RetrogeneDB ID: retro_mmul_1411

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:976354..976884(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1255
• Ensembl ID: ENSMMUG00000008784
• Aliases: None
• Description: lipopolysaccharide-induced TNF factor [Source:RefSeq peptide;Acc:NP_001245110]

Sequence

>retro_mmul_1411
GGGCCAACTACGGGGCTGGTGACAGGGCCTGGAGGGAAGGGCATGAATCCTGCTTCGTATTTTGCCAGCCAGCGCCCACC
CCCAGTAACAATCCAATTACCGTGCAGACGGTCTGTGTGCAGCACCCCATCCCCTTTTTGGACCGTCCTGTCCAAATGCG
TTGTCCTTCCTGCAACAAGATGAGCGTGAGTCAGCTGTCCTGTAACGCCGGTGCTCTGACCTGGCTGTCCCGCGGGAGCC
CGTGCCTGCTGGGGTGCGTGGCGGGCCTGCTGCTTCATCCCCTTCTGCGTGGACGCCCTGCAGGACGTGGACCGTTACTG
TCCCAGCTGCAGAGCTCTGGTGGGCACCTACAAGCGTTTGTAGGACTCAGCCAGACGGGGAGGGAGCCGGGTGCCGCAGG
AAGCCCTTTCCTCCTCTCATCAAGCTTCACACCTGGTGGAGGTTCTGCCCTGGTGGTCCCACCTCTCCAGGGGGCCCACC
TTCATGTCTTCTTTTGGGGGGAAATGTCGCAAAACAAACAAACCTCCAAA

Alignment

ORF - retro_mmul_1411 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.44 %
• Parental protein coverage: 78.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GPTTGLVTGPDGKGMNPPSYFT-QAAPIPNNNPITVQTVYVQHPISFLDRPVQMCCPSCNKMIVSQLSYN
          GPTTGLVTGP.GKGMNP.SYF..Q.AP.P.NNPITVQTV.VQHPI.FLDRPVQM.CPSCNKM.VSQLS.N
Retrocopy GPTTGLVTGPGGKGMNPASYFA<QPAPTPSNNPITVQTVCVQHPIPFLDRPVQMRCPSCNKMSVSQLSCN

Parental  AGALTWLSCGSLCLLGVRSGLLLHPLLRGRPAGRGPLLSQLQSSPGHLQAFVGLSQTWREPGAAGSPFHL
          AGALTWLS.GS.CLLG...GLLLHPLLRGRPAGRGPLLSQLQSS.GHLQAFVGLSQT.REPGAAGSPF.L
Retrocopy AGALTWLSRGSPCLLGCVAGLLLHPLLRGRPAGRGPLLSQLQSSGGHLQAFVGLSQTGREPGAAGSPFLL

Parental  SSSFTPGGGSALVVSPLQGAHLHVFFWGEVAKLTNLQTPK
          SSSFTPGGGSALVV.PLQGAHLHVFFWGE.....N.QT.K
Retrocopy SSSFTPGGGSALVVPPLQGAHLHVFFWGEMSQ--NKQTSK

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	0.00 RPM	18.38 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	29.03 RPM
SRP007412_cerebellum	0.00 RPM	14.46 RPM
SRP007412_heart	0.00 RPM	35.15 RPM
SRP007412_kidney	0.00 RPM	34.86 RPM
SRP007412_liver	0.00 RPM	42.24 RPM
SRP007412_testis	6.67 RPM	6.22 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1411 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1411 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1411 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006659	1 retrocopy	retro_cpor_704,
Macaca mulatta	ENSMMUG00000008784	1 retrocopy	retro_mmul_1411 ,
Monodelphis domestica	ENSMODG00000005014	4 retrocopies	retro_mdom_174, retro_mdom_574, retro_mdom_887, retro_mdom_911,
Otolemur garnettii	ENSOGAG00000028239	2 retrocopies	retro_ogar_1479, retro_ogar_2820,
Pteropus vampyrus	ENSPVAG00000009213	1 retrocopy	retro_pvam_261,
Rattus norvegicus	ENSRNOG00000002520	1 retrocopy	retro_rnor_2056,
Tupaia belangeri	ENSTBEG00000017097	1 retrocopy	retro_tbel_4388,
Tursiops truncatus	ENSTTRG00000010854	1 retrocopy	retro_ttru_1244,