RetrogeneDB ID: retro_mmul_1359

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 18:64883662..64884291(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPPL3
• Ensembl ID: ENSMMUG00000020650
• Aliases: None
• Description: signal peptide peptidase-like 3 [Source:RefSeq peptide;Acc:NP_001253621]

Sequence

>retro_mmul_1359
GTCACTGTAATTGCCTTTGTCTGCCTGCTGGGTCTCAAAGTCCCCTGTCTGCTTCTCTCAGGACTTTTAATCTATGATGT
CTTTTAGGTATTTTTCTCAGCCTACATCTTTAATAGCAATGTCATGGTGAACGTGGCCATGGCAGCTGGCTGAAAATCCC
CTTTACGTTCTGTCCTGGAAGCTCAACCTGGGGTCTGGTGTTGAGCGTGATGTTCCTCGACTGTCTTTGCCTAGAAAACT
GGTCTTCCCACATTCCACTGGGAGCCACTTCCTCATGTTGGGCATTGGAGACATTGTTATGCCTGGTCATCTGCTATGCT
TTGACCTTCGCTATGATAATTACAAAAAACAAGTCCGTGTGGACTCCTGTGGTGGCCCTGGACCTGCCAACATCTCTGGG
CACATGCAGAAGGTCTTTTACTTTCACTGCACCCTCATGGGATACTTTGTAGATCTGCTCACTGCTACTGTGGCCTCTCA
CATTCACCAGGCCGCCCAGCCTGCCCTTCTCTGTTTGGTGCCATTTACCTTATTGCCACTCCTCACGATGTATTTAAAGG
GTGACCTCCGGTGGATGTGGTCTGAGCTATTCCACTCCAAGACCAGTAAGCTCCCAATTCCTGGAAGTA

Alignment

ORF - retro_mmul_1359 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.13 %
• Parental protein coverage: 54.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VAMIAFVRLPSLKVSCLLLSGLLIYDVFWVFFSAYIFNSNVMVKVAT-QPADNPLDVLSRKLHLGPNVGR
          V..IAFV.L..LKV.CLLLSGLLIYDVF.VFFSAYIFNSNVMV.VA..Q.A.NPL.VLS.KL.LG..V.R
Retrocopy VTVIAFVCLLGLKVPCLLLSGLLIYDVF*VFFSAYIFNSNVMVNVAM>QLAENPLYVLSWKLNLGSGVER

Parental  DVPRLSLPGKLVFPSSTGSHFSMLGIGDIVMPGLLLCFVLRYDNYKKQASGDSCGAPGPANISGRMQKVS
          DVPRLSLP.KLVFP.STGSHF.MLGIGDIVMPG.LLCF.LRYDNYKKQ...DSCG.PGPANISG.MQKV.
Retrocopy DVPRLSLPRKLVFPHSTGSHFLMLGIGDIVMPGHLLCFDLRYDNYKKQVRVDSCGGPGPANISGHMQKVF

Parental  YFHCTLIGYFVGLLTATVASRIHRAAQPALLYLVPFTLLPLLTMAYLKGDLRRMWSEPFHSKSS-SSRFL
          YFHCTL.GYFV.LLTATVAS.IH.AAQPALL.LVPFTLLPLLTM.YLKGDLR.MWSE.FHSK.S.SS.FL
Retrocopy YFHCTLMGYFVDLLTATVASHIHQAAQPALLCLVPFTLLPLLTM-YLKGDLRWMWSELFHSKTS>SSQFL

Parental  EV
          EV
Retrocopy EV

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	0.00 RPM	43.25 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	46.17 RPM
SRP007412_cerebellum	0.00 RPM	37.13 RPM
SRP007412_heart	0.00 RPM	14.84 RPM
SRP007412_kidney	0.00 RPM	19.25 RPM
SRP007412_liver	0.00 RPM	8.19 RPM
SRP007412_testis	0.00 RPM	46.21 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1359 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1359 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1359 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000016589	1 retrocopy	retro_dnov_175,
Homo sapiens	ENSG00000157837	1 retrocopy	retro_hsap_1898,
Gorilla gorilla	ENSGGOG00000016245	1 retrocopy	retro_ggor_1392,
Myotis lucifugus	ENSMLUG00000012754	1 retrocopy	retro_mluc_672,
Macaca mulatta	ENSMMUG00000020650	1 retrocopy	retro_mmul_1359 ,
Pongo abelii	ENSPPYG00000005041	2 retrocopies	retro_pabe_1578, retro_pabe_1579,
Pan troglodytes	ENSPTRG00000005548	1 retrocopy	retro_ptro_1275,
Rattus norvegicus	ENSRNOG00000001178	1 retrocopy	retro_rnor_2157,
Sarcophilus harrisii	ENSSHAG00000015326	1 retrocopy	retro_shar_660,