RetrogeneDB ID: retro_ggor_1816

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2b:117456807..117457516(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000010590
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNF8
• Ensembl ID: ENSGGOG00000025290
• Aliases: None
• Description: None

Sequence

>retro_ggor_1816
AAGAAGCAAAGGACGGTCTTGGCTGAGGACTAGCTAGCCCACATGTCAAAGCTGTTGGGCATGTTCAAGACCAACCTGGA
GGAATTTGCCAGCAAGCACAAGCAGGAGATCCGGAAGGATCCTGAGTTCCATGTGCAGTTCCAGGATATGTGTGCAACCT
TTGGGGTGGAGCCTTTGGCCTCTGGAAAAGGATTTTGATCTGAGATGCTGGGTGTGGGGGATTTTTATTACGAACTAGGT
GTCCACATTATCAAAGTGTGCCTAGTGCTGAGCATTGGAGTGGAGGTCCAATAACTCTGGAGGAACGACATCAACAGGTG
TTAAAAGGAAGGGGCAAGTTCACCCAGGATATCAGTCAAGACGACCTGATCAGGGCCATCATGAAACTAAAGGCACTTGG
CACTGGCTTCAGCATCATCCCCATGAGTGGCACTTACCTCATTCAGTCTGTTCCAACTGAATTCAATATGGATCACACCA
TGGGGCTGCAGCTGGCAGAGAAAAATGGCTATTGACTGTCAGAGAGATCAAAGCCAGTCTTAAATGGGAGACCCAATGAG
CAGGGCAAGTGCCAGAACACCTGCTGAGAGAAGGGCTGGCGTGGCTGGACTTACAGGCCCCAGGGGAGATCCACTACTGG
CTGCCAGCTCTCTTCACCGACCTCTACTCCCAGGAGATTACAGCTGAGGAAGCCAGAGAAGTCTTCCCC

Alignment

ORF - retro_ggor_1816 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.33 %
• Parental protein coverage: 91.86 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KKADPQPAPDSIQQMSKQLDMFKTNLEEFASKHKQEIRKNPEFRVQFQDMCATIGVDPLASGKGFWSEML
          KK.....A.D....MSK.L.MFKTNLEEFASKHKQEIRK.PEF.VQFQDMCAT.GV.PLASGKGF.SEML
Retrocopy KKQRTVLAED*LAHMSKLLGMFKTNLEEFASKHKQEIRKDPEFHVQFQDMCATFGVEPLASGKGF*SEML

Parental  GVGDFYYELGVQIIEVCLAL-KHRNGGLITLEELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALGTGFGI
          GVGDFYYELGV.II.VCL.L..H..GG.ITLEE.HQQVLKGRGKF.QD.SQDDLIRAI.KLKALGTGF.I
Retrocopy GVGDFYYELGVHIIKVCLVL<EHWSGGPITLEERHQQVLKGRGKFTQDISQDDLIRAIMKLKALGTGFSI

Parental  IPVGGTYLIQSVPAELNMDHTVVLQLAEKNGY-VTVSEIKASLKWETERARQVLEHLLKEGLAWLDLQAP
          IP..GTYLIQSVP.E.NMDHT..LQLAEKNGY..TV.EIKASLKWET..A.QV.EHLL.EGLAWLDLQAP
Retrocopy IPMSGTYLIQSVPTEFNMDHTMGLQLAEKNGY<LTVREIKASLKWETQ*AGQVPEHLLREGLAWLDLQAP

Parental  GEAHYWLPALFTDLYSQEITAEEAREALP
          GE.HYWLPALFTDLYSQEITAEEARE..P
Retrocopy GEIHYWLPALFTDLYSQEITAEEAREVFP

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	30.45 RPM
SRP007412_cerebellum	0.00 RPM	24.43 RPM
SRP007412_heart	0.00 RPM	17.48 RPM
SRP007412_kidney	0.00 RPM	43.30 RPM
SRP007412_liver	0.00 RPM	22.24 RPM
SRP007412_testis	0.00 RPM	44.03 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_1816 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1816 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2394
Pongo abelii	retro_pabe_2161

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005062	1 retrocopy	retro_amel_164,
Canis familiaris	ENSCAFG00000016893	1 retrocopy	retro_cfam_1488,
Choloepus hoffmanni	ENSCHOG00000013760	1 retrocopy	retro_chof_1372,
Callithrix jacchus	ENSCJAG00000007322	2 retrocopies	retro_cjac_1175, retro_cjac_1922,
Echinops telfairi	ENSETEG00000000758	1 retrocopy	retro_etel_709,
Felis catus	ENSFCAG00000008944	2 retrocopies	retro_fcat_1291, retro_fcat_574,
Homo sapiens	ENSG00000159210	1 retrocopy	retro_hsap_2394,
Gorilla gorilla	ENSGGOG00000025290	1 retrocopy	retro_ggor_1816 ,
Macropus eugenii	ENSMEUG00000016638	1 retrocopy	retro_meug_663,
Mustela putorius furo	ENSMPUG00000015356	1 retrocopy	retro_mputfur_1425,
Mus musculus	ENSMUSG00000006058	1 retrocopy	retro_mmus_1050,
Nomascus leucogenys	ENSNLEG00000002743	1 retrocopy	retro_nleu_2520,
Oryctolagus cuniculus	ENSOCUG00000009156	2 retrocopies	retro_ocun_814, retro_ocun_996,
Pongo abelii	ENSPPYG00000008911	1 retrocopy	retro_pabe_2161,
Tarsius syrichta	ENSTSYG00000004576	1 retrocopy	retro_tsyr_843,