RetrogeneDB ID: retro_tbel_3738

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_150079:8635..9089(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000002729
• Aliases: None
• Description: None

Sequence

>retro_tbel_3738
GCCATGGTTTCTGAGTTCGACTTCTGCCTGGGGGTGCACGAAGTGGAAGTGGGGCTGAAATTCAGGTGGGTGCAGCAGCC
AAAGTTGGCGAACAAGTTCCCGGAGCCAAGGGCGGAGTGAACCCTGAGGCCAATGAGAACCGCCAGGGCGATGTGCACCA
GGAGGCCTTTGGCGAAGGCCAGGATCCTGGGCGGCAGCAGCCCGCAGAGGCGGCAGGCGCTGCTGCAGAGGGCCAAGGTG
CAGGTCTGGGCAGCCGCGAGCCGTGCGCACAAAGTTCACGCAGATGCAGCTGCAGGAGCTTGAGAGTATGTTCGAAGAAA
CTCAGTACCCTGATTGGCTGACCAGGAGGCAGCTTGCAAGACACATAGATGTGACTGAAAACAGAGTGCAGGCTTGGCTT
TAAGAATAGGCAGCCAAGTACAGGAAGGAAGAGAGGTCTTTAAGCGAGAGAAAC

Alignment

ORF - retro_tbel_3738 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.51 %
• Parental protein coverage: 89.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AMDPEFDFSLGVQEVEVV-AESQMAEAANVGDQVPDPEFGVNPEANENRQGEVHQEAAGEGQEPGQQPPA
          AM..EFDF.LGV.EVEV..AE.Q...AA.VG.QVP....GVNPEANENRQG.VHQEA.GEGQ.PG.Q.PA
Retrocopy AMVSEFDFCLGVHEVEVG<AEIQVGAAAKVGEQVPGAKGGVNPEANENRQGDVHQEAFGEGQDPGRQQPA

Parental  PAV-AAAEGQG-CGSGQPQGVRRKFTQVQLQELESVFEETHYPDWLTRRKLARRLDVTDKRVQAW-FKNR
          .A..AAAEGQG.C.SGQP..VR.KFTQ.QLQELES.FEET.YPDWLTRR.LAR..DVT..RVQAW.FKNR
Retrocopy EAAGAAAEGQG<CRSGQPRAVRTKFTQMQLQELESMFEETQYPDWLTRRQLARHIDVTENRVQAW>FKNR

Parental  R-AKYRRQQRALTESN
          ..AKYR...R.L.E.N
Retrocopy Q<AKYRKEERSLSERN

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_3738 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3738 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000009422	1 retrocopy	retro_pvam_753,
Ictidomys tridecemlineatus	ENSSTOG00000005297	1 retrocopy	retro_itri_735,
Tupaia belangeri	ENSTBEG00000002729	1 retrocopy	retro_tbel_3738 ,
Tupaia belangeri	ENSTBEG00000017505	1 retrocopy	retro_tbel_339,