RetrogeneDB ID: retro_tsyr_1246

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_36227:6178..7026(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTSYG00000012535
• Aliases: None
• Description: None

Sequence

>retro_tsyr_1246
GAGAGCATTTGAGCCAAGTGCATTCAGTACGTAGACCGGTGGGGAAAAGCTGAAGGATTTTTTACAAAGCAAAGAGAAGC
ATGGCAAAAAGCCAATGAGAACCAGAGTAGGGGCAAGGGCAGCGATAGTGACAGTGAAGGGGATGATCCGGAGAAAAAGA
AACTGCAAGAACAACTGATGGGTGCCATTGTGATGGAGAAACCCGCTATTCAGTGAAATGCTGTGGTCAGGTTGGAGGGG
GCCAAGGAGACCCTCAAAGAAGCTGTTACTTTGTCAATTAAATTCCCACACTTGTTCACAGACAAGTACACACCTTGGAG
AGGGATACTGCTCTTCAGATTCCCTGGCACAGGGAAATCCTACGTGGCCAAAGCTGTGGGCATGAAAGCCAACAACTCCA
CCTTCCTCTCTGTGTCTTCCTCAGATTTGATGTCCAAGTGGTTGGGAGAGAGTGAGAAGTTAATCAGGAACCTGTTTGAG
CTGACCAGATAGCACAACCCTCCAACATCTTTATCAATGAGGTGGATTCCCTCCTGCGGTCCCGAAATGGAAATGAGAGT
GAGGCTGCCTGAAGGATCAAAACAGAGTTCTTGGTCCAGATGCAGGGAGTGGGGCATAACAGGGAAGGGACCCTGTTTCT
TGGTGCCACAAACGTCCCATGGGTGTTGGATTTGGCCTTCAGAAGGCAGTTTGAAAAGTGAATTTATATCCCTTTGCCAG
AGGAAGCTGCCTGTGCCCAGATGCTTCGGTGGAATCTAGGGAGCAACCTCATGGATGCCAACAAACATGAGCTGGTGCAG
AAGACCCAAGGTTACTCCGGTACAGACATCAGCATCATCGTACGGGAC

Alignment

ORF - retro_tsyr_1246 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.96 %
• Parental protein coverage: 69.32 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ESIRAKCMQYLDRAEKLKDYLRNKEKHGKKPVKENQSEGKGSDSDSEGDNPEKKKLQEQLMGAIVMEKPN
          ESI.AKC.QY.DR..K.......K.........ENQS.GKGSDSDSEGD.PEKKKLQEQLMGAIVMEKP.
Retrocopy ESI*AKCIQYVDRWGKAEGFF-TKQREAWQKANENQSRGKGSDSDSEGDDPEKKKLQEQLMGAIVMEKPA

Parental  IRWNDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSVS
          I..N.V..LEGAKE.LKEAV.L.IKFPHLFT.K.TPWRGILLF..PGTGKSY.AKAV...ANNSTF.SVS
Retrocopy IQ*NAVVRLEGAKETLKEAVTLSIKFPHLFTDKYTPWRGILLFRFPGTGKSYVAKAVGMKANNSTFLSVS

Parental  SSDLMSKWLGESEKLVKNLFELARQH-KPSIIFIDEVDSLCGSRNENESEAARRIKTEFLVQMQGVGNNN
          SSDLMSKWLGESEKL..NLFEL.R.H..PS.IFI.EVDSL..SRN.NESEAA.RIKTEFLVQMQGVG.N.
Retrocopy SSDLMSKWLGESEKLIRNLFELTR*H<QPSNIFINEVDSLLRSRNGNESEAA*RIKTEFLVQMQGVGHNR

Parental  DGTLVLGATNIPWVLDSAIRRRFEKRIYIPLPEEAARAQMFRLHLGSTPHNLTDANIHELARKTEGYSGA
          .GTL.LGATN.PWVLD.A.RR.FEK.IYIPLPEEAA.AQM.R..LGS...NL.DAN.HEL..KT.GYSG.
Retrocopy EGTLFLGATNVPWVLDLAFRRQFEK*IYIPLPEEAACAQMLRWNLGS---NLMDANKHELVQKTQGYSGT

Parental  DISIIVRD
          DISIIVRD
Retrocopy DISIIVRD

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_1246 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
Macropus eugenii	ENSMEUG00000007309	1 retrocopy	retro_meug_1360,
Myotis lucifugus	ENSMLUG00000006550	2 retrocopies	retro_mluc_2432, retro_mluc_2513,
Mus musculus	ENSMUSG00000031913	1 retrocopy	retro_mmus_1038,
Otolemur garnettii	ENSOGAG00000016975	1 retrocopy	retro_ogar_391,
Tarsius syrichta	ENSTSYG00000012535	1 retrocopy	retro_tsyr_1246 ,