RetrogeneDB ID: retro_mmul_901

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:4403750..4404454(+)
• Located in intron of: ENSMMUG00000009885

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.18841
• Ensembl ID: ENSMMUG00000001544
• Aliases: None
• Description: leucine-rich repeat-containing protein 57 [Source:RefSeq peptide;Acc:NP_001181816]

Sequence

>retro_mmul_901
ATAGGAAACGGTGCCCTCGGTACTCAGGTGGAATGGGCACGCTAAACTGCTGTCTCCCAGTTTAAGGACTGTGGGCTGAC
CAAGTTCCTCTTAGAATTGCAGACACTAATGAGCAATCTCAGGACCATCGATTTGTCCAACAATAAGATGGAGAACCTAC
TGCCTTTGCTGATACAGAAGTTCACTGAGCTGAAGAACCTATCCCTGAACAACATAAACTGCTCTGCCTAATGAGATTAT
GCAATCCTAAACAAATCTAGAGATGCTATGCCTAAACAGCAGTCACCCGAGAAAGCTGCCATCTACCTTTGGGCAACTCT
CTACCCTCAAGACCCTGAGCCTCTCTGGGAACCAACTGGGAGCACTATCACCCAACATTGTAGCCTAGGCCACCAGAGGT
GGTGGACCTTTCCAGGAACCAGATTCAAAGTATACCTGACATAGTAGGAGAGCTGCAGGTCATCAGACTCATCCTCAACT
GGAAGAAGATATCTCAGGTCTCAGTAAAGATATCTTGCTGTCCTTGCATTAAAATTCTTTACCTAGAAGAGAACTGTCCT
GAGCTCATCATGGTTTCACAGAGCATCTGCAGTGACTCCCATATCTGTCCGCTTGCTATGGAAGGTGATCTTTTTGAAAT
AAAGAAACTTCAAGAACTGGAAGGTTATGATAAGTACATGGAGAGGTTCATGGCCACCAAGAAG

Alignment

ORF - retro_mmul_901 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.92 %
• Parental protein coverage: 98.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGNSALRAHVETAQKTGVFQLKDRGLTEFPADLQKLTSNLRTIDLSNNKIESLPPLLIGKFTLLKSLSLN
          .GN.AL...VE.A..T.V.Q.KD.GLT.F...LQ.L.SNLRTIDLSNNK.E.L.PLLI.KFT.LK...L.
Retrocopy IGNGALGTQVEWAR*TAVSQFKDCGLTKFLLELQTLMSNLRTIDLSNNKMENLLPLLIQKFTELKN--LS

Parental  NNKL-TVLPDEICNL-KKLETLSLNNNHLRELPSTFGQLSALKTLSLSGNQLGALP-LQLCSLRHL-DVV
          .N...T.LP.EI......LE.L.LN..H.R.LPSTFGQLS.LKTLSLSGNQLGAL...Q.CSL.H...VV
Retrocopy LNNI>TALPNEIMQS*TNLEMLCLNSSHPRKLPSTFGQLSTLKTLSLSGNQLGALS<TQHCSLGHQ<EVV

Parental  DLSKNQIRSIPDTVGELQVIELNLNQNQISQISVKISCCPRLKILRLEENCLELSMLPQSILSDSQICLL
          DLS.NQI.SIPD.VGELQVI.L.LN...ISQ.SVKISCCP..KIL.LEENC.EL.M..QSI.SDS.IC.L
Retrocopy DLSRNQIQSIPDIVGELQVIRLILNWKKISQVSVKISCCPCIKILYLEENCPELIMVSQSICSDSHICPL

Parental  AVEGNLFEIKKLRELEGYDKYMERFTATKK
          A.EG.LFEIKKL.ELEGYDKYMERF.ATKK
Retrocopy AMEGDLFEIKKLQELEGYDKYMERFMATKK

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	13.33 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	14.20 RPM
SRP007412_cerebellum	0.13 RPM	6.46 RPM
SRP007412_heart	0.06 RPM	3.30 RPM
SRP007412_kidney	0.00 RPM	9.86 RPM
SRP007412_liver	0.00 RPM	1.66 RPM
SRP007412_testis	0.00 RPM	57.18 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_901 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_901 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_901 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006482	1 retrocopy	retro_chof_2306,
Callithrix jacchus	ENSCJAG00000002991	1 retrocopy	retro_cjac_2819,
Homo sapiens	ENSG00000180979	1 retrocopy	retro_hsap_2163,
Gorilla gorilla	ENSGGOG00000009597	1 retrocopy	retro_ggor_1718,
Loxodonta africana	ENSLAFG00000005465	2 retrocopies	retro_lafr_1027, retro_lafr_767,
Macaca mulatta	ENSMMUG00000001544	1 retrocopy	retro_mmul_901 ,
Macaca mulatta	ENSMMUG00000016067	1 retrocopy	retro_mmul_712,
Nomascus leucogenys	ENSNLEG00000004485	1 retrocopy	retro_nleu_1812,
Otolemur garnettii	ENSOGAG00000007751	1 retrocopy	retro_ogar_3437,
Pan troglodytes	ENSPTRG00000006976	2 retrocopies	retro_ptro_1649, retro_ptro_1650,
Rattus norvegicus	ENSRNOG00000009143	1 retrocopy	retro_rnor_796,
Rattus norvegicus	ENSRNOG00000048310	1 retrocopy	retro_rnor_1732,