RetrogeneDB ID: retro_tbel_3386

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_139079:67898..68646(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000017539
• Aliases: None
• Description: None

Sequence

>retro_tbel_3386
GTGGAGAGAAGAAAAGACATCACAACTCAAGAAGAACTTTGGAAAATGAGTACTAGGAGAAGTCTAGAAGATTATTTGAC
CAATGACACGAGAGAGATCAGCATGCTGAAAAGGCCTGTGGTTTTGTATTTGCACCAAACAGCCCCTATTGATGAATTTG
ATCGCCCCTCAGAACTTCAGCACAAACAAAAACTTTTTCCAAAATGGTGCTTCCCAATTAAAATAGCTGCTATTGCATCA
TCTCTCACTTTTCTTTATACTCTTTTGAGAAAAATAATTTACCCTTCAGTAACTTCTCATCAACAATATTCTTATAGGGT
CCAATCCTGGTCATCCATGGAGTCTTGCCAATGGTTCCCATCACCCCTTGGCACTGGCTTATTTGCCTGGTGTGATAGCA
GAAGTTGTACAACTTCATAATGGAATGAAGTATAAGAAATCTCCACATTACTTGGATAGGTGGATGATAAAGCAATTTGG
GCTTCTCAGTTGCGTTTTTGCTCTACTGCATGCAATTTAGAGTCTGTCTTATCCAAAGAGGTGATCCTACAGATGCAAGT
TGCCACAGTGGGCATACCAACAGGTACAGAAAAATAGAGAAGATGCCCGGATTGAACATGATGTTTGGATAATGGAGATT
TATGTGTCTCTGGGAATTATGGGACTTGGAATACTGGCAGTGCTGGCTGTGACATCTATTCCATCTGTGAGTGACTCTTT
GACATGAAGAGAATTTCACCATATTCAG

Alignment

ORF - retro_tbel_3386 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.61 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MENRKDIINQEELWKMKPRRSLEEDYLTNDTREMSMLKRPVVLNLHQTVHVDEFDCPSELQHKQELFPKW
          .E.RKDI..QEELWKM..RRSLE.DYLTNDTRE.SMLKRPVVL.LHQT...DEFD.PSELQHKQ.LFPKW
Retrocopy VERRKDITTQEELWKMSTRRSLE-DYLTNDTREISMLKRPVVLYLHQTAPIDEFDRPSELQHKQKLFPKW

Parental  HLPMKIAAIVSSLTFLYTLLREIIYPLVTSHQQYFYRI-PILVINKVLPMVSITL-LALVYLPGVIAAVV
          ..P.KIAAI.SSLTFLYTLLR.IIYP.VTSHQQY.YR..PILVI..VLPMV.IT..LAL.YLPGVIA.VV
Retrocopy CFPIKIAAIASSLTFLYTLLRKIIYPSVTSHQQYSYRV<PILVIHGVLPMVPITP<LALAYLPGVIAEVV

Parental  QLHNGTKYKKFPHWLDRWMITRKQFGLLSFFFALLHAIYSLSYPMRRSYRYKLLNWAYQQVQQNKEDAWI
          QLHNG.KYKK.PH.LDRWMI..KQFGLLS..FALLHAI.SLSYP.R.SYR.KL..WAYQQVQ.N.EDA.I
Retrocopy QLHNGMKYKKSPHYLDRWMI--KQFGLLSCVFALLHAI*SLSYPKR*SYRCKLPQWAYQQVQKNREDARI

Parental  EHDVWRMEIYVSLGIMGLAVLALLAVTSIPSVSDSLTWREFHYIQ
          EHDVW.MEIYVSLGIMGL..LA.LAVTSIPSVSDSLT.REFH.IQ
Retrocopy EHDVWIMEIYVSLGIMGLGILAVLAVTSIPSVSDSLT*REFHHIQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_3386 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3386 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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
Tupaia belangeri	ENSTBEG00000017539	1 retrocopy	retro_tbel_3386 ,