RetrogeneDB ID: retro_tbel_3678

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_148232:11460..11940(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YAE1D1
• Ensembl ID: ENSTBEG00000010085
• Aliases: None
• Description: Yae1 domain containing 1 [Source:HGNC Symbol;Acc:24857]

Sequence

>retro_tbel_3678
ATGTCCTGGGTTCAAGCAGCACAGTTGGTCCGGGGCCCTGGTGATGAGGCAGACGTGTTTGACAAGGAAGCGGACAAGTC
TCTTGTGGTGCAGCAAGAATGGTGGAGTCACATGCAAAGACAAGTCAAAGAAGGTTATAGAGATGGAATAGACGCTGGCA
AAGCAGTTGCTCTTCAGCAGGGCTTCAATCAAGGTTATAAAGAAGGCGCAGAAGTCATTATCAACTACAGACAACTCAGG
GGAACATTGAGTGCTTTGCTCTCCTGGCGTCACCTTCATAGTAATAGTTCAACTTTAATCACTAAAATAAATCATCTTCT
GGAGGCAGTTGGCCAGTGTGAAGAGTATGTGCTCAAACATCTGAAATCAATCACTCCACAACCCTATGTTGTAGATTTAT
TGGACTCCATTGAGAATATGGACCTTTGTCATATAGTTCAAGCTGATAAAAAGACCAATGAAGCTGAAGATGAAAGACTC

Alignment

ORF - retro_tbel_3678 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.88 %
• Parental protein coverage: 70.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSWVQAASRVRGPGDEADVFDEEADESLVVQREWRSHMQRRVKEGYRDGIDAGKAVALQQGFNQGYKEGA
          MSWVQAA..VRGPGDEADVFD.EAD.SLVVQ.EW.SHMQR.VKEGYRDGIDAGKAVALQQGFNQGYKEGA
Retrocopy MSWVQAAQLVRGPGDEADVFDKEADKSLVVQQEWWSHMQRQVKEGYRDGIDAGKAVALQQGFNQGYKEGA

Parental  EVIINYGQLRGTLSALLSWCHLHGNSSTLITKINHLLDAVGQCEEYVLKHLKSITPQPHVVDLLDSIENM
          EVIINY.QLRGTLSALLSW.HLH.NSSTLITKINHLL.AVGQCEEYVLKHLKSITPQP.VVDLLDSIENM
Retrocopy EVIINYRQLRGTLSALLSWRHLHSNSSTLITKINHLLEAVGQCEEYVLKHLKSITPQPYVVDLLDSIENM

Parental  DLCHVVQADKKTNEAEDERL
          DLCH.VQADKKTNEAEDERL
Retrocopy DLCHIVQADKKTNEAEDERL

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_3678 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3678 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000075054	1 retrocopy	retro_mmus_152,
Rattus norvegicus	ENSRNOG00000013438	1 retrocopy	retro_rnor_2047,
Tupaia belangeri	ENSTBEG00000010085	2 retrocopies	retro_tbel_1201, retro_tbel_3678 ,