RetrogeneDB ID: retro_mmul_2077

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:43740773..43741141(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.873
• Ensembl ID: ENSMMUG00000022101
• Aliases: None
• Description: cold-inducible RNA-binding protein [Source:RefSeq peptide;Acc:NP_001248245]

Sequence

>retro_mmul_2077
GCAGATCATCCAGGAAAGCTCTTCTTTAGTGGTCTTAATACAGAAACAAATGAGAAAGCTCTTGAAGCAGTATTTGGCAA
ATATGGACGAATAGTGGAAGTACTCTTGATGAAAGACCCGGAAACCAACAAATCAGGAGGATTTGCTTTTGTCACCTTTG
AAGCCCAGCAGATGCTAAGGATGCAGCCAGAGACATGAATGGAAAGTCATTAGATGGAAAAGCCATCAAGGTGGAACAAG
TCACCAAACCATCATTTGAAAGTGGTAGACGTGGACCGCCTCCACCTCCAAGAAGTAGAGGCCCTCCAAGAGGTCTTAGA
GGTGGAAGACGAGGAAGTGGAGGAACCAGGGGACCTCCCTCACGGGGA

Alignment

ORF - retro_mmul_2077 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.81 %
• Parental protein coverage: 72.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFE-NIDDAKDAMMAMNGK
          A...GKLF..GL...TNE..LE.VF.KYG.I.EV...KD.ET..S.GF.FVTFE....DAKDA...MNGK
Retrocopy ADHPGKLFFSGLNTETNEKALEAVFGKYGRIVEVLLMKDPETNKSGGFAFVTFE<SPADAKDAARDMNGK

Parental  SVDGRQIRVDQAGKSSDNRSRGYRGGSAGGRGFFRGGRG--RGRGFSRGGGDRG
          S.DG..I.V.Q..K.S....R.........RG..RG.RG..RG.G..RG...RG
Retrocopy SLDGKAIKVEQVTKPSFESGRRGPPPPPRSRGPPRGLRGGRRGSGGTRGPPSRG

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	2.69 RPM	112.83 RPM
SRP007412_brain_prefrontal_cortex	5.79 RPM	121.14 RPM
SRP007412_cerebellum	3.10 RPM	163.83 RPM
SRP007412_heart	3.83 RPM	153.16 RPM
SRP007412_kidney	3.76 RPM	121.36 RPM
SRP007412_liver	1.15 RPM	85.22 RPM
SRP007412_testis	1.32 RPM	184.81 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2077 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2077 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2077 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Gadus morhua	ENSGMOG00000012137	1 retrocopy	retro_gmor_4,
Myotis lucifugus	ENSMLUG00000015007	1 retrocopy	retro_mluc_1975,
Macaca mulatta	ENSMMUG00000022101	4 retrocopies	retro_mmul_1101, retro_mmul_2077 , retro_mmul_510, retro_mmul_677,
Tursiops truncatus	ENSTTRG00000011049	1 retrocopy	retro_ttru_756,