RetrogeneDB ID: retro_mmul_638

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 10:58355463..58356505(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPAL1
• Ensembl ID: ENSMMUG00000018625
• Aliases: None
• Description: NIPA-like domain containing 1 [Source:HGNC Symbol;Acc:27194]

Sequence

>retro_mmul_638
AGTGCCACAGCTGCTTCTCCGGTCCTCTACACGGACCTGAATTCCAGCATAACCAACTTGAGCATTTCAGCAAACGTAGA
AAACAAATATAGTCTTTATGTGGGCTAGGTACTGGCAGTAACCTCCAGTATTTTTATTGGCTCCAGCTTCATATTGAAAA
AGAAGGGTCTCTTGCAACTGGTCAAAAAAGGCGTCACTAGAGCTGGACAAGGTGGACATTCTGACCTGAAAGATGGCTCT
AGGGGGCAGGAGTGCTAGCCATGGGAGCAGGAGAGGCTGTACATTTTGTGGCTTATGCTTTTGCACCTGCCATCTTGGTC
ACCCCCACCCTCCCGGCCCTCTGAGTGTTCTCGTAAGTGCAATATTATCTTCTTATTTTTTAAATGAGCACTTGAACATT
TATGGGAAAACAGGCTGCATATTGGGGTCAACTGTGATGGTTATCCATCCCCCACAAGAAGAGGAAGTCACTTCTTTGCA
TGAAATGGAAATGAAATTGAGAGACCCAGGATTTATTTCCTTTGCTGTGATCATAATTGTGATCTTCTTGGTACTGATTT
TGATTGTGGCTCCCAAGAAAGGACAGATCAATATATTGGTCTATATTTCAATCTGTTCTTTGACTGGAGCATTTTCAGTT
TCTTCTGCCAAAGGCCTGGGAATTGCCATTAAGGAATTACTAGAATGGAAGACAGTTTAGAAGCATCCCCTGGTCACTGT
TTTGCTGGCTATACTTGTGCTTTTGGTGACTACACAGATTAACTATCTCAAGGCACTGGACACCGTTACTACATCTCCTG
TGACTCCCATTTATTTTGCGTTCTTCACATCCATGGTAGTGACTTGCTCTGCCATCTTACTCCAAGGGTGGTATGGCATG
AAGGCTGGAGATATCATCAAGACCCTAAGTGGATTCTTCACTATTATCTTTGGCATCTTTCTTCTACATGCTTTTAAAAA
TACTGACATTACCCGGAGTAAGCTGACATCCACTGCTAAGAAGGAAGTCATCTCTCTGAATGGCAATGAGAGCAATCCTG
TT

Alignment

ORF - retro_mmul_638 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.38 %
• Parental protein coverage: 85.37 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SQLLASPVLYTDLNSSINNLSISANVENKYSLYVGLVLAVSSSIFIGSSFILKKKGLLQLASKGVTRAGQ
          S...ASPVLYTDLNSSI.NLSISANVENKYSLYVG.VLAV.SSIFIGSSFILKKKGLLQL..KGVTRAGQ
Retrocopy SATAASPVLYTDLNSSITNLSISANVENKYSLYVG*VLAVTSSIFIGSSFILKKKGLLQLVKKGVTRAGQ

Parental  GGHSYLKE-WLWWVGLLSM-GAGEAANFAAYAFAPATL--VTPLGALSVLISAILSSYFLNEHLNIHGKI
          GGHS.LK..WL...G.L.M.G......F....F....L....P.G.LSVL.SAILSSYFLNEHLNI.GK.
Retrocopy GGHSDLKD<WL*GAGVLAM<GSRRGCTFCGLCFCTCHLGHPHPPGPLSVLVSAILSSYFLNEHLNIYGKT

Parental  GCILSILGSTVMVIHAPQEEEVTSLHEMEMKLRDPGFISFAVIITVISLVLILIVAPKKGQTNILVYISI
          GC...ILGSTVMVIH.PQEEEVTSLHEMEMKLRDPGFISFAVII.VI.LVLILIVAPKKGQ.NILVYISI
Retrocopy GC---ILGSTVMVIHPPQEEEVTSLHEMEMKLRDPGFISFAVIIIVIFLVLILIVAPKKGQINILVYISI

Parental  CSLIGAFSVSSVKGLGIAIKELIEWKPVYKHPLVFVLLAVLVLSVTTQINYLNKALDTFNTSLVTPIYYV
          CSL.GAFSVSS.KGLGIAIKEL.EWK.V.KHPLV.VLLA.LVL.VTTQINYL.KALDT..TS.VTPIY..
Retrocopy CSLTGAFSVSSAKGLGIAIKELLEWKTV*KHPLVTVLLAILVLLVTTQINYL-KALDTVTTSPVTPIYFA

Parental  FFTSMVVTCSAVLFQEWYGMTAGDIIGTLSGFFTIIIGIFLLHAFKNTDITWSELTSTAKKEAISLNVNE
          FFTSMVVTCSA.L.Q.WYGM.AGDII.TLSGFFTII.GIFLLHAFKNTDIT.S.LTSTAKKE.ISLN.NE
Retrocopy FFTSMVVTCSAILLQGWYGMKAGDIIKTLSGFFTIIFGIFLLHAFKNTDITRSKLTSTAKKEVISLNGNE

Parental  NNYV
          .N.V
Retrocopy SNPV

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	0.00 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.08 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.59 RPM	1.06 RPM
SRP007412_kidney	0.00 RPM	2.11 RPM
SRP007412_liver	0.00 RPM	3.44 RPM
SRP007412_testis	0.23 RPM	0.19 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_638 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_638 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_638 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002047	1 retrocopy	retro_dnov_2048,
Homo sapiens	ENSG00000163293	1 retrocopy	retro_hsap_2463,
Gorilla gorilla	ENSGGOG00000009006	1 retrocopy	retro_ggor_1533,
Macaca mulatta	ENSMMUG00000003892	1 retrocopy	retro_mmul_1510,
Macaca mulatta	ENSMMUG00000018625	1 retrocopy	retro_mmul_638 ,
Nomascus leucogenys	ENSNLEG00000017377	1 retrocopy	retro_nleu_2814,
Pongo abelii	ENSPPYG00000014714	1 retrocopy	retro_pabe_1810,
Pan troglodytes	ENSPTRG00000016038	1 retrocopy	retro_ptro_1422,