RetrogeneDB ID: retro_ggor_1796

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2b:84320853..84321502(-)
• Located in intron of: ENSGGOG00000008893

Retrocopy information

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

Parental gene information

• Parental gene symbol: E2F3
• Ensembl ID: ENSGGOG00000011022
• Aliases: None
• Description: None

Sequence

>retro_ggor_1796
TCTGAGGATGAGGACATGCTGGCCCAATGTCAAGGCCTGTCAAAAGAAGCAACCAAGCTCAGTCAGGAAGAGAAAAAATT
AGATGAACTGATCCAAAGCTATACCCTGGACCTCAAACTATTAACCACAGATTCAGGGAATCAAAGGTTAGTTTATGTTA
CGTATCAAGATATTTGAAAACTTAGTGGTCTTAAAGACCAAACGGTTGTAAGTTGTGAAAGCCCCTCCAGAAACAAGACT
TGAAGCACTTTACTCAATAGAGAGCCTACAGATATATTTGGCAAGTACCCAAGGACCAATTGAGGTTTACTCCTGTCCAG
AAGAGATGGAAACACACAATCCAGTGAAAACAAACAACCAAGACCACAATGGGAATATCTCTAAACCCAATTCCAAAGAC
TTGGATTCAACCAACACAGGACATGGCGATTGGTCAATTTCTGTGGCAAACCTTTCTCCCTTGGCCTCCCCAGTCAACTT
TTTACAGCAGACTGAGGACCAAATTCCTTCTAACCTAGAAAGACCATTTGTAAACTTACTGCCTCCCCTGCTGCAGGAGG
ACTGTCTCCCGAGCCTTGGGGAGGAGGAAGGCATCAGTGATATCTTTGATGCTGATGATTTGGAAAAGCTTCCACTGGTG
GAAGACTTC

Alignment

ORF - retro_ggor_1796 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.87 %
• Parental protein coverage: 64.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SEDGGMLAQCQGLSKEVTELSQEEKKLDELIQSCTLDLKLLTEDSENQRLAYVTYQDIRKISGLKDQTVI
          SED..MLAQCQGLSKE.T.LSQEEKKLDELIQS.TLDLKLLT.DS.NQRL.YVTYQDI.K.SGLKDQTV.
Retrocopy SEDEDMLAQCQGLSKEATKLSQEEKKLDELIQSYTLDLKLLTTDSGNQRLVYVTYQDI*KLSGLKDQTVV

Parental  -VVKAPPETRLEVPDSIESLQIHLASTQGPIEVYLCPEETETHSPMKTNNQDHNGNIPKPASKDLASTNS
          .VVKAPPETRLE...SIESLQI.LASTQGPIEVY.CPEE.ETH.P.KTNNQDHNGNI.KP.SKDL.STN.
Retrocopy >VVKAPPETRLEALYSIESLQIYLASTQGPIEVYSCPEEMETHNPVKTNNQDHNGNISKPNSKDLDSTNT

Parental  GHSDCSISMGNLSPLASPANLLQQTEDQIPSNLEGPFVNLLPPLLQEDYLLSLGEEEGISDLFDAYDLEK
          GH.D.SIS..NLSPLASP.N.LQQTEDQIPSNLE.PFVNLLPPLLQED.L.SLGEEEGISD.FDA.DLEK
Retrocopy GHGDWSISVANLSPLASPVNFLQQTEDQIPSNLERPFVNLLPPLLQEDCLPSLGEEEGISDIFDADDLEK

Parental  LPLVEDF
          LPLVEDF
Retrocopy LPLVEDF

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	0.05 RPM	11.75 RPM
SRP007412_cerebellum	0.00 RPM	1.42 RPM
SRP007412_heart	0.00 RPM	1.34 RPM
SRP007412_kidney	0.00 RPM	12.35 RPM
SRP007412_liver	0.00 RPM	3.32 RPM
SRP007412_testis	0.00 RPM	5.70 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_1796 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1796 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1731
Pongo abelii	retro_pabe_2137

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021045	1 retrocopy	retro_btau_1523,
Choloepus hoffmanni	ENSCHOG00000008679	2 retrocopies	retro_chof_416, retro_chof_871,
Homo sapiens	ENSG00000112242	1 retrocopy	retro_hsap_1749,
Gorilla gorilla	ENSGGOG00000011022	2 retrocopies	retro_ggor_1796 , retro_ggor_2254,
Macaca mulatta	ENSMMUG00000017649	1 retrocopy	retro_mmul_955,
Pongo abelii	ENSPPYG00000016269	2 retrocopies	retro_pabe_1447, retro_pabe_2137,
Pan troglodytes	ENSPTRG00000023584	2 retrocopies	retro_ptro_1217, retro_ptro_1731,
Tupaia belangeri	ENSTBEG00000000171	1 retrocopy	retro_tbel_4457,