RetrogeneDB ID: retro_mmul_859

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:39365132..39366161(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.9602
• Ensembl ID: ENSMMUG00000012105
• Aliases: None
• Description: None

Sequence

>retro_mmul_859
ATTATTACAACCCAAAAGGAAGCAACTGCAAAATCAATGATAAATTAAGTACAACTTGCAGCAGCTTTTCATGAGGAATT
TGTTGTGAGAGAAGATTTAATGGAGGTGGCAATAGGAACACATGGTAGTAACATTCAGCAAGCTAGGAAGGTTCCTGGAG
TTACCGCCATTGAGCTAGATGAAGACACTGAAACATTAAGAATCTATAGAGAGAGTGCTGATGCTGTAAAAACGGCTAGA
GGTTTCTTGGAATTTGTGCAGGATTTTATTCAGGCTTCTAAGAACCTCACTGGAAAAGTAATTGGAAAAAAATGGCAAAG
TTATTCAAGAAATAGTAGACAAATCTGATACAGTTCAGGTGAGAATTGAAGGGGATAGTGAAAATAAACTACCCAGAGAA
GACGGTATGATTCCATTTGTATCTGTTGGCACTAAAGAAACCATTGGAAATGTGCAAGTTCTTTTAGAGTACCATATTGC
TTATCTAAAGGAAGTAAAACAGCTAAGAATGGAACGCCTACAGATTGATGAGCAGTTACAAGAGATTGGTTCTAGGTCTT
ATAGTGGAAGAGGCAGAGGTTGTCGGGGCCCTAATTACACCTCCAGTTATAGTACAAATTCTGAGCTGTCTAAACCCTCT
GAAATAGAATCTGAGGGTAAAGACAAGCTGAGTGATTGGTCATTGGCAGGAGATGATGATCGAGACAGCCGACATCAGCG
TGACAGCAGGAGACACCCAGGAGGAAGATGCAAAGTGTTTCAGGGGGTCAAGGTCGTGGTGGACCACATGGTGGCAAATC
CTCCATCATTTCTGTGCTCAAAGATCCAGACAGCAATCCATACAGCTTACTTGATAATACAGAATCAGATCAGACTGCAG
ACACTGATGCCAGCGAATCTCATCACAGTACTAATCGTCATATGAGGTCTCGTAGATGAAGGACTGACGAAGATGCTGTT
CTGATGGATGGAATGACTGAATCTGATACAGCTTCAATTACTGAAAATGGGCTAGGCAAAAGATGTGAT

Alignment

ORF - retro_mmul_859 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.48 %
• Parental protein coverage: 75.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLMSRNEEATKHLECTKQLAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYG
          ......E...K......QLAAAFHEEFVVREDLM..AIGTHGSNIQQARKVPGVTAIELDEDT.T.RIY.
Retrocopy IITTQKEATAKSMIN*VQLAAAFHEEFVVREDLMEVAIGTHGSNIQQARKVPGVTAIELDEDTETLRIYR

Parental  ESADAVKKARGFLEFVEDFIQVPRNLVGKVIGK-NGKVIQEIVDKSGVVRVRIEGDNENKLPREDGMVPF
          ESADAVK.ARGFLEFV.DFIQ...NL.GKVIGK.NGKVIQEIVDKS..V.VRIEGD.ENKLPREDGM.PF
Retrocopy ESADAVKTARGFLEFVQDFIQASKNLTGKVIGK>NGKVIQEIVDKSDTVQVRIEGDSENKLPREDGMIPF

Parental  VFVGTKESIGNVQVLLEYHIAYLKEVEQLRMERLQIDEQLRQIGSRSYSGRGRGRRGPNYTSGYGTNSEL
          V.VGTKE.IGNVQVLLEYHIAYLKEV.QLRMERLQIDEQL..IGSRSYSGRGRG.RGPNYTS.Y.TNSEL
Retrocopy VSVGTKETIGNVQVLLEYHIAYLKEVKQLRMERLQIDEQLQEIGSRSYSGRGRGCRGPNYTSSYSTNSEL

Parental  SNPSETESERKDELSDWSLAGEDDRDSRHQRDSRRRPGGRGR-SVSGGRGRGGPRGGKSSISSVLKDPDS
          S.PSE.ESE.KD.LSDWSLAG.DDRDSRHQRDSRR.PGGR...SVSGG.GRGGP.GGKSSI.SVLKDPDS
Retrocopy SKPSEIESEGKDKLSDWSLAGDDDRDSRHQRDSRRHPGGRCK<SVSGGQGRGGPHGGKSSIISVLKDPDS

Parental  NPYSLLDNTESDQTADTDASESHHSTNRRRRSRRRRTDEDAVLMDGMTESDTASVNENGLGKRCD
          NPYSLLDNTESDQTADTDASESHHSTNR..RSRR.RTDEDAVLMDGMTESDTAS..ENGLGKRCD
Retrocopy NPYSLLDNTESDQTADTDASESHHSTNRHMRSRR*RTDEDAVLMDGMTESDTASITENGLGKRCD

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	0.34 RPM	67.90 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	50.45 RPM
SRP007412_cerebellum	0.19 RPM	68.38 RPM
SRP007412_heart	0.00 RPM	98.28 RPM
SRP007412_kidney	0.00 RPM	52.35 RPM
SRP007412_liver	0.16 RPM	26.56 RPM
SRP007412_testis	0.30 RPM	762.01 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_859 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_859 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_859 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000012105	1 retrocopy	retro_mmul_859 ,
Nomascus leucogenys	ENSNLEG00000005928	1 retrocopy	retro_nleu_197,
Ochotona princeps	ENSOPRG00000009223	2 retrocopies	retro_opri_61, retro_opri_779,
Pan troglodytes	ENSPTRG00000015656	1 retrocopy	retro_ptro_691,