RetrogeneDB ID: retro_ggor_1994

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:170894277..170895184(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FHL1
• Ensembl ID: ENSGGOG00000010054
• Aliases: None
• Description: None

Sequence

>retro_ggor_1994
GCCCTTGCCAAATACGTCCTATTTGTCACACATCCAAAGTGAGGTCCCTCCAGCTATAAGGTGGGCACCATGGCAGAGAA
GTTTGACTGTCTCTACTGCAGGGACCCCTTGCAGAGGAAAAAGTATGTGAGGAAGGGTGACCAACACTGCTGCCTGAAAT
GTTTTGACAGGTTCTGTGCCAACACCTGCGTGGAATGCTGCAAGCCCATCCATGTGGACTCCAAGGAGGTGCACTATAAA
AACTGCTCCTGGCATGACCCCTGCTTCCACTGTGCCAAGTGCCTTCACCCCTTGCCAATGAGACCTTTGTGGCCAAGGAC
AACAAGATCCTGTGCAACAAGTTTGCCACTCAGGAGGACTCTCCCAAGTGTAAGGGGTGCTTCAAGGCCTTTGTGGCAGA
AGATAAAAAATGGAGTACAAGGGGACCATCTCGCACAAAGACCGCTTCACCTGTAGCAACTGCAAGCAAGTCATGGGGAC
TGGAAGCTTCTTCTCTAAAGGGAAGGACTTTTACTGTGTGACTTGCCATGAGAACAAGTTTGCTAAGCATTGTGTGAAGT
GCAACAAGACCATCGCATCTTGGGGAGTCACTTACCAGGATGAGCCCTGGCATGCTGAGTGCTTTGTGTGTGTTACCTGC
TCTAAGAAGCTGGCTGTGCAGCGTTTCACCACTGTGGAGGACCAGTAATACTGTGTGGATTGCTACAAGAACTTTGTGGC
CAAGAAGTGTGCTGGATGCAAGCACCCCATCACTGGGTTTGGTAAAGGCTCCAGTGTGGTGGCCTATGAAGGACAATCCT
GGCACGACTGCTGCTTCCACTGCAAAAAATGCTCTGTGAATCTGGCCAACAAGCACTTTGTTTTCCACGAGGAGCAAGTA
TATTGCCCTGACTGTGCCAAAAAGTTG

Alignment

ORF - retro_ggor_1994 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.37 %
• Parental protein coverage: 98.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLALELIWMLSSPAGPSSYKVGTMAEKFDCHYCRDPLQGKKYVQKDGHHCCLKCFDKFCANTCVECRKPI
          .LA...........GPSSYKVGTMAEKFDC.YCRDPLQ.KKYV.K...HCCLKCFD.FCANTCVEC.KPI
Retrocopy ALAKYVLFVTHPK*GPSSYKVGTMAEKFDCLYCRDPLQRKKYVRKGDQHCCLKCFDRFCANTCVECCKPI

Parental  GADSKEVHYKNRFWHDTCFRCAKCLHPL-ANETFVAKDNKILCNKCTTREDSPKCKGCFKAIVAGDQN-V
          ..DSKEVHYKN..WHD.CF.CAKCLHPL.ANETFVAKDNKILCNK..T.EDSPKCKGCFKA.VA.D....
Retrocopy HVDSKEVHYKNCSWHDPCFHCAKCLHPL<ANETFVAKDNKILCNKFATQEDSPKCKGCFKAFVAEDKK<M

Parental  EYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFAKHCVKCNKAITSGGITYQDQPWHADC
          EYKGT..HKD.FTCSNCKQV.GTGSFF.KG.DFYCVTCHE.KFAKHCVKCNK.I.S.G.TYQD.PWHA.C
Retrocopy EYKGTISHKDRFTCSNCKQVMGTGSFFSKGKDFYCVTCHENKFAKHCVKCNKTIASWGVTYQDEPWHAEC

Parental  FVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVAKKCAGCKNPITAGFGKGSSVVAYEGQSWHDYCFHCKK
          FVCVTCSKKLA.QRFT.VEDQ.YCVDCYKNFVAKKCAGCK.PIT.GFGKGSSVVAYEGQSWHD.CFHCKK
Retrocopy FVCVTCSKKLAVQRFTTVEDQ*YCVDCYKNFVAKKCAGCKHPIT-GFGKGSSVVAYEGQSWHDCCFHCKK

Parental  CSVNLANKRFVFHQEQVYCPDCAKKL
          CSVNLANK.FVFH.EQVYCPDCAKKL
Retrocopy CSVNLANKHFVFHEEQVYCPDCAKKL

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	0.29 RPM	162.76 RPM
SRP007412_cerebellum	0.47 RPM	131.08 RPM
SRP007412_heart	0.78 RPM	195.22 RPM
SRP007412_kidney	0.37 RPM	39.13 RPM
SRP007412_liver	0.18 RPM	67.61 RPM
SRP007412_testis	3.94 RPM	84.02 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_1994 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1994 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2878
Pongo abelii	retro_pabe_2382
Macaca mulatta	retro_mmul_1458

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000015644	2 retrocopies	retro_dord_299, retro_dord_722,
Homo sapiens	ENSG00000022267	1 retrocopy	retro_hsap_2878,
Gorilla gorilla	ENSGGOG00000010054	1 retrocopy	retro_ggor_1994 ,
Microcebus murinus	ENSMICG00000009342	1 retrocopy	retro_mmur_1438,
Myotis lucifugus	ENSMLUG00000014336	2 retrocopies	retro_mluc_311, retro_mluc_814,
Macaca mulatta	ENSMMUG00000007922	1 retrocopy	retro_mmul_1458,
Mus musculus	ENSMUSG00000023092	1 retrocopy	retro_mmus_51,
Pongo abelii	ENSPPYG00000020761	1 retrocopy	retro_pabe_2382,