RetrogeneDB ID: retro_tbel_1201

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4084:48772..49344(+)
• 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_1201
TGGGTTCAAGCTGTTCAATCAGTCTGAGGCCTTTAAGACAAGAGAGAGGTGTTTGATGAGGAAAGACATGAGTCTCTCCT
GGTGCCATGGGAATGGTGAGGTCACATATAAAGATGAGTCAAAGATTATAGAGATAGAATAGATACTGGCAAAGCAGTTA
CTCTTCAGCAAGGCTTCGATCAAGGCTAAAAAGAAGGTACAGAAGTCATCAACTATGGGAAACTCAGAGGAACATTAAAT
GCTTTGCTCTCTTGGTGTCACCTTCCTGATATAGTTTGACTTTAATCACTAAAATAAATAGTCCTCTGAATGCAGCTGGA
CAGTGTGAACACTATGTGCTTAAATGTATGAAATCAATCACTTCACAACCCCATGTTGTAGATTCATTGGACTCCACTGA
GAAAATGAACCTCTGTCATGTGTTTAAGGCTGAGAAAAAGATTGATGAAACTAAAAATGAAAGACTTAGTGAAAACAAAA
ACTGTAGCAAGAGTTCTGTTGAGATAGATTCTTCATATTTAGACTGTTGTACAACACAGGACCATGCATGAGCTAAAAAC
CCAGGTCTCACT

Alignment

ORF - retro_tbel_1201 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.81 %
• Parental protein coverage: 87.61 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WVQAASRVRGPGDEADVFDEEADESLVVQREWRSHMQRRVKEGYRDGIDAGKAVALQQGFNQGYKEGAEV
          WVQA...V.G..D...VFDEE..ESL.V..EW..H..R.VK..YRD.ID.GKAV.LQQGF.QG.KEG.EV
Retrocopy WVQAVQSV*GL*DKREVFDEERHESLLVPWEW*GHI*R*VKD-YRDRIDTGKAVTLQQGFDQG*KEGTEV

Parental  IINYGQLRGTLSALLSWCHLHG-NSSTLITKINHLLDAVGQCEEYVLKHLKSITPQPHVVDLLDSIENMD
          I.NYG.LRGTL.ALLSWCHL....S.TLITKIN..L.A.GQCE.YVLK..KSIT.QPHVVD.LDS.E.M.
Retrocopy I-NYGKLRGTLNALLSWCHLPD<YSLTLITKINSPLNAAGQCEHYVLKCMKSITSQPHVVDSLDSTEKMN

Parental  LCHVVQADKKTNEAEDERLCENNAEYNKNCSKSPVGLECSYVGCGRTEERAHAENPGLT
          LCHV..A.KK.....DE...E...E.NKNCSKS.V....SY..C..T...A.A.NPGLT
Retrocopy LCHVFKAEKKI----DETKNERLSE-NKNCSKSSVEIDSSYLDCCTTQDHA*AKNPGLT

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_1201 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1201 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,