RetrogeneDB ID: retro_ggor_2001

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:180478434..180479661(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LRRFIP1
• Ensembl ID: ENSGGOG00000008411
• Aliases: None
• Description: None

Sequence

>retro_ggor_2001
ATCAGGGAAATCAAGGACTCTCTAGCAGAAGTTGAAGAGAAATATAAGAAGGTTATGTTTTCCAATGCTCAGCTAGACAA
TGAAAAGACAAACTTCATTTACCAAGTTGACCCCCTGAAAGATATGTTGCTGGAGCTTGAAGAACAGCTGGCTGAATCTA
GGCGGCAGTACGAAGAGAAAAACAAAGAATTTGAAAGGGAAAAACACGCCCACAGTATACTGCAGTTTCAGTTTGCTGAA
GTCAAGGAGGCCCTGAAGCAAACAGAGGAAATGCTCGAGAAACATGGAATAATCCTAAATTCAGAAATAGTTACCAATGG
AGACACTTCCGACACTCTCAGTAATGTTGGATACCAAGATCCAACCAAGATGACGAAAGAAGAGTTAAATGCCCTCAAGT
CGACAGGGGATGGGACCCTAGGAAAGCCAGTGAAGTGGAGGTGAAGAATGAAATCGTGGCGAATGTGGGTAAAAGAGATA
TCTTGCACAATACTGAGAAAGAACAACACACAGAGGACACAGTGAAGGATTGTGTGGACATAGAGGTATTCACTGCTGGT
GAGAATGCCGAGGACCAGAAATCCTCTGAAGACACTGCCCCATTCCTAGGAACCTTAGCAGGTGCTACCTATGAGGAACA
GGTTCAAAGCCAAATTCTTGAGAGCGCTTCTCTCCCTGAAAACACAGCACAGGTTGAGTCAAATGAGGTCATGGGGTGCA
CCAGATGACAGGACCAGAACTCCCCTTGAGCCATCCAACTGTTGGAGTGACTTAGATGGTGGGAGCCACACAGAGAATGT
GGGAGAGGCAGCGGTGACTCAGGTTGGAGAGCAGGCAGACACAGTGGCCTCATGTCCTTCAGGGCATAGTGATGACACAG
TTAATCATGATGACAGATGTATGGTAGAGGTCCCCCAAGAGTTAGAGACAAGCATAGGGCATAGTTTAGAGAAAGAATTC
ACCAACCAGGAAGCAGCTGAGCCCAAGGAGGTTCCAGTGCAGAGTACAGAAGCAGGTAGGGATCACAACGAAGAAGAGGG
TGAAGAAAAAGGATTAAGAGATGAGAAACCAATCAAGACAGAAGTTCCTGGTTCTCCAGCAGGAACTGAGAGCAAGGGTC
AGGAGGCGACAGGTCCAAGTACAGTAGACACTCAAAGTGAACCCTCAGATATGAAAGAGCCAGATGAAGAAAAGAATGAC
CAACAGGGAGAGGCATTGGACTCATCG

Alignment

ORF - retro_ggor_2001 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.75 %
• Parental protein coverage: 50.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LKEMKDSLAEVEEKYKKAMVSNAQLDNEKTNFMYQVDTLKDMLLELEEQLAESRRQYEEKNKEFEREKHA
          ..E.KDSLAEVEEKYKK.M.SNAQLDNEKTNF.YQVD.LKDMLLELEEQLAESRRQYEEKNKEFEREKHA
Retrocopy IREIKDSLAEVEEKYKKVMFSNAQLDNEKTNFIYQVDPLKDMLLELEEQLAESRRQYEEKNKEFEREKHA

Parental  HSILQFQFAEVKEALKQREEMLEKHGIILNSEIATNGETSDTLNNVGYQGPTKMTKEELNALKSTGDGTL
          HSILQFQFAEVKEALKQ.EEMLEKHGIILNSEI.TNG.TSDTL.NVGYQ.PTKMTKEELNALKSTGDGTL
Retrocopy HSILQFQFAEVKEALKQTEEMLEKHGIILNSEIVTNGDTSDTLSNVGYQDPTKMTKEELNALKSTGDGTL

Parental  GR-ASEVEVKNEIVANVGKREILHNTEKEQHTEDTVKDCVDIEVFPAGENTEDQKSSEDTAPFLGTLAGA
          G..ASEVEVKNEIVANVGKR.ILHNTEKEQHTEDTVKDCVDIEVF.AGEN.EDQKSSEDTAPFLGTLAGA
Retrocopy GK<ASEVEVKNEIVANVGKRDILHNTEKEQHTEDTVKDCVDIEVFTAGENAEDQKSSEDTAPFLGTLAGA

Parental  TYEEQVQSQILESTSLPENTVQVESNEVL-GAPDDRTRTPLEPSNCWSDLDDGSHTENVGEAAVTQVEEQ
          TYEEQVQSQILES.SLPENT.QVESNEV..GAPDDRTRTPLEPSNCWSDLD.GSHTENVGEAAVTQV.EQ
Retrocopy TYEEQVQSQILESASLPENTAQVESNEVM>GAPDDRTRTPLEPSNCWSDLDGGSHTENVGEAAVTQVGEQ

Parental  AGTVASCPLGHSDDTVHHDDKCMVEVPQELETSTGHSLEKEFTNQEAAEPKEVPAHSTEVCRDHNEEEGE
          A.TVASCP.GHSDDTV.HDD.CMVEVPQELETS.GHSLEKEFTNQEAAEPKEVP..STE..RDHNEEEGE
Retrocopy ADTVASCPSGHSDDTVNHDDRCMVEVPQELETSIGHSLEKEFTNQEAAEPKEVPVQSTEAGRDHNEEEGE

Parental  ETGLRDEKPIKTEVPGSPAGTEGNGQEAAGPSTVDTQNEPLDMKEPDEEKNDQQGEALDSS
          E.GLRDEKPIKTEVPGSPAGTE..GQEA.GPSTVDTQ.EP.DMKEPDEEKNDQQGEALDSS
Retrocopy EKGLRDEKPIKTEVPGSPAGTESKGQEATGPSTVDTQSEPSDMKEPDEEKNDQQGEALDSS

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	0.96 RPM	63.78 RPM
SRP007412_cerebellum	1.02 RPM	37.07 RPM
SRP007412_heart	1.06 RPM	51.03 RPM
SRP007412_kidney	1.39 RPM	106.19 RPM
SRP007412_liver	1.00 RPM	45.69 RPM
SRP007412_testis	7.15 RPM	19.48 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_2001 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2001 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2887
Macaca mulatta	retro_mmul_1455

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000124831	1 retrocopy	retro_hsap_2887,
Gorilla gorilla	ENSGGOG00000008411	1 retrocopy	retro_ggor_2001 ,
Macaca mulatta	ENSMMUG00000003386	1 retrocopy	retro_mmul_1455,