RetrogeneDB ID: retro_tsyr_1456

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_44840:4114..4795(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTSYG00000006869
• Aliases: None
• Description: None

Sequence

>retro_tsyr_1456
AAGATGGAACATGAACCCAAAGCAGTGGACATTCCAAATTCTCCATCTAACCCTTCAAAAAATGATCCCGTGGTTTCCTC
TGAACCCAAGAAGACTTCTGCTGACCCAAAACTGAAAACAATGAGTCAAACCAAAAGAAAGAAAAGGTCTGATAGCTCGC
TTAGTGGTAGCAGTGACGGCGAAGAAGAATTGCATGAGGAGGAGTATTTTGATGATAGCACAGAAGAAAGGTTTTACAAA
CAGTCTTCCATGTCCGAGGAAAGTGATAGTGGTGATGACTTCTTCATTGGGAAAGTCAGACGGACACGAGAGGATAGTAG
TTGAGATTCTCCTGTTAAGGAACAAAAACCTCTCCAAAAAGTGTTACGCAAAGAAGATACACATGAAACTCATTGGGATA
TAAGAAGTGACAAAAATAAGCAAAGTACAGATGCCAGAAAGTTAGAGTCAGTGTTGTTTCACACTTTATCTGGATCTAAA
GGCTCTAGAAGAGATCACAAAGAACAGGCTCCAAAGAGTAAAACCCCTGTTATTCCACAGAGTGGACCTCAGATCAAGAA
TCAGTTTAATAAGAAGCCACAAAGAGGACTTGAAAATACAAAACAGCAATTGCAACTGCCTCTTTGTCCTTCATGGGAAG
CAGGCAAAAGGCGAAAAGAACAGCAATCTAAAATTGCTGTG

Alignment

ORF - retro_tsyr_1456 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.58 %
• Parental protein coverage: 54.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KMEHGPKAVDISNSPSKPLKNDPVVSSESRKTSADPKLKTVRQNKRNKRSDTLLSGSSDGSEEIEEKEYF
          KMEH.PKAVDI.NSPS.P.KNDPVVSSE..KTSADPKLKT..Q.KR.KRSD..LSGSSDG.EE..E.EYF
Retrocopy KMEHEPKAVDIPNSPSNPSKNDPVVSSEPKKTSADPKLKTMSQTKRKKRSDSSLSGSSDGEEELHEEEYF

Parental  HDSPEQRFYKQSSMSEDSDSGDDFFVGKVRQTRKKESSCHSSVKEQKPLQKVLPKEDTHETHWDISSDKN
          .DS.E.RFYKQSSMSE.SDSGDDFF.GKVR.TR...SS..S.VKEQKPLQKVL.KEDTHETHWDI.SDKN
Retrocopy DDSTEERFYKQSSMSEESDSGDDFFIGKVRRTRE-DSS*DSPVKEQKPLQKVLRKEDTHETHWDIRSDKN

Parental  KESTDGRKLESVLFHTLSGSKGSRRDYKEQAPKSKTLGFPQSGPQIKNQFSKKPQRGFENTKQQLQLPLR
          K.STD.RKLESVLFHTLSGSKGSRRD.KEQAPKSKT...PQSGPQIKNQF.KKPQRG.ENTKQQLQLPL.
Retrocopy KQSTDARKLESVLFHTLSGSKGSRRDHKEQAPKSKTPVIPQSGPQIKNQFNKKPQRGLENTKQQLQLPLC

Parental  PSWEASKRQKKQQSKIAV
          PSWEA.KR.K.QQSKIAV
Retrocopy PSWEAGKRRKEQQSKIAV

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_1456 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017177	1 retrocopy	retro_cjac_1132,
Monodelphis domestica	ENSMODG00000013487	2 retrocopies	retro_mdom_1304, retro_mdom_1705,
Otolemur garnettii	ENSOGAG00000032423	1 retrocopy	retro_ogar_1270,
Tarsius syrichta	ENSTSYG00000006869	1 retrocopy	retro_tsyr_1456 ,