RetrogeneDB ID: retro_mmul_1524

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:96852228..96852665(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFU1
• Ensembl ID: ENSMMUG00000000435
• Aliases: None
• Description: None

Sequence

>retro_mmul_1524
CAGCCTCTGCATCAATTTGTAGAAAGACTACTTTTCCCACTACCTGCAGCCTTTTGTAACCCAGTGAGACACATGTTTAT
TCAAACACAGATATCCCAAATCCTAATAGTTTAAAGTTTATACCATGGAAACCAGTTTTTGAGACAAGGCTCATGGATTT
TCCTACCCCAGCTGCAGCATTTCACTCTCCTTTGGCTAGGCAGTTATTTAGGATTGAAGGAGTAAAAAGTGTTTTCTTTG
GGCCAGATTTCTTCACTGTCACAAAGGAAAATGAAAAATTAGACTGGAATTTACTAAAACCAGATATATACACAACAACC
ATGGACTTCTTTGCATCTGGTTTACCCCTAGTTACTGAGGAAACATCTTCAGGAGAAGCAGGATATGAAGATGATGAAGT
TGTGGCAATGATTAAGGAAGTGTTAGATACTAGAATA

Alignment

ORF - retro_mmul_1524 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.76 %
• Parental protein coverage: 58.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QPLHQFVQRPLFPLPAAFCNPGRFIFIM-NNQTLGPNFLKKIPSLPHTDTRTFSFYLNISLLRIYLRVFV
          QPLHQFV.R.LFPLPAAFCNP.R..FI..N.....PN.LK.IP..P...TR...F..........L....
Retrocopy QPLHQFVERLLFPLPAAFCNPVRHMFIQ<NTDIPNPNSLKFIPWKPVFETRLMDFPTPAAAFHSPLARQL

Parental  FRRIEGVKSVFFGPDFITVTKENEDLDWNLLKPDIYATIMDFFASGLPLVTEETPSGEAGKEKRRENVYM
          FR.IEGVKSVFFGPDF.TVTKENE.LDWNLLKPDIY.T.MDFFASGLPLVTEET.SGEAG.E...E.V.M
Retrocopy FR-IEGVKSVFFGPDFFTVTKENEKLDWNLLKPDIYTTTMDFFASGLPLVTEETSSGEAGYED-DEVVAM

Parental  LKKILVSKI
          .K..L...I
Retrocopy IKEVLDTRI

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	1.01 RPM	9.41 RPM
SRP007412_brain_prefrontal_cortex	0.48 RPM	4.20 RPM
SRP007412_cerebellum	1.16 RPM	8.72 RPM
SRP007412_heart	1.12 RPM	13.07 RPM
SRP007412_kidney	1.41 RPM	12.68 RPM
SRP007412_liver	0.24 RPM	3.44 RPM
SRP007412_testis	2.56 RPM	17.30 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1524 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1524 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1524 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2638
Pan troglodytes	retro_ptro_1778
Pongo abelii	retro_pabe_2329

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005978	1 retrocopy	retro_chof_456,
Callithrix jacchus	ENSCJAG00000019156	1 retrocopy	retro_cjac_1573,
Echinops telfairi	ENSETEG00000019002	1 retrocopy	retro_etel_1371,
Homo sapiens	ENSG00000169599	1 retrocopy	retro_hsap_2638,
Macaca mulatta	ENSMMUG00000000435	1 retrocopy	retro_mmul_1524 ,
Monodelphis domestica	ENSMODG00000011805	1 retrocopy	retro_mdom_1395,
Mustela putorius furo	ENSMPUG00000006663	1 retrocopy	retro_mputfur_67,
Mus musculus	ENSMUSG00000029993	1 retrocopy	retro_mmus_1401,
Nomascus leucogenys	ENSNLEG00000010101	1 retrocopy	retro_nleu_646,
Ochotona princeps	ENSOPRG00000016760	2 retrocopies	retro_opri_380, retro_opri_48,
Pongo abelii	ENSPPYG00000012339	1 retrocopy	retro_pabe_2329,
Pan troglodytes	ENSPTRG00000012016	1 retrocopy	retro_ptro_1778,
Tupaia belangeri	ENSTBEG00000008616	1 retrocopy	retro_tbel_525,
Tarsius syrichta	ENSTSYG00000013765	1 retrocopy	retro_tsyr_108,