RetrogeneDB ID: retro_mmul_860

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:41214407..41214931(-)
• Located in intron of: ENSMMUG00000000205

Retrocopy information

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

Parental gene information

• Parental gene symbol: IQCF1
• Ensembl ID: ENSMMUG00000004352
• Aliases: None
• Description: None

Sequence

>retro_mmul_860
AAAGATGAGCCTCAGCAGAAGGAGATGCTGGGCCATTTTTCTTCAGAACCATTAACCTCAAAGTCGAAGGCAGAGGCCAA
AACTCTGGCTCTGGTTAAGACACAAACAGTGGATAATGCGAATGAGAAATTCAGAAACCCCCCAGAAAACCAAAAGAAGC
TCTCTGACAAAGATACGGCAATCATCAAGATCCAAACCTAGTGGCGGGGCACCCTGGTGGACCAGGCACTGTGGCACACA
GCCCTTAGCACCTGGATCATTCAGTGCTGCTGGCAGCTGATACCGTCCAGGATTCTGGAGATGAGGCAGTGGACGGCACT
GGAGGCCTTCTCACGGGAGAAGTGGGCAGCAGTCACACTGCAGTCCCTGGCCCACATGTGCCACATCTGCCAGTGCTAAT
GCCACATTCTCAATGCTGTCTGCATCATCCAGGACGACTGGAGGTGCCTCTGTGTTTCTTGGAGGCTCATCAAGGTTCGT
TACAGAGTGATGGCCAACCACTGCCTCTTGAGCTGGAGATCTTG

Alignment

ORF - retro_mmul_860 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.28 %
• Parental protein coverage: 84.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EDEPQQKETLTHLSLE---AEWKAEAKTPVLVETQRVDNANEKLEKPPENQKKLSDKDMVATKIQAWWRG
          .DEPQQKE.L.H.S.E......KAEAKT..LV.TQ.VDNANEK...PPENQKKLSDKD....KIQ..WRG
Retrocopy KDEPQQKEMLGHFSSEPLTSKSKAEAKTLALVKTQTVDNANEKFRNPPENQKKLSDKDTAIIKIQT*WRG

Parental  TLVRRALLHAALSACIIQCWWRLILSKILEKRRRAALEAFSREEWAAVTLQSQARMWRIRRRYCQVLNAV
          TLV..AL.H.ALS..IIQC.W.LI.S.ILE.R...ALEAFSRE.WAAVTLQS.A.M..I....C..LNAV
Retrocopy TLVDQALWHTALSTWIIQCCWQLIPSRILEMRQWTALEAFSREKWAAVTLQSLAHMCHICQC*CHILNAV

Parental  RIIQAYWRCRSCASRGFIKGQYRVTANQ-LHLQLEIL
          .IIQ..WRC..C.S...IK..YRV.AN..L.L.LEIL
Retrocopy CIIQDDWRC-LCVSWRLIKVRYRVMANH<LPLELEIL

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	0.11 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	0.48 RPM
SRP007412_cerebellum	0.00 RPM	0.32 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	135.88 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_860 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_860 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_860 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1109
Pan troglodytes	retro_ptro_689

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000173389	1 retrocopy	retro_hsap_1109,
Gorilla gorilla	ENSGGOG00000012462	1 retrocopy	retro_ggor_867,
Macaca mulatta	ENSMMUG00000004352	1 retrocopy	retro_mmul_860 ,
Pan troglodytes	ENSPTRG00000014977	1 retrocopy	retro_ptro_689,