RetrogeneDB ID: retro_mmul_955

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:59641314..59641979(-)
• Located in intron of: ENSMMUG00000005622

Retrocopy information

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

Parental gene information

• Parental gene symbol: E2F3
• Ensembl ID: ENSMMUG00000017649
• Aliases: None
• Description: E2F transcription factor 3 [Source:HGNC Symbol;Acc:3115]

Sequence

>retro_mmul_955
GTGAGCTGCAGTCTGTCTGAGGATGAGGGCATGCTGGTCCAGTGTCAAGGCCTGTCAAAAGAAGCAACCAAGCTGAGTCA
GGAAGAGAAAAAATTAGATGAACTGATCCAGAGCTGCACCCTGGACCTCAAACTATTGACCACAGATTCAGATAACCAAA
GGTTAGTTTATGTTACATATCAAGACATTTGAAAACTTAGTGGCCTTAAAGACCAAACCGTTATAAGTTGTTAAAGCCTC
TCCAGAAACAAGACTTGAAAGCCTTGACTCAATAGAGAGCCTACAAACATATTTGGCAAGTACCCAAGGACCCGTTGAGG
TTTACTCCTGTCCAGAAGAGATGGAAACACACAATCCAGTGAAAACAAACAACCAAGACCACAATGGGAATATCTCTAAA
CTCAATTCCAAAGACTTGGATTCAGCCAACTCAGGACATAGCAATTGGTCAATTTCTATAGTAAACCTTTCTCCCTTGGC
CTCCTCAGCCAACTTTTTACAGCAGACTGTGAACCAAATTCCTTCTAACCTAGAAGGACCGTTTGTGAACTCACTGCTTC
CCCTGCTGCAAGAGGACTGTCTCCTGAGCCTTGGGGAGGAGGGAAGGCATCAGTGATCTCTTTGATGCTGATGATTTGGA
AAAGCTTCCACTGGTGGAAGACTTC

Alignment

ORF - retro_mmul_955 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.89 %
• Parental protein coverage: 66.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGCSLSEDGGMLAQCQGLSKEVTELSQEEKKLDELIQSCTLDLKLLTEDSENQRYPFSYVTYQDIRKISG
          ..CSLSED.GML.QCQGLSKE.T.LSQEEKKLDELIQSCTLDLKLLT.DS.NQR....YVTYQDI.K.SG
Retrocopy VSCSLSEDEGMLVQCQGLSKEATKLSQEEKKLDELIQSCTLDLKLLTTDSDNQR--LVYVTYQDI*KLSG

Parental  LKDQTVI-VVKAPPETRLEVPDSIESLQIHLASTQGPIEVYLCPEETETHSPMKTNNQDHNGNIPKPTSK
          LKDQTVI.VVKA.PETRLE..DSIESLQ..LASTQGP.EVY.CPEE.ETH.P.KTNNQDHNGNI.K..SK
Retrocopy LKDQTVI>VVKASPETRLESLDSIESLQTYLASTQGPVEVYSCPEEMETHNPVKTNNQDHNGNISKLNSK

Parental  DLASTNSGHSDCSISMGNLSPLASPANLLQQTEDQIPSNLEGPFVNLLPPLLQEDYLLSLGEE-EGISDL
          DL.S.NSGHS..SIS..NLSPLAS.AN.LQQT..QIPSNLEGPFVN.L.PLLQED.LLSLGEE.EGISDL
Retrocopy DLDSANSGHSNWSISIVNLSPLASSANFLQQTVNQIPSNLEGPFVNSLLPLLQEDCLLSLGEE>EGISDL

Parental  FDAYDLEKLPLVEDF
          FDA.DLEKLPLVEDF
Retrocopy FDADDLEKLPLVEDF

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	0.11 RPM	19.05 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	20.15 RPM
SRP007412_cerebellum	0.00 RPM	2.58 RPM
SRP007412_heart	0.00 RPM	8.60 RPM
SRP007412_kidney	0.00 RPM	8.33 RPM
SRP007412_liver	0.00 RPM	3.92 RPM
SRP007412_testis	0.04 RPM	4.64 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_955 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_955 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_955 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 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 ,
Macaca mulatta	ENSMMUG00000023225	1 retrocopy	retro_mmul_87,
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,