RetrogeneDB ID: retro_mmul_1679

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:50444330..50444820(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THOC4
• Ensembl ID: ENSMMUG00000012884
• Aliases: THOC4, ALYREF
• Description: Aly/REF export factor [Source:RefSeq peptide;Acc:NP_001247942]

Sequence

>retro_mmul_1679
CTCGCCAGCTGTGGACCAGCGGGTGGTGCCGGCGTGGAGACGGGTGGGAAACTGCTGGTATCCAATCTAGATTTTGGAGT
GTCAGACGCCGATATTCGGGAACTCCTTGCAGAATCCGGAACGCTGAAGAAGACGGCTGTGCACTATAATCGCTCTGGCC
GCCCCTTAGGATCAGCAGACATGCACTTTGAGCGGAAGGCACACGCCCTGAAAGCCATGAAGCAGTACCACGGCGCCCCT
CTGGCTGGCTGCCCCGTGAACATTCAGCTTGTCACATCACAGATCGAAACACAGCAGACACCTGCACAGAGCGTAAACAG
AGGTGGCATGACTAGAAACCATGAGGCTGGAGGTTTTGGTGGTAGCGGAGGCACCCGGGGAGGCACCCATGGAGGCGCCC
AGGAAAGAGACAGAGGCGCCGGCAGGAATTCAAAGCAGCAGCTTTTCGGCAGAGGAGGGGGACGCCTATAATGCGAGAAT
GGACACCAGT

Alignment

ORF - retro_mmul_1679 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.57 %
• Parental protein coverage: 63.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADAL
          L...G..GGAGVETGGKLLVSNLDFGVSDADI.EL.AE.GTLKK.AVHY.RSGR.LG.AD.HFERKA.AL
Retrocopy LASCGPAGGAGVETGGKLLVSNLDFGVSDADIRELLAESGTLKKTAVHYNRSGRPLGSADMHFERKAHAL

Parental  KAMKQYNGVPLDGRPMNIQLVTSQIDTQRRPAQSVNRGGMTRNRGAGGFGGGGGTRRGTRGGARGRGRGA
          KAMKQY.G.PL.G.P.NIQLVTSQI.TQ..PAQSVNRGGMTRN..AGGFGG.GGTR.GT.GGA..R.RGA
Retrocopy KAMKQYHGAPLAGCPVNIQLVTSQIETQQTPAQSVNRGGMTRNHEAGGFGGSGGTRGGTHGGAQERDRGA

Parental  GRNSKQQL-SAEELDAQLDAYNARMDTS
          GRNSKQQL.SAEE.DA....YNARMDTS
Retrocopy GRNSKQQL>SAEEGDA----YNARMDTS

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	10.20 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	18.48 RPM
SRP007412_cerebellum	0.00 RPM	9.17 RPM
SRP007412_heart	0.00 RPM	13.84 RPM
SRP007412_kidney	0.00 RPM	10.45 RPM
SRP007412_liver	0.00 RPM	9.70 RPM
SRP007412_testis	0.00 RPM	85.15 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1679 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1679 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1679 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2523

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005877	1 retrocopy	retro_cfam_1395,
Gorilla gorilla	ENSGGOG00000013935	1 retrocopy	retro_ggor_2523,
Macaca mulatta	ENSMMUG00000012884	1 retrocopy	retro_mmul_1679 ,
Mus musculus	ENSMUSG00000025134	1 retrocopy	retro_mmus_286,
Sarcophilus harrisii	ENSSHAG00000010459	1 retrocopy	retro_shar_332,
Tupaia belangeri	ENSTBEG00000005834	7 retrocopies	retro_tbel_237, retro_tbel_2432, retro_tbel_251, retro_tbel_2690, retro_tbel_2918, retro_tbel_3933, retro_tbel_3934,