RetrogeneDB ID: retro_ggor_1184

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 15:21644506..21645575(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RUSC1
• Ensembl ID: ENSGGOG00000000408
• Aliases: None
• Description: None

Sequence

>retro_ggor_1184
AAAGCCCTTTGCTCCTCCCTCAGAATGAATGGAGACCAGAGATCAGATGTTTATGTCCAAGAAAAGCAGGATTTCGTTCA
GTACTTCTCCCAGATCATTGGGGATGAGATGAGGCACCCATAGACAGGAGATGCTATCACCCAGCTGAAGGAGGTCCTGT
AGTACAATGCCATTGGAGGCAAGTATCACCGGGGTTTCACAGTGCTAGTAGCATTCTGGGAGCTGGTGGAGCCAAGGAAA
CAGGATGCTGAGAGTCTCCAGCGGGCCCTGACTGTGGGCTGGTGTGTGGAACTGCTGCAAGCTTTGTTCCTGGTGGCAAA
TGACATCACGGATTCATTGCTCACCGCTGGGAACAGATCTGCTGGTTTCAGAAGCCGGGCGTGGGTTTGGATGCCATCAG
TGATGCTATCCTTGTGGAAGCATGTATCTACTGCCTGCTGAAGCTCTATTGCTGGGAGCAGCCCTATTGCCAGAACCTGA
TCCAGCTCTTCCTGCAGAGTTTCTATCAGATTGAGATTGGGCAGACCCTGGACCTCATCACAGCACCCCAGGGCAATGCG
GATCTTGGCAGATTCACTGAAAAGAGGTACAAATCTACTGTCAAGTACAAGGCAGTTTCTACTTCTACATTCCTGTAGCT
GCAGCCATGTACATGGCAGGCATTGATGGCGAGAAGGAGCACGACAATGCCAAGAAGATCCTGCTGGAGATGGGAGAGGG
AGAGTTCTTTCAGATCAGGATGATTACCTTCACCTCTTTTGGGGACCCCAGTGTGACCAGCAAAGTTGGCACTGACATCC
AGGACAATAAATGCAGCTGGCTGCTGGTTCAGTGTCTGCAACGGGCCACTCCGGAACACTACCAGATCCTGAAGGAGAAT
TACAGGCAGAAGGAGACCAAGAAGGTGGCCCCGGTGAAGGCAGTATATGAGGAGCTGGATCTGCCGGCCGTGTTCTTGCA
ATAATAGGAAGACAGTTACAGCCACATTATGGGTCTCATTGAACAGTACGCAGCTCCCCTGTCCCCAGCCATCTTTCTAG
GGCTGACATGCAAAATCTACAAAAGTAAA

Alignment

ORF - retro_ggor_1184 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.51 %
• Parental protein coverage: 85.92 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RALCSSLRMNGDQNSDVYAQEKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYNAIGGKYNRGL
          .ALCSSLRMNGDQ.SDVY.QEKQDFVQ.FSQ.......DEM.HP..GDAI..LKEVL.YNAIGGKY.RG.
Retrocopy KALCSSLRMNGDQRSDVYVQEKQDFVQYFSQ----IIGDEMRHP*TGDAITQLKEVL*YNAIGGKYHRGF

Parental  TVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLT-RRGQICWYQKPGVGLDAIND
          TV.VAF.ELVEPRKQDA.SLQRA.TVGWCVELLQA.FLVA.DI.DS.LT.R..QICW.QKPGVGLDAI.D
Retrocopy TVLVAFWELVEPRKQDAESLQRALTVGWCVELLQALFLVANDITDSLLT<RWEQICWFQKPGVGLDAISD

Parental  ANLLEACIYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKT
          A.L.EACIY.LLKLYC.EQPY..NLI.LFLQS.YQ.EIGQTLDL.TAPQGN.DL.RFTEKRYKS.VKYK.
Retrocopy AILVEACIYCLLKLYCWEQPYCQNLIQLFLQSFYQIEIGQTLDLITAPQGNADLGRFTEKRYKSTVKYKA

Parental  -AFYSFYLPIAAAMYMAGIDGEKEHANAKKILLEMGE--FFQI-QDDYLDLF-GDPSVTGKIGTDIQDNK
          ..FY.FY.P.AAAMYMAGIDGEKEH.NAKKILLEMGE..FFQI.QDDYL.LF.GDPSVT.K.GTDIQDNK
Retrocopy <SFY-FYIPVAAAMYMAGIDGEKEHDNAKKILLEMGEGEFFQI<QDDYLHLF>GDPSVTSKVGTDIQDNK

Parental  CSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAAPL
          CSWL.VQCLQRATPE.YQILKENY.QKE..KVA.VKA.YEELDLPAVFLQ..EDSYSHIM.LIEQYAAPL
Retrocopy CSWLLVQCLQRATPEHYQILKENYRQKETKKVAPVKAVYEELDLPAVFLQ**EDSYSHIMGLIEQYAAPL

Parental  PPAVFLGLARKIYKRR
          .PA.FLGL..KIYK..
Retrocopy SPAIFLGLTCKIYKSK

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	0.24 RPM	147.46 RPM
SRP007412_cerebellum	0.08 RPM	128.56 RPM
SRP007412_heart	0.00 RPM	34.43 RPM
SRP007412_kidney	0.00 RPM	103.20 RPM
SRP007412_liver	0.00 RPM	119.84 RPM
SRP007412_testis	0.00 RPM	91.48 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_1184 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1184 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1558
Pan troglodytes	retro_ptro_1048
Pongo abelii	retro_pabe_1290

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000000408	4 retrocopies	retro_ggor_1162, retro_ggor_1184 , retro_ggor_1185, retro_ggor_2608,