RetrogeneDB ID: retro_tsyr_1760

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_57306:16..1031(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TM9SF3
• Ensembl ID: ENSTSYG00000000322
• Aliases: None
• Description: transmembrane 9 superfamily member 3 [Source:HGNC Symbol;Acc:21529]

Sequence

>retro_tsyr_1760
CTTCCATTCTGTGTGGGGTCAAAAAAATGTATCAGTCATTACCATGAAACTCTGGGAGAAGCACTTCAAGGAGTTGAATT
GGAATTTAGCAGTCTGGATATTAAATTTAAAGATGATGTGATGCCAGCCACTTACTGTGAAATTGACTTAGGTAAAGAAA
AGAGAGATGCGTTTGTATATGCCATCAAAAATCACTACTGGTACCAAATGTACATAGATGACTTACCAATATGGGGCATT
GTTGGTGAGGCTGATGAAAATGGAGAAGATTACTATCTTTGGACCTACAAAAAACTTGAAATGGGTTTTAACAGAAATTG
AATTGTTAATGTTAACCTAACTAGTGAAGGAAAGGTGAAACTGGTTCCAAATACTAAAATCCAGATGTCCTATCCAGTGA
AAGGAAAAAGTCAGATGTAAAATTTGAAGATCGATTTGACAAATATCTTGATCTGTCAGTTTTTCAACATCGGATTCATT
GGTTTTCAATTTTCAACTCCTTCATGATGGTGATCTTCTTGGTGGGCTTAGTTTCAATGATTTTAATGAGAACCTTAAGG
AAAATTATGCCTGATACAATAAAGAAGAAATAATGGATGACATGGACAGAGACCTAGGAGATGAGTAAGGGTGGAAGCAA
GTGCATGGAGATGTGTTCAGACCTTCAAGTCAACCCCTGATATTCTCCTCCCTCATTGACTCTGGCTGCCAGATATTTGC
CGTATCTCTCATTGTCATTATTGTTGCAATGATAGAAGATCTCGATACAGAGAGGGGATCGAAGTTTAGCATGGCCATAT
TTGTTTATGCTGCTACGTCTCCAGTGAATGGTTATTTCGGAGGAAGTCTGTATGTGAGACAAGGAGGAAGAAGATGGATA
AAATAGATGTTTATTGGAGCATTCCTCATCCCAGCCATGGTGTGTGGCACCACCTTTTTCATCAATTTCATAGCCATTTA
CTACCATACTTCAAGAGCCATTCCTTTTGGGACAATGGTGGCCGTTTGTTGCATC

Alignment

ORF - retro_tsyr_1760 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.5 %
• Parental protein coverage: 61.08 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LPFCVGSKKSISHYHETLGEALQGVELEFSGLDIKFKDDMMPATYCEIDLDKEKRDAFVYAIKNHYWYQM
          LPFCVGSKK.ISHYHETLGEALQGVELEFS.LDIKFKDD.MPATYCEIDL.KEKRDAFVYAIKNHYWYQM
Retrocopy LPFCVGSKKCISHYHETLGEALQGVELEFSSLDIKFKDDVMPATYCEIDLGKEKRDAFVYAIKNHYWYQM

Parental  YIDDLPIWGIVGEADENGEDYYLWTYKKLEIGFNGNRIVDVNLTSEGKVKLVPNTKIQMSYSVKWK-KSD
          YIDDLPIWGIVGEADENGEDYYLWTYKKLE.GFN.N.IV.VNLTSEGKVKLVPNTKIQMSY.VK.K.KSD
Retrocopy YIDDLPIWGIVGEADENGEDYYLWTYKKLEMGFNRN*IVNVNLTSEGKVKLVPNTKIQMSYPVKGK<KSD

Parental  VKFEDRFDKYLDPSFFQHRIHWFSIFNSFMMVIFLVGLVSMILMRTLRK-DYARYSKEEEMDDMDRDLGD
          VKFEDRFDKYLD.S.FQHRIHWFSIFNSFMMVIFLVGLVSMILMRTLRK..YA.Y.KEE.MDDMDRDLGD
Retrocopy VKFEDRFDKYLDLSVFQHRIHWFSIFNSFMMVIFLVGLVSMILMRTLRK<NYA*YNKEEIMDDMDRDLGD

Parental  EYGWKQVHGDVFRPSSHPLIFSSLIGSGCQIFAVSLIVIIVAMIEDLYTERGSMLSTAIFVYAATSPVNG
          E.GWKQVHGDVFRPSS.PLIFSSLI.SGCQIFAVSLIVIIVAMIEDL.TERGS..S.AIFVYAATSPVNG
Retrocopy E*GWKQVHGDVFRPSSQPLIFSSLIDSGCQIFAVSLIVIIVAMIEDLDTERGSKFSMAIFVYAATSPVNG

Parental  YFGGSLYARQGGRRWIKQMFIGAFLIPAMVCGTAFFINFIAIYYHASRAIPFGTMVAVCCI
          YFGGSLY.RQGGRRWIK.MFIGAFLIPAMVCGT.FFINFIAIYYH.SRAIPFGTMVAVCCI
Retrocopy YFGGSLYVRQGGRRWIK*MFIGAFLIPAMVCGTTFFINFIAIYYHTSRAIPFGTMVAVCCI

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_1760 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000013527	1 retrocopy	retro_nleu_387,
Tarsius syrichta	ENSTSYG00000000322	2 retrocopies	retro_tsyr_1760 , retro_tsyr_1903,