RetrogeneDB ID: retro_mmul_850

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:25369677..25370599(-)
• Located in intron of: ENSMMUG00000015374

Retrocopy information

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

Parental gene information

• Parental gene symbol: MLF1IP
• Ensembl ID: ENSMMUG00000012176
• Aliases: None
• Description: None

Sequence

>retro_mmul_850
AAGAACATTTTATGAAGAACACATTCTATGAAAGATAAAGCTTGTCAAAAGTGCAAGCCTACCAATGTGTTTGATTTTCC
TATGTAATTCTGCCGTCTGAAGAATTGGCAGGCTTGTTGAAAATAAGAAAGATGAAGAACCTTATGAAACCTTTGATCCT
CCTTTACACAGCTCATCTATGTATGCCAATGAAGAATTCTCCAAATATTGTGGATTATCTATCACTTCAACTCCTTTAGG
AAAAGAAGCAAAAAGAAGCTCGAGCACTTCTGAAAATGAAGGAAGTGAAAATGAATCTGCAAAAATGAGTGCAAAAACAC
CAGGAAGAAAACTCAAACCCATTAGCAATGAGTCTGAAAGCACTGAAGAAAGTGATGTGAGAAGAAAAGTTAAATCAGTG
GAGAAAATAAGGACCCAACAACACAAAGCTATTCCAACTGCAGCATCTTCAGACCTTTCAGAGAAACCAGCTGACTCAGT
CACTTCCAAAAAGATAGGACCCATTAGTGCCCAGCCATCTGTTGAAAAAGACACACTGACAACAGAAAGTCAAGCAAAAA
CTCAGAAAAAAAGGGAATACATCTTATGGCAAAAGGAAGGTATCAAGAAGTGAAGCCATAGTCTCAGATATTTCCAACAT
TGTGAATATTTAGTGTCTAGAAGGAAAGAAAACCAACAACATCATGGAATTGAATATTGTTTTGCCTGCATTTGAGAAAA
CTCTCATCCAGTATAAACATAGAATAGAATCTAAAATTTGTAAGAAAGCCATCAATAAATTTTATTTTAATAGTAAATAA
GAACTCAACAAAATGTTTAAAAAGTCCAGATATTGAAAAATCTGAAAAAGAAGAATGCTAAGGTAATTTCAGATATTAAA
AAGAAATGGCAGTGTTTGACTGATGTCCAGGATGAACTGCTT

Alignment

ORF - retro_mmul_850 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.51 %
• Parental protein coverage: 73.35 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KNTLERTHSVKDKAGQKCKPIDVFDFPD-NSDVSSIGRLGENEKDEEPDETFVLFPPLLFTAMKERRERF
          KN.L.RTHS.KDKA.QKCKP..VFDFP..NS.V..IGRL.EN.KDEEP.ET...F.P.L........E.F
Retrocopy KNIL*RTHSMKDKACQKCKPTNVFDFPM>NSAV*RIGRLVENKKDEEPYET---FDPPLHSSSMYANEEF

Parental  YEHKILVLGYTNDGPYAWDCSDTSGNEASAIESVKLVQKRQPGRKLKPISDDSESTEGSDTRRKVKSAEK
          .....L....T..G..A...S.TS.NE.S..ES.K...K..PGRKLKPIS..SESTE.SD.RRKVKS.EK
Retrocopy SKYCGLSITSTPLGKEAKRSSSTSENEGSENESAKMSAKT-PGRKLKPISNESESTEESDVRRKVKSVEK

Parental  TNIQRHEVIPTTASSELSEKPAESVTSKKTGPLSAQPSVEKENLALESQSKTQ-KKGKMSHGKKKKSRSK
          ...Q.H..IPT.ASS.LSEKPA.SVTSKK.GP.SAQPSVEK..L..ESQ.KTQ.KKG..S.GK.K.SRS.
Retrocopy IRTQQHKAIPTAASSDLSEKPADSVTSKKIGPISAQPSVEKDTLTTESQAKTQ>KKGNTSYGKRKVSRSE

Parental  AVGSDTSDTVDIWCLEGMKTSDIKELNIVLPEFEKTHIEHKERTESKVCRAAIDTFYVNVKEQVIKLLKE
          A..SD.S..V.I.CLEG.KT..I.ELNIVLP.FEKT.I..K.R.ESK.C..AI..FY.N.K....K..K.
Retrocopy AIVSDISNIVNI*CLEGKKTNNIMELNIVLPAFEKTLIQYKHRIESKICKKAINKFYFNSK*ELNKMFKK

Parental  S-QMLKNLKRKNAKMISDIEKKRQRMIEVQDELL
          S.Q.LKNLK.KNAK.ISDI.KK.Q....VQDELL
Retrocopy S<QILKNLKKKNAKVISDIKKKWQCLTDVQDELL

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	0.34 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	0.71 RPM
SRP007412_cerebellum	0.00 RPM	1.55 RPM
SRP007412_heart	0.06 RPM	0.24 RPM
SRP007412_kidney	0.00 RPM	0.94 RPM
SRP007412_liver	0.00 RPM	0.24 RPM
SRP007412_testis	0.00 RPM	110.55 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_850 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_850 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_850 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1096
Pan troglodytes	retro_ptro_697
Gorilla gorilla	retro_ggor_862

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000151725	1 retrocopy	retro_hsap_1096,
Gorilla gorilla	ENSGGOG00000011892	1 retrocopy	retro_ggor_862,
Microcebus murinus	ENSMICG00000013084	1 retrocopy	retro_mmur_836,
Macaca mulatta	ENSMMUG00000012176	1 retrocopy	retro_mmul_850 ,
Nomascus leucogenys	ENSNLEG00000010967	1 retrocopy	retro_nleu_1628,
Oryctolagus cuniculus	ENSOCUG00000003903	1 retrocopy	retro_ocun_1174,
Pongo abelii	ENSPPYG00000015238	1 retrocopy	retro_pabe_979,
Pan troglodytes	ENSPTRG00000016643	1 retrocopy	retro_ptro_697,