RetrogeneDB ID: retro_mmul_304

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:112737326..112737899(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000006016
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SAR1B
• Ensembl ID: ENSMMUG00000004417
• Aliases: None
• Description: SAR1 homolog B [Source:RefSeq peptide;Acc:NP_001247957]

Sequence

>retro_mmul_304
ATGTCTTTCATCTTTGAGTGGATCTACCGAGGCTTCAGCAGTGTGCCCCAGTTCCTAGGACTTGACAAGAAATCTGGAAA
ACTTGGGTTCTTAGGTGTAAACAATACAGGCAAAACAATTCTTCTTCACATGATCAAAGATGACAGATTGGGCCAACATA
TTCCAACACTACATCTGACATCAGAAGAGCTAACAATTGCTGGAATGACTTTTACAACTTTTCACCTTGGTCGGCACGAG
CAAGCATGCCGGGTTTGGAAAAATTGTCTCCCAGCAATGAATGGGATTGTCTTTCTGGTGGACTGTGCAGATCTTTCTTA
CCTTATGGAATCCAAAGTTGAGCTTAATGCTTTAATGACTGATGAAACAATATCCAATGTGCCAATCCTTATCTTGGGTA
ACAAAATTGACAGAACAGATACAATCAATGCAGAAAAACTCCATGAGATATTTGAGCTTTATGGACAGACCACAAGAAAG
GGCAATGTGACCCTGAAAGAGCTGAATGTTCACCCTGTGGAAGTGTTCATGTGCAGTGCACTCAAGAGGCAAGCCTACAG
GGAGGGTTTCTGA

Alignment

ORF - retro_mmul_304 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.32 %
• Parental protein coverage: 95.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSFIFDWIYSGFSSVLQFLGLYKKTGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMT
          MSFIF.WIY.GFSSV.QFLGL.KK.GKL.FLG..N.GKT.LLHM.KDDRLGQH.PTLH.TSEELTIAGMT
Retrocopy MSFIFEWIYRGFSSVPQFLGLDKKSGKLGFLGVNNTGKTILLHMIKDDRLGQHIPTLHLTSEELTIAGMT

Parental  FTTFDLGGHVQARRVWKNYLPAINGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPE
          FTTF.LG.H.QA.RVWKN.LPA.NGIVFLVDCAD...L.ESK.EL..LMTDETI.NVPILILGNKIDR..
Retrocopy FTTFHLGRHEQACRVWKNCLPAMNGIVFLVDCADLSYLMESKVELNALMTDETISNVPILILGNKIDRTD

Parental  AISEERLREMFGLYGQTTGKGSVSLKELNARPLEVFMCSVLKRQGYGEGF
          .I..E.L.E.F.LYGQTT.KG.V.LKELN..P.EVFMCS.LKRQ.Y.EGF
Retrocopy TINAEKLHEIFELYGQTTRKGNVTLKELNVHPVEVFMCSALKRQAYREGF

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	0.78 RPM	15.01 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	11.50 RPM
SRP007412_cerebellum	1.42 RPM	17.63 RPM
SRP007412_heart	1.30 RPM	20.37 RPM
SRP007412_kidney	1.41 RPM	23.47 RPM
SRP007412_liver	1.46 RPM	44.61 RPM
SRP007412_testis	0.75 RPM	62.27 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_304 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_304 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_304 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2976
Pan troglodytes	retro_ptro_2011
Gorilla gorilla	retro_ggor_144
Pongo abelii	retro_pabe_2468

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013784	3 retrocopies	retro_dnov_1584, retro_dnov_1804, retro_dnov_919,
Equus caballus	ENSECAG00000012409	1 retrocopy	retro_ecab_948,
Loxodonta africana	ENSLAFG00000001021	1 retrocopy	retro_lafr_1043,
Macaca mulatta	ENSMMUG00000004417	3 retrocopies	retro_mmul_1825, retro_mmul_2507, retro_mmul_304 ,