RetrogeneDB ID: retro_tsyr_343

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_101272:3248..4118(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AGFG1
• Ensembl ID: ENSTSYG00000001787
• Aliases: None
• Description: ArfGAP with FG repeats 1 [Source:HGNC Symbol;Acc:5175]

Sequence

>retro_tsyr_343
GGAAGTGCTGGATCCGTAAATGCTAATTTTGCTCATTTTGATAACTTCCCCAAATCCTCCAGTGCTGATCTTGGAACCTT
CAATACTTCCCAGAGTCATCAAACAGCACCAGCTGCTACTAAAGTTTCAACGAACAAAGACGGATTACAGACAGCAGACA
AATATGCAGCACTTGCTAATTTAGACAATATCTTCAGTGCTGGGCAAGGTGGGGATCAGGGAAGTGGCTTTGGGACCAAA
GGTAAATCTCCTGTTGGTTCTGTGGTTTCAGTTCCCAGTCAGTCAAGTGCATCTTCAGACAAGTATGCAGCCCTGGCAGA
ACTGGACAGCGTTCTCAGTTCTGCAGCCACCTCCAGGAATGCGTATACTTCCACAAGTAATGCTAGCAGCAACGTTTTTG
GAACAGTGCCAGTGGGTGCTTCTGCACAGACACAGCCTGCTTCTTCAAGTGTGCCTGCTCCGTTTGGAGCTACGCCTTCC
ACAAATCCCTTTGTTGCTGCTGCTGGTCCTTCTGTGGCATCTTCTCCAAATCTATTTCAGACCAATGCCAGAGGAGCAAC
AACGGCAACCTTTGGCACTGCATCCATGAGCATGCCTGCGGGGTTCGACACCCCTGCTCCCTATAGTCTTCCCACCGGCT
TTAGTGGCAGCTTCCAGCAGCCTGCTTTCCCAGCCCAAGCAGCTTTCCCTCAACAAACAGCTTTTTCTCAACAGCCCAAT
GGTGCAGGTTTTGCAGCATTTGGACAAACAAAGCCAGTGGTGACCCCTTTTGGTCAAGTTGCAGCTTCTGGGGTATCTAG
TAATCCTTTTATGACTGGTGCACCGACAGGACAATTTCCAACAGGAAGCTCATCAACCAATCCTTTCTTA

Alignment

ORF - retro_tsyr_343 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.66 %
• Parental protein coverage: 60.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSAGSVNANFAHFDNFPKSSSADFGTFNTSQSHQTASAVTKVSTNKAGLQTADKYAALANLDNIFSAGQG
          GSAGSVNANFAHFDNFPKSSSAD.GTFNTSQSHQTA.A.TKVSTNK.GLQTADKYAALANLDNIFSAGQG
Retrocopy GSAGSVNANFAHFDNFPKSSSADLGTFNTSQSHQTAPAATKVSTNKDGLQTADKYAALANLDNIFSAGQG

Parental  GDQGSGFGTTGKTPVGSVVSVPSQSSASSDKYAALAELDSVFSSAATSSNAYTS-SNASSNVFGTVPVGA
          GDQGSGFGT.GK.PVGSVVSVPSQSSASSDKYAALAELDSV.SSAATS.NAYTS.SNASSNVFGTVPVGA
Retrocopy GDQGSGFGTKGKSPVGSVVSVPSQSSASSDKYAALAELDSVLSSAATSRNAYTSTSNASSNVFGTVPVGA

Parental  SAQTQPASSSVPAPFGATPSTNPFVAAAGPSVASSTNPFQTNARGATAATFGTASMSMPTGFGTPAPYSL
          SAQTQPASSSVPAPFGATPSTNPFVAAAGPSVASS.N.FQTNARGAT.ATFGTASMSMP.GF.TPAPYSL
Retrocopy SAQTQPASSSVPAPFGATPSTNPFVAAAGPSVASSPNLFQTNARGATTATFGTASMSMPAGFDTPAPYSL

Parental  PTSFSGS-QQPAFPAQAAFPQQTAFXXXXXXAGFAAFGQTKPVVTPFGQVAATGVSSNPFMTGAPTGQFP
          PT.FSGS.QQPAFPA..........XXX...AGFAAFGQTKPVVTPFGQVAA.GVSSNPFMTGAPTGQFP
Retrocopy PTGFSGSFQQPAFPAXXXXXXXXXXXXXPNGAGFAAFGQTKPVVTPFGQVAASGVSSNPFMTGAPTGQFP

Parental  TGSSSTNPFL
          TGSSSTNPFL
Retrocopy TGSSSTNPFL

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_343 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Tarsius syrichta	ENSTSYG00000001787	3 retrocopies	retro_tsyr_343 , retro_tsyr_769, retro_tsyr_942,
Vicugna pacos	ENSVPAG00000012101	1 retrocopy	retro_vpac_563,