RetrogeneDB ID: retro_tsyr_1390

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_423078:138..858(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LGALS3
• Ensembl ID: ENSTSYG00000009020
• Aliases: None
• Description: lectin, galactoside-binding, soluble, 3 [Source:HGNC Symbol;Acc:6563]

Sequence

>retro_tsyr_1390
CTTAATGATGCGTTAACTGGGTCTGGAAACCCAATCCCTCAAGGATGGCCTGGTCAGTGGGGGAACCAGCCTGCTGGGGC
AGGGGGCTACCCAGGGGCCCATCCTCATCCCGGAGTCCAGCCTGGGACAGGCTCCTCTGGGGCTCTACCCTGGCCCAATA
GCTTGGCCCAACAACTCTGGGAGCTTATCCTGGACCACCCACACCCAGAGTCTACCCAGGGTAGCCTGGGGCCTACCCAC
TGCCCACACAGACAAGTGCTCCCAGAGCTTACCCTGCTGCCGGCCCCTTTGGTTTCCTGCTGGGCCACTGACCATGTCCT
ATGATCTGCCTCTGTCCGGGGAAATCATGCCTCGCATGCTGATCACCATCCTGGTCACGGTGAAGTCCAACACAAACCGA
ATTGTCTTAGATTTCAAGAAGGGGAACGATGTTGCCTTCCACTTTAACCCACACTTCAAGGAGGATAGCCAGAGAGTCAT
TATTTGCAATACCAAGGTGCATGATGCCTGGGGAAAGGAAGAAAGACATGCACAATTCCCACTGGAAAGGGGTAAACCAT
TCAAGCTGCAAGTTCCAGTTGAATCTGACCATTTCAAGGTTGCAGTCAATGATGGCTCACTTGTTGCAATACAATCATCT
GATGAAAAAATCTCAATGAAATCAGCAAACTGGGAATTGCTGTTGACATAGACCTCACCAGTGCTTCGCACACTGTGATA

Alignment

ORF - retro_tsyr_1390 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.6 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LNDALSGSGNPNPQGWPGQWGNQPAGAGGYPGAHPYPGAYPG-QAPPGAYPGQAPPAAYPGAPGT-YPGP
          LNDAL.GSGNP.PQGWPGQWGNQPAGAGGYPGAHP.PG..PG.QAP.G.YPG...P.A.P...G..YPGP
Retrocopy LNDALTGSGNPIPQGWPGQWGNQPAGAGGYPGAHPHPGVQPG>QAPLGLYPG---PIAWPNNSGS>YPGP

Parental  PAPGAYPGQPGGPGAYPPPAQPSAPGAYPAAGPFGV-PAGPLTVPYELPLPAGVMPRMLITILGTVKPNA
          P.P..Y...PG.PGAYP.P.Q.SAP.AYPAAGPFG..PAGPLT..Y.LPL....MPRMLITIL.TVK.N.
Retrocopy PTPRVY---PG*PGAYPLPTQTSAPRAYPAAGPFGF<PAGPLTMSYDLPLSGEIMPRMLITILVTVKSNT

Parental  NRIALDFKKGNDVAFHFNPRFKEDNQRVIVCNTKVHDAWGREERHAQFPFKSGQPFKIQILVESDHFKVA
          NRI.LDFKKGNDVAFHFNP.FKED.QRVI.CNTKVHDAWG.EERHAQFP...G.PFK.Q..VESDHFKVA
Retrocopy NRIVLDFKKGNDVAFHFNPHFKEDSQRVIICNTKVHDAWGKEERHAQFPLERGKPFKLQVPVESDHFKVA

Parental  VND-AHLLQYNHRM-KNLNEITKLGISGDIDLTSASHAMI
          VND.AHLLQYNH.M.KNLNEI.KLGI..DIDLTSASH..I
Retrocopy VND>AHLLQYNHLM>KNLNEISKLGIAVDIDLTSASHTVI

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_1390 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 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015013	1 retrocopy	retro_cfam_2018,
Mustela putorius furo	ENSMPUG00000005725	2 retrocopies	retro_mputfur_115, retro_mputfur_535,
Pteropus vampyrus	ENSPVAG00000016067	1 retrocopy	retro_pvam_103,
Tarsius syrichta	ENSTSYG00000009020	4 retrocopies	retro_tsyr_1233, retro_tsyr_1390 , retro_tsyr_1784, retro_tsyr_625,