RetrogeneDB ID: retro_tsyr_1068

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_29570:17364..18177(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTSYG00000003440
• Aliases: None
• Description: None

Sequence

>retro_tsyr_1068
TGGGAGGTGATCAGCAATGAGCATGGCATCGACCCCACTAGCACCTACCAGAGGGACAGTGACCTGCAGCTAGAGTGCAT
CGATGTGTACTACAACGAGGCCACCAATGGCAAGTGCATGCCCCGCGCCATGCTCGTGGACCTGGAGCCTGGCACCATGG
ACACGGTGCACTCCAAGCCCTTTGAACAGATCTTCAGGCCGGACAACTTCACCTTTGGTCAGAGCAGGGCCGGGAACAAC
TGGGTCATGGGCCACTCCACAGAGGGCATAGAGCTGGTCGACTCAATGCTGGACATCGTGAGGAAGGAGGCTGAGAGCTG
TGACTGCCTCCAGGGCTTCCAGCTGACCCACTCCCGGGTGAGGGGGCTGGGTCTGGGAATGGGTACCCTCCTCATTAGCA
AGATTCAGGAGGAGTACCCGGACAGGATCATGAACATCTTCAGCATGGTGCGCTTCCCCAAGGTGTCAGACATGGTGGTC
GAGCCCTACAATGCCACCCTCTCAGTTCACCAACTGGTGGAAAACGCAGACGAGACCTACTGCATTGACAACGAGGCGCT
CTATGACATTTGCTTCCATACCCTCAAGCTGACCATGCCCACCTACTGTGACCTGAAGCACCTAGTGTCTGCCACCATGA
GTGGGGTCACCACCTGCCTGTGCTTCCCCAGCCAGCTCAAAGACAACCTGCGCAAGCTGGCTGTGAACATGGTGCTCTTT
CCCCACCTGCACTTTTTCATGCCCAGCTTCGCCCCGCTGACCAGCTGGGGCAGCCAGCAGTACTGGGCCCTGATGGTGCC
TGAGCTCACCCAG

Alignment

ORF - retro_tsyr_1068 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.31 %
• Parental protein coverage: 63.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYAPWAIIGDLEPGTMDSGQGFGPFGQIFRPDN
          WEVIS.EHGIDPT..Y..DSDLQLE.I.VYYNEAT..K..P.A...DLEPGTMD......PF.QIFRPDN
Retrocopy WEVISNEHGIDPTSTYQRDSDLQLECIDVYYNEATNGKCMPRAMLVDLEPGTMDTVHS-KPFEQIFRPDN

Parental  FVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEY
          F.FGQS.AGNNW..GH.TEG.ELVDS.LD.VRKE.ESCDCLQGFQLTHS...G.G.GMGTLLISKI.EEY
Retrocopy FTFGQSRAGNNWVMGHSTEGIELVDSMLDIVRKEAESCDCLQGFQLTHSRVRGLGLGMGTLLISKIQEEY

Parental  PDRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLV
          PDRIMN.FS....PKVSD.VVEPYNATLSVHQLVEN.DETYCIDNEALYDICF.TLKLT.PTY.DL.HLV
Retrocopy PDRIMNIFSMVRFPKVSDMVVEPYNATLSVHQLVENADETYCIDNEALYDICFHTLKLTMPTYCDLKHLV

Parental  SATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQ
          SATMSGVTTCL.FP.QL...LRKLAVNMV.FP.LHFFMP.FAPLTS.GSQQY.AL.VPELTQ
Retrocopy SATMSGVTTCLCFPSQLKDNLRKLAVNMVLFPHLHFFMPSFAPLTSWGSQQYWALMVPELTQ

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_1068 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017637	1 retrocopy	retro_cjac_1649,
Myotis lucifugus	ENSMLUG00000016179	1 retrocopy	retro_mluc_401,
Tupaia belangeri	ENSTBEG00000004854	9 retrocopies	retro_tbel_2291, retro_tbel_3456, retro_tbel_3944, retro_tbel_4113, retro_tbel_413, retro_tbel_4390, retro_tbel_4439, retro_tbel_961, retro_tbel_962,
Tarsius syrichta	ENSTSYG00000002994	1 retrocopy	retro_tsyr_569,
Tarsius syrichta	ENSTSYG00000003440	2 retrocopies	retro_tsyr_1068 , retro_tsyr_2125,