RetrogeneDB ID: retro_tbel_4280

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_74920:3334..3869(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000009016
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ELAVL3
• Ensembl ID: ENSTBEG00000006133
• Aliases: None
• Description: ELAV (embryonic lethal, abnormal vision, Drosophila)-like 3 (Hu antigen C) [Source:HGNC Symbol;Acc:3314]

Sequence

>retro_tbel_4280
TCTGGCAGCACAGAGGGTAGCAAGACCAACTTTAGTAGTTAACCACCTGCCGCAGAACACGAGACAGGAGGGATTCAAGA
GTCTTTTGGGAAGCATTGGTGAGATAGAGTCCTGTAAGCTTGTAAGAGACAAAGCAACAGGACAGAGCTCGGGATGTGGC
TTTGTGAACTACATTGACCCCGAGGATGCAGAGAAAGCTATCAACACCCTGAATGGATTGTGACTTCAAACCAAAACAAT
CAAAGTTTCCTCTGCTCACCCAAGTTCAGCTTCTATCAGAGTTGCAAATGTATATGTCAGTGGACTTCCAAAAACAATGA
CCCAAAAGGAGTTGGAACAGCTGATTTCGCAGTATGGACGCATCATTACTTGTCGTCTTCTTGTTGGCCAGGTCACTGGC
ATATCCGGGGTTGTAGGGCTCATTCGATTTGACAAGCGGATTGAGGCAGAAGAAGCTATCAAAGGCCTCAATGGCCAGAA
ACCTCCTGGTGCCACAGAGCCAATCACTGAAAAGTTTGCTAATAATCCAAGCCAA

Alignment

ORF - retro_tbel_4280 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.77 %
• Parental protein coverage: 54.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NGATDDSKTN-LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIST
          .G.T..SKTN.L.VN.LPQN..Q..FKSL.GSIG.IESCKLVRDK.TGQS.G.GFVNY.DP.DA.KAI.T
Retrocopy SGSTEGSKTN>LVVNHLPQNTRQEGFKSLLGSIGEIESCKLVRDKATGQSSGCGFVNYIDPEDAEKAINT

Parental  LNGLKLQTKTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGVSRGVG
          LNGL.LQTKTIKVS.A.PSSASIR.AN.YVSGLPKTM.QKE.EQL.SQYGRIIT.R.LV.QVTG.S..VG
Retrocopy LNGL*LQTKTIKVSSAHPSSASIRVANVYVSGLPKTMTQKELEQLISQYGRIITCRLLVGQVTGISGVVG

Parental  FIRFDKRIEAEEAIKGLNGQKPLGAAEPITVKFANNPSQ
          .IRFDKRIEAEEAIKGLNGQKP.GA.EPIT.KFANNPSQ
Retrocopy LIRFDKRIEAEEAIKGLNGQKPPGATEPITEKFANNPSQ

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_4280 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4280 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Tupaia belangeri	ENSTBEG00000006133	1 retrocopy	retro_tbel_4280 ,
Tupaia belangeri	ENSTBEG00000015038	1 retrocopy	retro_tbel_3670,