RetrogeneDB ID: retro_mmul_1101

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:64931144..64931486(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000008588
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1101
GCGGATCGCCCGGGGAAGCTGTTCATTGGAGGCCTCAACCTCGAAACCGACGAGAAAGCCCTCGAAGCCGAGTTTGGCAA
GTATGGCCGCATCGTCGAGGTGCTCCTGATGAAAGACCGAGAAACCAACAAGTCGAGGGGCTTCGCGTTCGTCACCTTCG
AAAGCCCCGCAGACGCCAAGGCCGCCGCCAGAGACATGAACGGCAAGTCCCTGGATGGTAAGGCCATCAAGGTGGCCCAG
GCCACCAAACCGGCGTTCGAGAGCAGCCGGCGAGGCCCGCCGCCTCCTCGCAGCCGCGGTCGCCCGAGGTTCCTGCGCGG
AACCCGCGGAGGTGGCGGCGGC

Alignment

ORF - retro_mmul_1101 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.63 %
• Parental protein coverage: 65.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKS
          A...GKLF.GGL...T.E..LE..F.KYG.I.EV...KDRET..SRGF.FVTFE...DAK.A...MNGKS
Retrocopy ADRPGKLFIGGLNLETDEKALEAEFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADAKAAARDMNGKS

Parental  VDGRQIRVDQAGKSS-DNRSRGYRGGSAGGRGFF-RGGRGRGRG
          .DG..I.V.QA.K.......RG.......GR..F.RG.RG.G.G
Retrocopy LDGKAIKVAQATKPAFESSRRGPPPPRSRGRPRFLRGTRGGGGG

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	112.83 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	121.14 RPM
SRP007412_cerebellum	0.00 RPM	163.83 RPM
SRP007412_heart	0.12 RPM	153.16 RPM
SRP007412_kidney	0.00 RPM	121.36 RPM
SRP007412_liver	0.00 RPM	85.22 RPM
SRP007412_testis	22.20 RPM	184.81 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1101 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1101 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1101 has 0 orthologous retrocopies within eutheria group .

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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,