RetrogeneDB ID: retro_mmul_301

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:91371904..91372636(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000030225
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FGF13
• Ensembl ID: ENSMMUG00000012484
• Aliases: None
• Description: fibroblast growth factor 13 [Source:RefSeq peptide;Acc:NP_001252772]

Sequence

>retro_mmul_301
ATGGCGGCGGCTATCGCCAGCTCGCTCATCCGTCAGAAGAGGCAAGGCCGCGAGCGCGAGAAATCCAACGCCTGCAAGTG
CAGTCCCAGCAAAGGCAAGACCAGCTGCGACAAAAACAAGTTAAATGTCTTTTCCCGGGTCAAACTCTTCGGCTCCAAGA
AGAGGCCCCGAAGAAGACCAGAGCCTCAGCTTAAGGGTGTAGTTACCAAGCTATACAGCCGACAAGGCTACCACTTGCAG
CTGCAGGCGGATGGAACCATTGATGGCACCAAAGATGAGGACAGCACTTACACTCTGTTTAACCTCATCCCTGTGGGTCT
GCGAGTGGTGGCTATGCAAGGAGTTCAAACCAAGCTGTACTTGGCAATGAACAGTGAGGGATCCTTGTACACTTCGGAAC
TTTTCACACCTGAGTGCAAATTCAAAGAATCAGTGTTTGAAAATTATTATGTGACATATTCATCAATGATATACCGTCAG
CAGCAGTCAGGCCGAGGGTGGTATCTGGGTCTGAACAAAGAAGGAGAGATCATGAAAGGCAACCATGTGAAGAAGAACAA
GCCTGCAGCTCATTTTCTGCCCAAACCACTAAAAGTGGCCATGTACAAGGAGCCATCACTGCACGACCTCACGGAGTTCT
CCCGATCTGGAAGCGGGACCCCAACCAAGAGCAGAAGTGTCTCTGGCGTGCTGAACGGAGGCAAATCCATGAGCCACAAT
GAATCAACGTAG

Alignment

ORF - retro_mmul_301 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.14 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAIASSLIRQKRQAREREKSNACKCVSSPSKGKTSCDKNKLNVFSRVKLFGSKKRRRRRPEPQLKGIV
          MAAAIASSLIRQKRQ.REREKSNACKC..SPSKGKTSCDKNKLNVFSRVKLFGSKKR.RRRPEPQLKG.V
Retrocopy MAAAIASSLIRQKRQGREREKSNACKC--SPSKGKTSCDKNKLNVFSRVKLFGSKKRPRRRPEPQLKGVV

Parental  TKLYSRQGYHLQLQADGTIDGTKDEDSTYTLFNLIPVGLRVVAIQGVQTKLYLAMNSEGYLYTSELFTPE
          TKLYSRQGYHLQLQADGTIDGTKDEDSTYTLFNLIPVGLRVVA.QGVQTKLYLAMNSEG.LYTSELFTPE
Retrocopy TKLYSRQGYHLQLQADGTIDGTKDEDSTYTLFNLIPVGLRVVAMQGVQTKLYLAMNSEGSLYTSELFTPE

Parental  CKFKESVFENYYVTYSSMIYRQQQSGRGWYLGLNKEGEIMKGNHVKKNKPAAHFLPKPLKVAMYKEPSLH
          CKFKESVFENYYVTYSSMIYRQQQSGRGWYLGLNKEGEIMKGNHVKKNKPAAHFLPKPLKVAMYKEPSLH
Retrocopy CKFKESVFENYYVTYSSMIYRQQQSGRGWYLGLNKEGEIMKGNHVKKNKPAAHFLPKPLKVAMYKEPSLH

Parental  DLTEFSRSGSGTPTKSRSVSGVLNGGKSMSHNEST
          DLTEFSRSGSGTPTKSRSVSGVLNGGKSMSHNEST
Retrocopy DLTEFSRSGSGTPTKSRSVSGVLNGGKSMSHNEST

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	0.22 RPM	34.29 RPM
SRP007412_brain_prefrontal_cortex	0.40 RPM	31.26 RPM
SRP007412_cerebellum	0.13 RPM	1.74 RPM
SRP007412_heart	0.00 RPM	2.94 RPM
SRP007412_kidney	0.23 RPM	2.35 RPM
SRP007412_liver	0.00 RPM	0.04 RPM
SRP007412_testis	0.04 RPM	0.64 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_301 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_301 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_301 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004376	1 retrocopy	retro_chof_774,
Macaca mulatta	ENSMMUG00000012484	1 retrocopy	retro_mmul_301 ,