RetrogeneDB ID: retro_mmul_1264

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 16:55644390..55644761(-)
• Located in intron of: ENSMMUG00000008199

Retrocopy information

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

Parental gene information

• Parental gene symbol: SH3GL1
• Ensembl ID: ENSMMUG00000000273
• Aliases: None
• Description: None

Sequence

>retro_mmul_1264
ATGCAGGAAGCTTCCTCAGGTTCCAAGCGGCAGTATAAGCCCAAGTCCCGGGAGCCCTTTGACCTCGGAGAGCCTGAGCA
GTCCAACGGGGGCTTCCCCAGCACCACAGTCCCCAAGATCGCAGCTTCGTCTTTCCGATCTTCCGACAAGCCCATCTGGA
CTCCTAGCAGGAGCATGCTGCCCCTAGACGAGCGGAGCTGCAAGGTGCTGTACAACTTCGAACCCTAGAACCATGGGGAG
CTGGGCTTCCATGATGGTGACGTCATCACCTTGACCAACCAGATCAACTACAACTGGTATAGGGCATGCTGGATGGCCAG
TCGGGCTTCTTCCTGCTCAGCTACATGGACACGCTCGTGCCCCTGCCGCAG

Alignment

ORF - retro_mmul_1264 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.37 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MREASSRPRREYKPKPREPFDLGEPEQSNGGFPCTTAPKIAASSSFRSSDKPIRTPSRSMLPLDQPSCKA
          M.EASS...R.YKPK.REPFDLGEPEQSNGGFP.TT.PKIAA.SSFRSSDKPI.TPSRSMLPLD..SCK.
Retrocopy MQEASSGSKRQYKPKSREPFDLGEPEQSNGGFPSTTVPKIAA-SSFRSSDKPIWTPSRSMLPLDERSCKV

Parental  LYDFEPENDGELGFREGDVITLTNQIDENWYE-GMLDGQSGFFPLSYVEVLVPLPQ
          LY.FEP.N.GELGF..GDVITLTNQI..NWY..GMLDGQSGFF.LSY...LVPLPQ
Retrocopy LYNFEP*NHGELGFHDGDVITLTNQINYNWYR<GMLDGQSGFFLLSYMDTLVPLPQ

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	12.66 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	44.74 RPM
SRP007412_cerebellum	0.00 RPM	10.72 RPM
SRP007412_heart	0.00 RPM	10.01 RPM
SRP007412_kidney	0.00 RPM	22.07 RPM
SRP007412_liver	0.00 RPM	34.16 RPM
SRP007412_testis	0.23 RPM	44.06 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1264 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1264 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1264 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010823	1 retrocopy	retro_amel_1668,
Choloepus hoffmanni	ENSCHOG00000001689	2 retrocopies	retro_chof_1007, retro_chof_24,
Cavia porcellus	ENSCPOG00000003970	1 retrocopy	retro_cpor_1384,
Homo sapiens	ENSG00000141985	3 retrocopies	retro_hsap_1742, retro_hsap_1745, retro_hsap_1859,
Gorilla gorilla	ENSGGOG00000008198	3 retrocopies	retro_ggor_2151, retro_ggor_2258, retro_ggor_675,
Macropus eugenii	ENSMEUG00000015197	1 retrocopy	retro_meug_523,
Macaca mulatta	ENSMMUG00000000273	1 retrocopy	retro_mmul_1264 ,
Macaca mulatta	ENSMMUG00000013669	1 retrocopy	retro_mmul_1265,
Monodelphis domestica	ENSMODG00000000931	1 retrocopy	retro_mdom_1530,
Nomascus leucogenys	ENSNLEG00000003122	2 retrocopies	retro_nleu_2914, retro_nleu_3075,
Pongo abelii	ENSPPYG00000009405	6 retrocopies	retro_pabe_1488, retro_pabe_1516, retro_pabe_1530, retro_pabe_1542, retro_pabe_1700, retro_pabe_3542,
Pan troglodytes	ENSPTRG00000020792	1 retrocopy	retro_ptro_576,