RetrogeneDB ID: retro_ggor_1697

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2a:82883189..82883793(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP4A
• Ensembl ID: ENSGGOG00000016091
• Aliases: None
• Description: None

Sequence

>retro_ggor_1697
GAGGAGATGGTAATCAAGAAACAGGAGTTTCTGGAGCAGACAATTCAACATGAATTGTTCATTAGCAGCATTGAGAACAG
ACTTTCAAAGAACCATGGTTCCAAGAATAAGAAAGCTGCTCTGCAGGCTTTACAGGGGAAAAAAAGATGGGAACAGCAGC
TGGCACAAACTGATAGAACATCATCCACCCTAGAGTTTCAGCATGAAGTCATTGAGAATGCCACTACCAATGCAAAAATG
CTTTGTACTTTGTAGTTAGCTGCCTGAGGCATGGTTAGCTGCCTACCAGGACCTGGACATTGGCAAGGTAGATGAACCGA
TGGATGACATCACAGAATAGCAGGAGGTGGCCCAGCAGATCTCAGATGCCATTTCTTGACCTGTGGGTTTTGAAGAAGAT
GTGGGTGATCATGAACTGTTGGAGGAACTAGAGAAGCTGGAGGAGGAATTGGCCCAAGAATTGTTAAATGTGGGGCAACA
AGGAGGAAGTGAACCCCAGTCAAATGGCTAGTGTATCCTCCACACTATCTGCCTTCCTGGGAGGGTCGGCTCCCAAAGCA
GATGAAGACAAAGAAGCACTAAAGGAGTGGCTGCGTGGGAATCC

Alignment

ORF - retro_ggor_1697 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.62 %
• Parental protein coverage: 76.89 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EEAIQKLKETEKILIKKQEFLEQKIQQELQTAKKYGTKNKRAALQALRRKKRFEQQLAQTDGTLSTLEFQ
          EE...K..E.....I....F.......E....K..G.KNK.AALQAL..KKR.EQQLAQTD.T.STLEFQ
Retrocopy EEMVIKKQEFLEQTIQHELFISSI---ENRLSKNHGSKNKKAALQALQGKKRWEQQLAQTDRTSSTLEFQ

Parental  REAIENATTNAEVLRTMELAA-QSMKKAYQDMDIDKVDELMTDITEQQEVAQQISDAISRPMGFGDDVDE
          .E.IENATTNA..L.T..LAA......AYQD.DI.KVDE.M.DITE.QEVAQQISDAIS.P.GF..DV..
Retrocopy HEVIENATTNAKMLCTL*LAA>EAWLAAYQDLDIGKVDEPMDDITE*QEVAQQISDAIS*PVGFEEDVGD

Parental  DELLEELEELEQEELAQELLNV-GDKEEEPPVKLPSVPST--HLPAGPAPKVDEDEEALKQ-LAEWVS
          .ELLEELE.LE.EELAQELLNV.G.KEE..P....SV.ST......G.APK.DED.EALK...A.W.S
Retrocopy HELLEELEKLE-EELAQELLNV>GNKEEVNPSQMASVSSTLSAFLGGSAPKADEDKEALKE<VAAWES

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	29.16 RPM
SRP007412_cerebellum	0.00 RPM	27.26 RPM
SRP007412_heart	0.00 RPM	13.10 RPM
SRP007412_kidney	0.00 RPM	55.90 RPM
SRP007412_liver	0.00 RPM	23.08 RPM
SRP007412_testis	0.00 RPM	36.67 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_1697 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1697 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2284
Pongo abelii	retro_pabe_1937
Macaca mulatta	retro_mmul_1035

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000254505	1 retrocopy	retro_hsap_2284,
Gorilla gorilla	ENSGGOG00000007775	1 retrocopy	retro_ggor_29,
Gorilla gorilla	ENSGGOG00000016091	1 retrocopy	retro_ggor_1697 ,
Microcebus murinus	ENSMICG00000001732	1 retrocopy	retro_mmur_1101,
Macaca mulatta	ENSMMUG00000012476	2 retrocopies	retro_mmul_1035, retro_mmul_1694,
Pongo abelii	ENSPPYG00000005691	1 retrocopy	retro_pabe_1937,
Sorex araneus	ENSSARG00000008328	1 retrocopy	retro_sara_530,