RetrogeneDB ID: retro_ptro_1275

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 18:67480504..67481529(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPPL3
• Ensembl ID: ENSPTRG00000005548
• Aliases: None
• Description: Pan troglodytes signal peptide peptidase like 3 (SPPL3), mRNA. [Source:RefSeq mRNA;Acc:NM_001246615]

Sequence

>retro_ptro_1275
GAGAGTACACAGAAAGACAATAATAGTTCTTCTGGGTCTTTCAATGGCAACAGCACCAATAATAGCATCAAATAATTGAA
TCTACCCAGGCTCCATTCCTTCCAATTGGAGCATCTGTCTCTCTTTTATTGTTGTTTTGCTTCTTTGACTGAGCTCAAGT
AGTTTTCACAATATGTACAGCAGTTCTTACAATGATAACTTTTGCTTTTCTTCTTCTCCTGATGTGCCAGTATTTAACGA
GACTCTATTCACCTCAGAACAAGATTTCCCTGGGTTTCCCTGGATGTTTCACTGCTGCTGAGTTGTTGTTATTATCTCTG
TCTGTCGTGCTCATCCTCACCTGGGTTCTCACTGGCCATTGACTTCTCATGGATGCATTGGCTGTGGGTCTCCATCTCAC
TGTAATTTTCTTTGTCTGCCTGTTGGGCCTCAAAGTCCCCTGCCTGCTTCTCTCAGGGCTTTTAATCTATGATGTCTTTT
AGGTAGTTTTCTCAGCCTACATCTTTAATAGCAGTGTCATGGTGAATGTGGCCATGGCAGCTGGCTGAAAATCCCCTTTA
CGTTCTATCCCAGAAGCTCAACCTGGGGCCCGGTGTTGGGCGTGATGTTCCTCGCCTGTCTCTGCGTGGAAAACTGGTCT
TCCCACGTTCCACTGGGAGCCACTTCCTCATGTTGGGCATTGGAGACATTGTTATGCCTGGTCATCTGCTATGCTTTGAC
CTTCACTATGACAATTACAAAATCAAGCCCGTGGGGACTCCTGTGGTGGCCCTGGACCTGCCAACATCTCTGGGCGCATG
CAGAAGGTCTTCTACTTTCACTGCACCCTCATGGGATACTTTGTAGATCTGCTCACGGCTACTGTGGCCTCTCACATTCA
CCAGGCCGCCCAGCCTGCCCTTCTCTGTTTGGTGCCATTTACCTTATTGCCACTCCTCATGATGGCCTATTTAAAGGGTG
ACTTCCGGTGGATGTGGTCTAAGCTATTCCACTCCAAGACCAGTAGCTCCCAATTCCTGGAAGTA

Alignment

ORF - retro_ptro_1275 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.26 %
• Parental protein coverage: 89.06 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QDKEKDSNSSSGSFNGNSTNNSI-QTIDSTQALFLPIGASVSLLVMFFFFDSVQVVFTICTAVLATIAFA
          ....KD.NSSSGSFNGNSTNNSI.Q.I.STQA.FLPIGASVSLL..F.FFD..QVVFTICTAVL..I.FA
Retrocopy ESTQKDNNSSSGSFNGNSTNNSI<QIIESTQAPFLPIGASVSLLLLFCFFD*AQVVFTICTAVLTMITFA

Parental  FLLLPMCQYLTRPCSPQNKISFGCCGRFTAAELLSFSLSVMLVLIWVLTGHWLLMDALAMGLCVAMIAFV
          FLLL.MCQYLTR..SPQNKIS.G..G.FTAAELL..SLSV.L.L.WVLTGH.LLMDALA.GL....I.FV
Retrocopy FLLLLMCQYLTRLYSPQNKISLGFPGCFTAAELLLLSLSVVLILTWVLTGH*LLMDALAVGLHLTVIFFV

Parental  RLPSLKVSCLLLSGLLIYDVFWVFFSAYIFNSNVMVKVAT-QPADNPLDVLSRKLHLGPNVGRDVPRLSL
          .L..LKV.CLLLSGLLIYDVF.V.FSAYIFNS.VMV.VA..Q.A.NPL.VLS.KL.LGP.VGRDVPRLSL
Retrocopy CLLGLKVPCLLLSGLLIYDVF*VVFSAYIFNSSVMVNVAM>QLAENPLYVLSQKLNLGPGVGRDVPRLSL

Parental  PGKLVFPSSTGSHFSMLGIGDIVMPGLLLCFVLRYDNYK-KQASGDSCGAPGPANISGRMQKVSYFHCTL
          .GKLVFP.STGSHF.MLGIGDIVMPG.LLCF.L.YDNYK..QA.GDSCG.PGPANISGRMQKV.YFHCTL
Retrocopy RGKLVFPRSTGSHFLMLGIGDIVMPGHLLCFDLHYDNYK<NQARGDSCGGPGPANISGRMQKVFYFHCTL

Parental  IGYFVGLLTATVASRIHRAAQPALLYLVPFTLLPLLTMAYLKGDLRRMWSEPFHSKSSSSRFLEV
          .GYFV.LLTATVAS.IH.AAQPALL.LVPFTLLPLL.MAYLKGD.R.MWS..FHSK.SSS.FLEV
Retrocopy MGYFVDLLTATVASHIHQAAQPALLCLVPFTLLPLLMMAYLKGDFRWMWSKLFHSKTSSSQFLEV

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	43.51 RPM
SRP007412_cerebellum	0.00 RPM	37.28 RPM
SRP007412_heart	0.00 RPM	11.95 RPM
SRP007412_kidney	0.00 RPM	35.98 RPM
SRP007412_liver	0.00 RPM	16.14 RPM
SRP007412_testis	0.00 RPM	55.96 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1275 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1275 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1275 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1898
Gorilla gorilla	retro_ggor_1392
Pongo abelii	retro_pabe_1578

---

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,
Pan troglodytes	ENSPTRG00000005548	1 retrocopy	retro_ptro_1275 ,
Pan troglodytes	ENSPTRG00000007070	1 retrocopy	retro_ptro_1054,
Rattus norvegicus	ENSRNOG00000001178	1 retrocopy	retro_rnor_2157,
Sarcophilus harrisii	ENSSHAG00000015326	1 retrocopy	retro_shar_660,