RetrogeneDB ID: retro_tsyr_882

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_229388:3349..3800(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: M6PR
• Ensembl ID: ENSTSYG00000005689
• Aliases: None
• Description: mannose-6-phosphate receptor (cation dependent) [Source:HGNC Symbol;Acc:6752]

Sequence

>retro_tsyr_882
TTTGATAGCACTGTAATCCAGGGCTCATACACATACATCTACATGTTCAGGGAATGCCAGAAATCTACAATTCACATCTC
TGGGGAACGTCTGATGCATATCAACCTCCGTAAGAAAACAGTAGGAGCATGACTCAACCAGACTCACATCTTTCAATGGA
AGCAGTTGTATCATGCTGATCTATAAGGAGGGTGAATATGACAACCATTGTAGCAAGGAGCAGCATTGTCATGCAGTGGT
GATGATCTTATATTATTGACAAACCCTAGTGGACAATTTTATCCCTGTGTCTGAAGTGTAAGACAAAGTCCAAGATTGTT
TCTACCTCTTTGAGATGGATAGCAGCCTGGTCTGATCCTTAGAACTCTCCCACCTCAGTGTGGGTTCGATCTTACTTGTC
ACAATTGCATCATTGGTTGCTATCTGTGTGGTCAGGGAGCTCCTATAGCAA

Alignment

ORF - retro_tsyr_882 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.69 %
• Parental protein coverage: 69.72 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FESTVGQGSDTYIYIFRVCREAGNQTSGAGLVQINKSNWKETVVGRLNETHVF-NGSNWIMLIYKGGDEY
          F.STV.QGS.TYIY.FR.C.......SG..L..IN....K.TV...LN.TH.F.NGS..IMLIYK.G.EY
Retrocopy FDSTVIQGSYTYIYMFRECQKSTIHISGERLMHINLR--KKTVGA*LNQTHIF>NGSSCIMLIYKEG-EY

Parental  DSHCGKEQR-RAVVMISCNRHTLAGNFNPVSEERGKVQDCFYLFEMDSSLACSPEISHLSVGSILLVTFA
          D.HC.KEQ...AVVMI.....TL..NF.PVSE...KVQDCFYLFEMDSSL..S.E.SHLSVGSILLVT.A
Retrocopy DNHCSKEQHCHAVVMILYY*QTLVDNFIPVSEV*DKVQDCFYLFEMDSSLV*SLELSHLSVGSILLVTIA

Parental  SLVAVYVIGGFLYQ
          SLVA..V....L.Q
Retrocopy SLVAICVVRELL*Q

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_882 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000003538	1 retrocopy	retro_dnov_2250,
Mus musculus	ENSMUSG00000007458	1 retrocopy	retro_mmus_2192,
Oryctolagus cuniculus	ENSOCUG00000017823	1 retrocopy	retro_ocun_1931,
Otolemur garnettii	ENSOGAG00000005610	1 retrocopy	retro_ogar_629,
Tarsius syrichta	ENSTSYG00000005689	2 retrocopies	retro_tsyr_1665, retro_tsyr_882 ,