RetrogeneDB ID: retro_mmul_2235

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:70057662..70058013(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1867
• Ensembl ID: ENSMMUG00000002197
• Aliases: None
• Description: gamma-aminobutyric acid receptor-associated protein-like 1 [Source:RefSeq peptide;Acc:NP_001247615]

Sequence

>retro_mmul_2235
ATGAAGTTCCAGTACAAGGAGGACCATCCCTTTGAGTAGCGGAAAAGGGAAGCAGAAAATATCCGGAAGAAATATCCGGA
CAGGGTACCTGTGATTGTAGAGAAGGCTCCAAAAGCCAGGGTGCCTGATCTGGACAAGAGGAAGTACCTAGTGCCCTCCG
ACCTTACCAATGGCCAGTTCTACTTCTTAATCCGGAAGAGAATCCACCTGAGACCTGAGGACGCCTTATTCTTCTTTGTC
AACAACACAATCCCTCCCACTAGTGCTACCGTGGGCCAACTGTATGAGGACAGTCATGAGGAAGATGATTTTCTGTATGT
GGCCTACAGTAATGAGAGTGTCTATGGGAAA

Alignment

ORF - retro_mmul_2235 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKFQYKEDHPFEYRKKEGEKIRKKYPDRVPVIVEKAPKARVPDLDKRKYLVPSDLTVGQFYFLIRKRIHL
          MKFQYKEDHPFE.RK.E.E.IRKKYPDRVPVIVEKAPKARVPDLDKRKYLVPSDLT.GQFYFLIRKRIHL
Retrocopy MKFQYKEDHPFE*RKREAENIRKKYPDRVPVIVEKAPKARVPDLDKRKYLVPSDLTNGQFYFLIRKRIHL

Parental  RPEDALFFFVNNTIPPTSATMGQLYEDNHEEDYFLYVAYSDESVYGK
          RPEDALFFFVNNTIPPTSAT.GQLYED.HEED.FLYVAYS.ESVYGK
Retrocopy RPEDALFFFVNNTIPPTSATVGQLYEDSHEEDDFLYVAYSNESVYGK

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	395.09 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	380.15 RPM
SRP007412_cerebellum	0.13 RPM	303.63 RPM
SRP007412_heart	0.00 RPM	229.77 RPM
SRP007412_kidney	0.00 RPM	354.69 RPM
SRP007412_liver	0.00 RPM	184.50 RPM
SRP007412_testis	0.15 RPM	53.52 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2235 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2235 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2235 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_122

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000002197	1 retrocopy	retro_mmul_2235 ,
Macaca mulatta	ENSMMUG00000005759	2 retrocopies	retro_mmul_2369, retro_mmul_540,
Macaca mulatta	ENSMMUG00000010545	1 retrocopy	retro_mmul_155,
Macaca mulatta	ENSMMUG00000017613	1 retrocopy	retro_mmul_15,
Oryctolagus cuniculus	ENSOCUG00000016834	3 retrocopies	retro_ocun_1380, retro_ocun_496, retro_ocun_697,
Sarcophilus harrisii	ENSSHAG00000007434	1 retrocopy	retro_shar_82,
Ictidomys tridecemlineatus	ENSSTOG00000002246	1 retrocopy	retro_itri_391,
Tursiops truncatus	ENSTTRG00000009099	3 retrocopies	retro_ttru_1451, retro_ttru_1563, retro_ttru_1629,