RetrogeneDB ID: retro_mmul_1089

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:113613..114032(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS24
• Ensembl ID: ENSMMUG00000002405
• Aliases: None
• Description: None

Sequence

>retro_mmul_1089
CCTTGCGCTGGGCGCGCCCTGCACACCTCCGCCGTCCGCGACGAGAACCGGCGGCCCGAGTCCGCGGAGGCCGGGGGACA
AGCCGGCGACCTAGGAGGACGCACACGCGCCGCACTTCGTCGCCCGCCTGAGGGCCGGAGGTCGCTCGCACGCGGAGCCC
GGACGGGAGGGCCGTGCGGCGGAGCGAACCGTGGAGGGCGTTTCCGTGGCGCATTCATGTCGGGGCCTTCCCGGGCGCCC
GGCTGACCAGCGGGTGGTGCCGCTCCGGGCGAGCCGTTGGGAGAGCTGCGCCCCGGTCCTGAGGCACTTGCCTGCCCGCA
CGTTCTGCTTCCTCGTGGGCCACAGGGAAACTTCGCTGTCCCACTTGCCACGTGTCCTCTGCCCTCCACGTCCAAACAGC
GCCGTCGGAGGCTGTGTAC

Alignment

ORF - retro_mmul_1089 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.02 %
• Parental protein coverage: 85.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PCAWRALHTSAVCAKNR-AARVRVGK-GDKPVTYEEAHAPHYIAHRKGWLSLHTGNLDGEDHAAERTVED
          PCA.RALHTSAV...NR.AARVR.G..GDKP.T.E.AHAPH..A........H......E..AAERTVE.
Retrocopy PCAGRALHTSAVRDENR<AARVRGGR<GDKPAT*EDAHAPHFVARLRAGGRSH-AEPGREGRAAERTVEG

Parental  VFLRKFMWGTFPGCLADQLVLKRRGNQLEICALVLRNLPPHKYYFLVGYSETLLSYFYK-CPV-RLHLQT
          V.......G..PG..ADQ.V...R....E.CA.VLR.LP.....FLVG..ET.LS.....CP...LH.QT
Retrocopy VSVAHSCRG-LPGRPADQRVVPLRASRWESCAPVLRHLPARTFCFLVGHRETSLSHLPR<CPL<ALHVQT

Parental  VPSKVVY
          .PS..VY
Retrocopy APSEAVY

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	1.23 RPM	13.78 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	34.67 RPM
SRP007412_cerebellum	0.65 RPM	12.27 RPM
SRP007412_heart	1.53 RPM	28.85 RPM
SRP007412_kidney	0.82 RPM	30.40 RPM
SRP007412_liver	1.62 RPM	29.93 RPM
SRP007412_testis	0.75 RPM	16.32 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1089 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1089 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1089 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017491	1 retrocopy	retro_amel_1126,
Bos taurus	ENSBTAG00000007398	1 retrocopy	retro_btau_411,
Choloepus hoffmanni	ENSCHOG00000003106	1 retrocopy	retro_chof_2334,
Dasypus novemcinctus	ENSDNOG00000016853	3 retrocopies	retro_dnov_1195, retro_dnov_153, retro_dnov_2049,
Echinops telfairi	ENSETEG00000016782	1 retrocopy	retro_etel_1350,
Homo sapiens	ENSG00000062582	1 retrocopy	retro_hsap_836,
Gorilla gorilla	ENSGGOG00000005692	1 retrocopy	retro_ggor_687,
Loxodonta africana	ENSLAFG00000011905	1 retrocopy	retro_lafr_426,
Macaca mulatta	ENSMMUG00000002405	1 retrocopy	retro_mmul_1089 ,
Monodelphis domestica	ENSMODG00000013889	1 retrocopy	retro_mdom_1785,
Pan troglodytes	ENSPTRG00000019127	1 retrocopy	retro_ptro_583,
Pteropus vampyrus	ENSPVAG00000015911	4 retrocopies	retro_pvam_1129, retro_pvam_1360, retro_pvam_180, retro_pvam_978,
Tursiops truncatus	ENSTTRG00000002938	1 retrocopy	retro_ttru_1860,