RetrogeneDB ID: retro_ggor_1392

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 18:69582836..69583852(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPPL3
• Ensembl ID: ENSGGOG00000016245
• Aliases: None
• Description: None

Sequence

>retro_ggor_1392
CAGAAAGACAATAATAGTTCTTCTGGGTCTTTCAATGGCAACAGCACCAATAATAGCATCAAATAATTGAATCTACCCAG
GCTCTGTTCCTTCCGATTGGAGCATCTGTCTCTCTTTTATTGTTGTTTTGCTTGTTTGACTGAGCTCAAGTAGTTTTCAC
AATATGTACAGCAGTTCTTACAACGATAACTTCTGCTTTTCTTCTTCTCCGGATGTGCCAGTATTTAACGAGACTCTATT
CACCTCAGAACAAGATTTCCCTGGGTTTCCCTGAATGTTTCACTGCTGCTGAGTTGTTGTTATTATCTCTATCTGTCGTG
CTCATCCTCACCTGGGTTCTCACTGGCCATTGACTTCTCATGGATGCATTGGCTGTGGGTCTCCGTCTCACTGTAATTTT
CTTTGTCTGCCTGTTGGGCCTCAAAGTCCCCTGCCTGCTTCTCTCAGGGCTTTTAATCTCTGATGTCTTTTAGGTAGTTT
TCTCAGCCTACATCTTTAATAGCAGTGTCATGGTGAATGTGGCCATGGCAGCTGGCTGAAAATCCCCTTTACGTTCTATC
CCTGAAGCTCAACCTGGGGCCCGGTGTTGGGCGTGATGTTCCTCGCCTGTCTCTGCCTGGAAAACTGGTCTTCCCATGTT
CCACTGGGAGCCACTTCCTCAGGTAGGGCATTGGAGACATTGTTATGCCTGGTCATCTGCTATGCTTTGACCTTCACTAT
GACAATTACAAAATCAAGCCCGTGGGGACTCCTGTGGTGGCCTTGGACCTGCCAACATCTCTGGGCGCATGCAGAAGGTC
TTCTACTTTCACTGCACCCTCATGGGGTACTTTGTAGATCTGCTCATGGCTACTGTGGCCTCTCACATTCACCAGGCCGC
CCAGCCTGCCCTTCTCTGTTTGGTGCCATTTACCTTATTGCCACTCCTCATGATGGCCTATTTAAAGGGTGACCTCCGGT
GGATGTGGTCTAAGCTATTCCACTCCAAGACCAGTAGCTCCCAATTCCTGGAAGTA

Alignment

ORF - retro_ggor_1392 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 96.86 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EKDSNSSSGSFNGNSTNNSI-QTIDSTQALFLPIGASVSLLVMFFFFDSVQVVFTICTAVLATIAFAFLL
          .KD.NSSSGSFNGNSTNNSI.Q.I.STQALFLPIGASVSLL..F..FD..QVVFTICTAVL.TI..AFLL
Retrocopy QKDNNSSSGSFNGNSTNNSI<QIIESTQALFLPIGASVSLLLLFCLFD*AQVVFTICTAVLTTITSAFLL

Parental  LPMCQYLTRPCSPQNKISFGCCGRFTAAELLSFSLSVMLVLIWVLTGHWLLMDALAMGLCVAMIAFVRLP
          L.MCQYLTR..SPQNKIS.G....FTAAELL..SLSV.L.L.WVLTGH.LLMDALA.GL....I.FV.L.
Retrocopy LRMCQYLTRLYSPQNKISLGFPECFTAAELLLLSLSVVLILTWVLTGH*LLMDALAVGLRLTVIFFVCLL

Parental  SLKVSCLLLSGLLIYDVFWVFFSAYIFNSNVMVKVAT-QPADNPLDVLSRKLHLGPNVGRDVPRLSLPGK
          .LKV.CLLLSGLLI.DVF.V.FSAYIFNS.VMV.VA..Q.A.NPL.VLS.KL.LGP.VGRDVPRLSLPGK
Retrocopy GLKVPCLLLSGLLISDVF*VVFSAYIFNSSVMVNVAM>QLAENPLYVLSLKLNLGPGVGRDVPRLSLPGK

Parental  LVFPSSTGSHFSMLGIGDIVMPGLLLCFVLRYDNYK-KQASGDSCGAPGPANISGRMQKVSYFHCTLIGY
          LVFP.STGSHF...GIGDIVMPG.LLCF.L.YDNYK..QA.GDSCG..GPANISGRMQKV.YFHCTL.GY
Retrocopy LVFPCSTGSHFLR*GIGDIVMPGHLLCFDLHYDNYK<NQARGDSCGGLGPANISGRMQKVFYFHCTLMGY

Parental  FVGLLTATVASRIHRAAQPALLYLVPFTLLPLLTMAYLKGDLRRMWSEPFHSKSSSSRFLEV
          FV.LL.ATVAS.IH.AAQPALL.LVPFTLLPLL.MAYLKGDLR.MWS..FHSK.SSS.FLEV
Retrocopy FVDLLMATVASHIHQAAQPALLCLVPFTLLPLLMMAYLKGDLRWMWSKLFHSKTSSSQFLEV

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	29.64 RPM
SRP007412_cerebellum	0.00 RPM	29.98 RPM
SRP007412_heart	0.00 RPM	6.38 RPM
SRP007412_kidney	0.00 RPM	29.81 RPM
SRP007412_liver	0.00 RPM	17.25 RPM
SRP007412_testis	0.00 RPM	46.93 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1392 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1392 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1898
Pan troglodytes	retro_ptro_1275
Pongo abelii	retro_pabe_1578

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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	ENSGGOG00000013154	1 retrocopy	retro_ggor_1191,
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,