RetrogeneDB ID: retro_mmul_1916

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:145867981..145868875(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.18663
• Ensembl ID: ENSMMUG00000010620
• Aliases: None
• Description: WD repeat domain phosphoinositide-interacting protein 4 [Source:RefSeq peptide;Acc:NP_001253949]

Sequence

>retro_mmul_1916
CTTCTGGTCTTGGTGGGTGGTAGTAGTAGCCCCAAGTTCTCAGAGATCTCAGTGCTGATCTGGGACGATGCCCGGGAGGG
CAAGGACTCCAAAGAGAAGCTGGTGCTGGAGTTCACCTTCACTAAGCCAGTGCTTTCTGTGCTCATGCGCCATGACAAGA
TCGTGATGGTGCTGAAGAACCGCATCTGTGTGTACTCCTTCCCAGACAATCCCTGAAAGCTGTTTGAGTTTGATACCTGG
GACAACCCCAAGGGGCTCTGTGACCTCTGCCCCAGCCTGGAGAAGCAACTGTTAAGTGTTCCTGGGACACAAGTGTGGGA
GTCTGCAACTTGTGGACCTGGCGAGCACAATGCCTGGCACCTCGTCTTCTCCATTCACCATCAATGCACACCAGAGTGAC
ATAGCCTGTGTGTCTCTAAACCAGCCAGGGACTGTAGTGGCCTCAGCCTCCCAGAAGGGTACCCTTATTCACCTCTTTGA
CACACCATCCAAGGAGAAACTGGTAGAGCTGCGCCGAGGCACTGACCCTGCCACCGTCTACTGCATTAACTTCAGCCACG
ACTCCTCCTTCCTCTGTACTTCCAGTGATAAAGGCACCGTCCATATCTTTGCTCTCAAGGATACCCGCCTCAACCGCTGC
TCTGCACTGGCTCACTGTGGGCAAGGGCCTATCATTGAGCAGTACGTGGACCCTCAGTGGAGCCTGGCGAGCTTCACTGT
GCCTGCTGAGTCAGCTTGCATCTGCGTCTTCTGTCGCAATACTTCCAAGAACGTCAATTGTGTCATTGCCATCTGCGTAG
ATGGGACCTTCCACAAATAGTCTTCACTCCTGATGGAAACTGCAACAGAGAGGCTTTTGACGCGTACCTTGACATCTGTG
ATGATGATGACTTT

Alignment

ORF - retro_mmul_1916 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.37 %
• Parental protein coverage: 83.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LLALVGGGSSPKFSEISVLIWDDAREGKDSKEKLVLEFTFTKPVLSVRMRHDKIVIVLKNRIYVYSFPDN
          LL.LVGG.SSPKFSEISVLIWDDAREGKDSKEKLVLEFTFTKPVLSV.MRHDKIV.VLKNRI.VYSFPDN
Retrocopy LLVLVGGSSSPKFSEISVLIWDDAREGKDSKEKLVLEFTFTKPVLSVLMRHDKIVMVLKNRICVYSFPDN

Parental  PRKLFEFDTRDNPKGLCDLCPSLEKQLL-VFPGHKCGSLQLVDLASTKPGTSSAPFTINAHQSDIACVSL
          P.KLFEFDT.DNPKGLCDLCPSLEKQLL.VF.GHKCGSLQLVDLAST.PGTSS.PFTINAHQSDIACVSL
Retrocopy P*KLFEFDTWDNPKGLCDLCPSLEKQLL>VFLGHKCGSLQLVDLASTMPGTSSSPFTINAHQSDIACVSL

Parental  NQPGTVVASASQKGTLIRLFDTQSKEKLVELRRGTDPATLYCINFSHDSSFLCASSDKGTVHIFALKDTR
          NQPGTVVASASQKGTLI.LFDT.SKEKLVELRRGTDPAT.YCINFSHDSSFLC.SSDKGTVHIFALKDTR
Retrocopy NQPGTVVASASQKGTLIHLFDTPSKEKLVELRRGTDPATVYCINFSHDSSFLCTSSDKGTVHIFALKDTR

Parental  LNRRSALARVGKVGPMIGQYVDSQWSLASFTVPAESACICAFGRNTSKNVNSVIAICVDGTFHK-YVFTP
          LNR.SALA..G..GP.I.QYVD.QWSLASFTVPAESACIC.F.RNTSKNVN.VIAICVDGTFHK..VFTP
Retrocopy LNRCSALAHCGQ-GPIIEQYVDPQWSLASFTVPAESACICVFCRNTSKNVNCVIAICVDGTFHK<IVFTP

Parental  DGNCNREAFDVYLDICDDDDF
          DGNCNREAFD.YLDICDDDDF
Retrocopy DGNCNREAFDAYLDICDDDDF

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	18.82 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	32.76 RPM
SRP007412_cerebellum	0.00 RPM	16.60 RPM
SRP007412_heart	0.00 RPM	21.49 RPM
SRP007412_kidney	0.12 RPM	31.81 RPM
SRP007412_liver	0.00 RPM	35.82 RPM
SRP007412_testis	0.00 RPM	1.92 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1916 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1916 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1916 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2075

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000002062	3 retrocopies	retro_etel_1291, retro_etel_688, retro_etel_712,
Gorilla gorilla	ENSGGOG00000000589	1 retrocopy	retro_ggor_2075,
Macaca mulatta	ENSMMUG00000010620	1 retrocopy	retro_mmul_1916 ,
Macaca mulatta	ENSMMUG00000021803	1 retrocopy	retro_mmul_1330,
Pongo abelii	ENSPPYG00000020333	1 retrocopy	retro_pabe_2481,