RetrogeneDB ID: retro_tsyr_1915

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_66495:7142..7701(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLEC4A
• Ensembl ID: ENSTSYG00000001154
• Aliases: None
• Description: C-type lectin domain family 4, member A [Source:HGNC Symbol;Acc:13257]

Sequence

>retro_tsyr_1915
CTGCTCTGTGCCTCATTGCTGATAATTTCTCTGCTATTAGAAACTTCGTTCTTTATTGCTTTTATCATTTTCTTTCAAAA
ACATTCTCAGTTTCTTGAAGAAAGCAAGGCTACAAAAGTGTTGGTGTGTATGAAAGAAAACCTGACCGTGGAAGAGAGTC
TGGGGTTACTGCCCAGAGAATTGAAAGCTGTTTAGTTCCGACAGCTACTTTATTTCTACTGAATTAAAATCTTGGAATGC
AAGTGAAAAGAACTGCTCTAGAATAGAGGCTCATCTGCTAGTGATCAACATCAAGGATAAGCAGGATTTCATCGTTCAAT
ATCTGCATAAAAATTCTGTTTATTTTGTGGAATTGTCAGATCCAGAGGGTCAGAATCATTGGCAATGGGCTGATCAGACA
CCATACCCCAAAAGACCCATATTCTGGCATCAAAAAGAGTCCAGTGAGCCCAAAGACTATTGCGCTGTGCTAAATTATCA
TGGGTGGCCCAAAGAGGTGTGGGGCTGGAATATTTCTGATCCTCAAAGTTTAGTTTGTGAGATGATGAAAATCCACTTA

Alignment

ORF - retro_tsyr_1915 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.11 %
• Parental protein coverage: 79.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LILFLLLAISFFIAFIIFFQKHSQFIEGKKTTKESIHTKLVCEKENVTTEE-KVWSCCPVNWKPFSSSCY
          L....LL.IS.......F......F........ES..TK.........T.E..VW..CP.N.K.FSS..Y
Retrocopy LLCASLLIISLLLETSFFIAFIIFFQKHSQFLEESKATKVLVCMKENLTVE>RVWGYCPEN*KLFSSDSY

Parental  FISTAPKPWSESEKNCSRMEAHLLVINTEGEQDFIIQHLKTNFAYFVGLSDPEGQNHWQWVDQTPYNKKS
          FIST..K.W..SEKNCSR.EAHLLVIN....QDFI.Q.L..N..YFV.LSDPEGQNHWQW.DQTPY.K..
Retrocopy FISTELKSWNASEKNCSRIEAHLLVINIKDKQDFIVQYLHKNSVYFVELSDPEGQNHWQWADQTPYPKRP

Parental  TFWHRWEPSNSAERCVMLNYRGVPRK-WGWNDIRCSDEQGSVCEMMKIHL
          .FWH..E.S.....C..LNY.G.P...WGWN....SD.Q..VCEMMKIHL
Retrocopy IFWHQKESSEPKDYCAVLNYHGWPKEVWGWN---ISDPQSLVCEMMKIHL

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_1915 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Tarsius syrichta	ENSTSYG00000001154	1 retrocopy	retro_tsyr_1915 ,