RetrogeneDB ID: retro_mmul_1222

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 16:25305433..25305967(+)
• Located in intron of: ENSMMUG00000012118

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.17675
• Ensembl ID: ENSMMUG00000020204
• Aliases: None
• Description: syntaxin-18 [Source:RefSeq peptide;Acc:NP_001247460]

Sequence

>retro_mmul_1222
TGTGTAAACTTTACTCAGAACAAAGAGCCATCCGAGTTAAGAGTGGTGGATAAGAAAAGATTATCTAAGCTGAAACCAGA
ACCAAATACAAAGACAAGATAATCCACATCTGAGAAAGTTTCACAGAGTCCTTCAAAAGACTCTGAAGAAAACCCTGCCA
CTGAAGAACATCCAGAAAAGATTTTGGCTGAAACACAACCTGAATTGGGAACCTGGGGAGATGGCAAAGGTGAAGATGAA
TTATCCCCAGAAGAAATACAAATGTTTGAACTGGAAAATCAGCGACGAATTGGTGAAATGAACATCTTGTTTGATGAAGT
GAGGCAGATCGAAGGGAGAGTGGTTGAGATTTCCAGACTTCAAGAGATATTCACGGAAAAGGTTTTGCCACAGGAAACTG
AGATTGATAGCATTCACCAGTTAGTTGTGGGGGCAACTGAAAATATCAAGGAAGGCAACAAAGACATAAGAGAGGCCATT
AACAACAACGCTGGCTTCCACGTGTGGATCCTCTTCTTCCCCATGATGTGTGCT

Alignment

ORF - retro_mmul_1222 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.47 %
• Parental protein coverage: 53.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CKLYSEQRAIRVKRVVDKKRLSKLEPEPNTKTRESTSSEKVSQSPSKDSEENPATEEHPEKILAETQPEL
          C............RVVDKKRLSKL.PEPNTKTR.ST.SEKVSQSPSKDSEENPATEEHPEKILAETQPEL
Retrocopy CVNFTQNKEPSELRVVDKKRLSKLKPEPNTKTR*ST-SEKVSQSPSKDSEENPATEEHPEKILAETQPEL

Parental  GTWGDGKGEDELSPEEIQMFEQENQRLIGEMNSLFDEVRQIEGRVVEISRLQEIFTEKVLQQEAEIDSIH
          GTWGDGKGEDELSPEEIQMFE.ENQR.IGEMN.LFDEVRQIEGRVVEISRLQEIFTEKVL.QE.EIDSIH
Retrocopy GTWGDGKGEDELSPEEIQMFELENQRRIGEMNILFDEVRQIEGRVVEISRLQEIFTEKVLPQETEIDSIH

Parental  QLVVGATENIKEGNEDIREAIKNNAGFRVWILFFLVMCS
          QLVVGATENIKEGN.DIREAI.NNAGF.VWILFF..MC.
Retrocopy QLVVGATENIKEGNKDIREAINNNAGFHVWILFFPMMCA

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	0.22 RPM	17.59 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	15.87 RPM
SRP007412_cerebellum	0.13 RPM	17.50 RPM
SRP007412_heart	0.06 RPM	11.72 RPM
SRP007412_kidney	0.00 RPM	19.95 RPM
SRP007412_liver	0.00 RPM	8.31 RPM
SRP007412_testis	0.41 RPM	109.08 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1222 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1222 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1222 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000168818	1 retrocopy	retro_hsap_1741,
Microcebus murinus	ENSMICG00000009557	1 retrocopy	retro_mmur_1372,
Macaca mulatta	ENSMMUG00000020204	1 retrocopy	retro_mmul_1222 ,
Mustela putorius furo	ENSMPUG00000007952	1 retrocopy	retro_mputfur_1453,