RetrogeneDB ID: retro_mmul_214

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:73591719..73592523(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000031259
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SNAI1
• Ensembl ID: ENSMMUG00000019719
• Aliases: None
• Description: None

Sequence

>retro_mmul_214
ATGCCGCGCTCTTTCCTCGTCAGGAAGCCCTCTGACCCTGATCGGAAGCCTAACTACAGCGAACTGCCGGACTCTAATCC
AGAGTTTACCTTCCAGCAGCCCTACCACCGGGCCCACCTGCTGGCAGCCATGCCACGTTCGGAGATCCTTAACCCCTCTG
CTTCGCCGCCAACACTCATCTGGGACGCTTTCCTGGCGCTCCAAGCCCAACCAACTGCCAGGGCCTCCCTCCAACTGGGA
CTCTCCCAGGAGAGTCCCAAGGTGGCAGAACTGACCTCGCTGTCAGATGAGGACAGCGGGAAAGGCTCCCAGTCCCCCAG
CCCACCCTCACAGGCTCCTTCGTCTTTCTCCTCCACTTCAGCTTCTTCCTTGGAGGCAGAGGCCGATGCCACCTCCCCAG
GCTTGGGCCAGGTGCCCAAGCAGCTGGCCCAGGTCTCTGAAGCCAAGGATTCCCAGTTTCAAAAAGCCTTCAACTGCCAA
TACTGCAATAAGGAATGCCTCAGCCTGGGTGTCCTCAAGAGACACATCCGAAGCCACACGCTGCCCTTCGTCTGCGGAAC
CTGCGGGAAGGCCTTCTCCAGACCCTGGCTGCTGCGGGGCCATGTCCGGACCCACACCGGTGAGAAGCCCTTCTCCTGTC
CCCACTGCAGCCGTGCCTTCGCCGACCGCTCCAACCTGCGGGCCCACCTCCAGACCCACTTGGACATCAAGAAGTACCAG
TGCCAGGCGTGCACTCGAACCTTCTCCCGAATGGCCCTGCTCCACAAGCACCAAGAGTCGGGCTGCTCAGGGGGCCCCTG
CTGA

Alignment

ORF - retro_mmul_214 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.83 %
• Parental protein coverage: 99.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPRSFLVRKPSDPNRKPNYSELQDSNPEFTFQQPYDQAHLLAAIPPPEILNPTASLPMLIWDSVLAPQAQ
          MPRSFLVRKPSDP.RKPNYSEL.DSNPEFTFQQPY..AHLLAA.P..EILNP.AS.P.LIWD..LA.QAQ
Retrocopy MPRSFLVRKPSDPDRKPNYSELPDSNPEFTFQQPYHRAHLLAAMPRSEILNPSASPPTLIWDAFLALQAQ

Parental  PIAWASLR---PQESPRAAELTSLSDEDSGKGSQPPSPPSPATSSFSSTSASSLEAEAYAAFPGLGQVPK
          P.A.ASL.....QESP..AELTSLSDEDSGKGSQ.PSPPS.A.SSFSSTSASSLEAEA.A..PGLGQVPK
Retrocopy PTARASLQLGLSQESPKVAELTSLSDEDSGKGSQSPSPPSQAPSSFSSTSASSLEAEADATSPGLGQVPK

Parental  QLAQLSEAKDLQSRKAFNCKYCNKEYLSLGALKMHIRSHTLPCVCGTCGKAFSRPWLLQGHVRTHTGEKP
          QLAQ.SEAKD.Q..KAFNC.YCNKE.LSLG.LK.HIRSHTLP.VCGTCGKAFSRPWLL.GHVRTHTGEKP
Retrocopy QLAQVSEAKDSQFQKAFNCQYCNKECLSLGVLKRHIRSHTLPFVCGTCGKAFSRPWLLRGHVRTHTGEKP

Parental  FSCPHCSRAFADRSNLRAHLQTHSDVKKYQCQACARTFSRMSLLHKHQESGCSGCP
          FSCPHCSRAFADRSNLRAHLQTH.D.KKYQCQAC.RTFSRM.LLHKHQESGCSG.P
Retrocopy FSCPHCSRAFADRSNLRAHLQTHLDIKKYQCQACTRTFSRMALLHKHQESGCSGGP

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	0.22 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.24 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.77 RPM
SRP007412_kidney	0.00 RPM	1.41 RPM
SRP007412_liver	0.00 RPM	1.50 RPM
SRP007412_testis	0.08 RPM	1.51 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_214 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_214 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_214 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000518	1 retrocopy	retro_cjac_2770,
Myotis lucifugus	ENSMLUG00000015053	2 retrocopies	retro_mluc_117, retro_mluc_726,
Macaca mulatta	ENSMMUG00000019719	1 retrocopy	retro_mmul_214 ,