RetrogeneDB ID: retro_mmul_1042

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:106106624..106107098(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF3
• Ensembl ID: ENSMMUG00000014306
• Aliases: None
• Description: None

Sequence

>retro_mmul_1042
ATGCATTGTGATTCCTGTCCATTGGACTGTAAGGTTTGTGTAGGCAATCTTGGAAACAATGGCAACAAGACTGAATTGGA
ACGGGCTTTTGGCTACTATGGACCATTCTGAAGTGTGTGGGTTGCTAGAAACCCTGCCGGCTTTGCTTTTGTTGAATTTG
AAGATCCCCGAGGTGCAGCTGATGCGATCCGAGAGCTAGATGGAAGAACACTATGTGGCCGCTGTGTGACAGTGGAACTG
TCGAATGATGAAAAAAGAAGTAGAAATCGTGGCCCACCTCCCTCTCGGGGTCGTCGCCCTCGAGATGATTATCGCAGGAG
GCGTCCTCCACCTCGTCGCAGATCTCCAAGGAGAAGCCTCTCTCGCTGCGGGAGCAGGTCCCTTTCTAGAGTTAGGAGAA
GAGAGAGATCGCTGTCTCCGGAGAGAAATCACAAGCCGTCGGGATCCTTCTCTAGGTCTCGGAGCCCATGTAGG

Alignment

ORF - retro_mmul_1042 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.16 %
• Parental protein coverage: 96.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT
          MH.DSCPLDCKV.VGNLGNNGNKTELERAFGYYGP..SVWVARNP.GFAFVEFEDPR.AADA.RELDGRT
Retrocopy MHCDSCPLDCKVCVGNLGNNGNKTELERAFGYYGPF*SVWVARNPAGFAFVEFEDPRGAADAIRELDGRT

Parental  LCGCRVRVELSNGEKRSRNRGPPPSWGRRPRDDYRRRSPPPRRRSPRRRSFSRSRSRSLSRDRRRERSLS
          LCG..V.VELSN.EKRSRNRGPPPS.GRRPRDDYRRR.PPPRRRSP.RRS.SR..SRSLSR.RRRERSLS
Retrocopy LCGRCVTVELSNDEKRSRNRGPPPSRGRRPRDDYRRRRPPPRRRSP-RRSLSRCGSRSLSRVRRRERSLS

Parental  RERNHKPSRSFSRSRSRSR
          .ERNHKPS.SFSRSRS..R
Retrocopy PERNHKPSGSFSRSRSPCR

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	75.63 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	61.00 RPM
SRP007412_cerebellum	0.06 RPM	107.84 RPM
SRP007412_heart	0.00 RPM	91.04 RPM
SRP007412_kidney	0.12 RPM	86.50 RPM
SRP007412_liver	0.00 RPM	51.10 RPM
SRP007412_testis	0.45 RPM	140.14 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1042 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1042 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1042 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016062	5 retrocopies	retro_cjac_1035, retro_cjac_1969, retro_cjac_2006, retro_cjac_620, retro_cjac_746,
Echinops telfairi	ENSETEG00000010117	2 retrocopies	retro_etel_2064, retro_etel_445,
Loxodonta africana	ENSLAFG00000018193	2 retrocopies	retro_lafr_1219, retro_lafr_80,
Myotis lucifugus	ENSMLUG00000010671	6 retrocopies	retro_mluc_1205, retro_mluc_1312, retro_mluc_1554, retro_mluc_2283, retro_mluc_278, retro_mluc_51,
Macaca mulatta	ENSMMUG00000014306	4 retrocopies	retro_mmul_1007, retro_mmul_1042 , retro_mmul_1642, retro_mmul_2359,
Macaca mulatta	ENSMMUG00000016494	1 retrocopy	retro_mmul_2154,
Mus musculus	ENSMUSG00000071172	9 retrocopies	retro_mmus_100, retro_mmus_1347, retro_mmus_1749, retro_mmus_2294, retro_mmus_2337, retro_mmus_2433, retro_mmus_2654, retro_mmus_2933, retro_mmus_3629,
Otolemur garnettii	ENSOGAG00000000502	6 retrocopies	retro_ogar_1850, retro_ogar_1959, retro_ogar_2131, retro_ogar_2783, retro_ogar_597, retro_ogar_803,
Sus scrofa	ENSSSCG00000001564	1 retrocopy	retro_sscr_1038,
Ictidomys tridecemlineatus	ENSSTOG00000014280	5 retrocopies	retro_itri_123, retro_itri_502, retro_itri_664, retro_itri_857, retro_itri_901,