RetrogeneDB ID: retro_mmul_2595

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:72273057..72273604(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LRRFIP2
• Ensembl ID: ENSMMUG00000022539
• Aliases: None
• Description: None

Sequence

>retro_mmul_2595
ACTTCTGGTTCTGGAAGGAAAACATCAATGAAAGCCTGATTTTCTGCAGAAGATGAAGCTTTGAGTAACATGCCAAAAAG
GCAGAGGCAAGGCTGGCAGTAAAATGAGTTGCCTGGGCAAAAGCAAGAGATATACACATGAGCAAACTGGAACAATGAAA
AGAGTTGGATGAAAAATCTGACAAACAGTGTGCTAAAAATTATGCAAGGCCTTTATCTTGAAATTCTGCTCTGCAACAAA
CACCCTAGGTGGAAATTGATCCAGATAAGGAAGTGGGAACACCAGCAGCTTAATAGGTCCAGATACCTAGCTGAGTGACT
TGTCTTTGTCTAAAGTGAAAGAGAAATGTAAGAAAACCATGGTTTCCAGTGCATAGTTATACAACAAGAACAATTTAGCC
CACCAGATAGATACCCTCAAGCTTTTTATTGAAGAACAGGAGGAACAGATGATGGAATTTTATAGAGATAATGAAGAATG
ATCAAAGAAGATAGAAAGACAGAAACATATGTGTAGTGCACTGCAGCATACAATGGATAAACTTAAG

Alignment

ORF - retro_mmul_2595 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.95 %
• Parental protein coverage: 71.21 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TPGSGRKRTPVKDRFSAEDEALSNI-AREAEARLAAKRAARAEARDIRMRELERQQKELDEKSDKQYAEN
          T.GSGRK.T..K..FSAEDEALSN..A..AEARLA.K..A.A.ARDI.M..LE.Q.KELDEKSDKQ.A.N
Retrocopy TSGSGRK-TSMKA*FSAEDEALSNM<AKKAEARLAVK*VAWAKARDIHMSKLE-Q*KELDEKSDKQCAKN

Parental  YTRPSSRNSA-SATTPLSGNSSRRGSGDTSSLIDPDTSLSELRESLSEVEEKYKKAMVSNAQLDNEKNNL
          Y.RP.S.NSA.SAT..L.GN.SR.GSG.TSSLI.PDT.LS.L..SLS.V.EK.KK.MVS.A.L.N.KNNL
Retrocopy YARPLS*NSA<SATNTLGGN*SR*GSGNTSSLIGPDT*LSDL--SLSKVKEKCKKTMVSSA*LYN-KNNL

Parental  IYQVDTLKDVIEEQEEQMAEFYRENEEKSKELERQKHMCSVLQHKMEELK
          ..Q.DTLK..IEEQEEQM.EFYR.NEE.SK..ERQKHMCS.LQH.M..LK
Retrocopy AHQIDTLKLFIEEQEEQMMEFYRDNEE*SKKIERQKHMCSALQHTMDKLK

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	12.77 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	7.54 RPM
SRP007412_cerebellum	0.00 RPM	19.18 RPM
SRP007412_heart	0.00 RPM	62.77 RPM
SRP007412_kidney	0.00 RPM	11.15 RPM
SRP007412_liver	0.00 RPM	5.94 RPM
SRP007412_testis	0.00 RPM	49.42 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2595 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2595 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2595 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000003386	1 retrocopy	retro_mmul_1455,
Macaca mulatta	ENSMMUG00000022539	1 retrocopy	retro_mmul_2595 ,
Ictidomys tridecemlineatus	ENSSTOG00000023775	1 retrocopy	retro_itri_1458,