHKFSETHAD-PHNSRRGFFFSHVGWLLVRKHPAVKEKGATLDLSDLEAEKLVMFQRRYY
          .YEWA.DH.AHHKFSETHAD...NSR.GF.FSHVGWL...KH.AVKEKG.TLDLSDLEAEKLVMFQR.YY
Retrocopy IYEWAHDHHAHHKFSETHAD<SRNSRHGFVFSHVGWLC--KHSAVKEKGGTLDLSDLEAEKLVMFQRGYY

Parental  KPGLLL-MCFILPTLVPWCFWGETFQHSVFVATFLRYAIVLNVTWLVNSAAHLFGYRPYDKNISPRENIL
          KP.....MCF.LPTLVPWCFWGETFQHS.F.ATFLRYA.VL..TWLVNSAAHLFGYRPYDKNISPREN.L
Retrocopy KPRFAADMCFTLPTLVPWCFWGETFQHSLFIATFLRYAVVLHATWLVNSAAHLFGYRPYDKNISPRENVL

Parental  VSLGAVGEGFHNYHHSFPYDYSASEYRWHINFTTFFIDCMA
          VS.GAVGEGFH.YHHSFPYDY.ASEY.WHI.FTTFFIDCMA
Retrocopy VSPGAVGEGFHEYHHSFPYDYCASEYCWHISFTTFFIDCMA

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	0.90 RPM	42.69 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	41.41 RPM
SRP007412_cerebellum	0.06 RPM	30.03 RPM
SRP007412_heart	0.47 RPM	26.32 RPM
SRP007412_kidney	0.35 RPM	30.05 RPM
SRP007412_liver	3.17 RPM	186.04 RPM
SRP007412_testis	0.19 RPM	42.07 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1636 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1636 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1636 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,