RetrogeneDB ID: retro_pabe_1578

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18:84643255..84644269(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPPL3
• Ensembl ID: ENSPPYG00000005041
• Aliases: None
• Description: signal peptide peptidase like 3 [Source:HGNC Symbol;Acc:30424]

Sequence

>retro_pabe_1578
AAAGACAATAATAGTTCTTGTGGATCTTTCAATGGCAACAGCACCAATAATAGCATCAAATAATTGAATCTACCCAGGCT
CTATTCCTTCCTATTGGAGCATCTGTCTCTCTTTTATTGTTGTTTTGCTTCTTTGACTGAGCTGAAGTAGTTTTCACAAT
ATGTACAGAAGTTCTTACAATGATAACTTTTGCTTTTCTTCTTCTCCTTATGTGCCAATATTTAACGAGACTCTGTTCAC
CTCAGAACAAGATTTCCCTGGGTTTCTGTGGGTGTTTCACTACTGCTGAGTTGTTGTTATTATCTCTGTCTGTCGTGCTC
ATCCTCACCTGGGTTCTCACTGGCCATTGACTTCTCATGGATGCATTGGCTATGGGTCTCCGTGTCACTGTAATTTTCTT
TGTCTGCCTGTTGGGCCTCAAAGTCCCCTGCCTGCTTCTCTCAGGGCTTTTAATCTATGATGTCTTTTAGGTATTTTTCT
CAGCCTACATCTTTAATAGCAGTGTCATGGTGAACGTGGCCATGGCAGCTGGCTGAAAATCCCCTTTACGTTCTATCCTG
GAAGCTCAACCTGGGGCCCAGTGTTGGGCGTGATGTTCCTCACCTGTCTCTGCCTGGAAAACTGGTCTTCCCACGTTCCA
CTGGGAGCCACTTCCTCATGTTGGGCATTGGAGACATTGTTATGCCTAGTTGTCTGCTATGCTTTGACCTTTGCTATGAC
AATTACAAAAAACAAGCCCGTGGGGACTCTTGTGGTGGCCCTGGACCTGCCAACATCTCTGGGCACATGCAGAAGGTCTT
CTACTTTCACTGGCCCGTCATGGGATACCTTGTAGATCTGCTCACTGCTACTGTGGCCTCTCACATTCACCAGGCCGCCC
AGCCTGTGCTTCTCTGTTTGGTGCCATTTACCTTATTGCCACTCCTCATGATGGCCTATTTAAAGGGTGACCTCTGGTGG
ATGTGGTCTAAGCTATTCCACTCCAAGACCAGTAGCTCCCAATTCCTGGAAGTA

Alignment

ORF - retro_pabe_1578 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.24 %
• Parental protein coverage: 97.41 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KDSNSSSGSFNGNSTNNSI-QTIDSTQALFLPIGASVSLLVMFFFFDSVQVVFTICTAVLATIAFAFLLL
          KD.NSS.GSFNGNSTNNSI.Q.I.STQALFLPIGASVSLL..F.FFD...VVFTICT.VL..I.FAFLLL
Retrocopy KDNNSSCGSFNGNSTNNSI<QIIESTQALFLPIGASVSLLLLFCFFD*AEVVFTICTEVLTMITFAFLLL

Parental  PMCQYLTRPCSPQNKISFGCCGRFTAAELLSFSLSVMLVLIWVLTGHWLLMDALAMGLCVAMIAFVRLPS
          .MCQYLTR.CSPQNKIS.G.CG.FT.AELL..SLSV.L.L.WVLTGH.LLMDALAMGL.V..I.FV.L..
Retrocopy LMCQYLTRLCSPQNKISLGFCGCFTTAELLLLSLSVVLILTWVLTGH*LLMDALAMGLRVTVIFFVCLLG

Parental  LKVSCLLLSGLLIYDVFWVFFSAYIFNSNVMVKVAT-QPADNPLDVLSRKLHLGPNVGRDVPRLSLPGKL
          LKV.CLLLSGLLIYDVF.VFFSAYIFNS.VMV.VA..Q.A.NPL.VLS.KL.LGP.VGRDVP.LSLPGKL
Retrocopy LKVPCLLLSGLLIYDVF*VFFSAYIFNSSVMVNVAM>QLAENPLYVLSWKLNLGPSVGRDVPHLSLPGKL

Parental  VFPSSTGSHFSMLGIGDIVMPGLLLCFVLRYDNYKKQASGDSCGAPGPANISGRMQKVSYFHCTLIGYFV
          VFP.STGSHF.MLGIGDIVMP..LLCF.L.YDNYKKQA.GDSCG.PGPANISG.MQKV.YFH....GY.V
Retrocopy VFPRSTGSHFLMLGIGDIVMPSCLLCFDLCYDNYKKQARGDSCGGPGPANISGHMQKVFYFHWPVMGYLV

Parental  GLLTATVASRIHRAAQPALLYLVPFTLLPLLTMAYLKGDLRRMWSEPFHSKSSSSRFLEV
          .LLTATVAS.IH.AAQP.LL.LVPFTLLPLL.MAYLKGDL..MWS..FHSK.SSS.FLEV
Retrocopy DLLTATVASHIHQAAQPVLLCLVPFTLLPLLMMAYLKGDLWWMWSKLFHSKTSSSQFLEV

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	0.00 RPM	32.01 RPM
SRP007412_cerebellum	0.00 RPM	30.77 RPM
SRP007412_heart	0.00 RPM	6.74 RPM
SRP007412_kidney	0.00 RPM	18.63 RPM
SRP007412_liver	0.00 RPM	9.88 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1578 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1578 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1578 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1898
Pan troglodytes	retro_ptro_1275
Gorilla gorilla	retro_ggor_1392

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 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,
Pongo abelii	ENSPPYG00000006472	1 retrocopy	retro_pabe_1293,
Pan troglodytes	ENSPTRG00000005548	1 retrocopy	retro_ptro_1275,
Rattus norvegicus	ENSRNOG00000001178	1 retrocopy	retro_rnor_2157,
Sarcophilus harrisii	ENSSHAG00000015326	1 retrocopy	retro_shar_660,