RetrogeneDB ID: retro_tbel_3434

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_140321:21..407(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DTD1
• Ensembl ID: ENSTBEG00000000242
• Aliases: None
• Description: D-tyrosyl-tRNA deacylase 1 [Source:HGNC Symbol;Acc:16219]

Sequence

>retro_tbel_3434
TGTGTCAGCCAGTTCACCCTGCAGTGTGTCCTTACGGGGAACAAGCCCGACTTCCACCTAGCGATGCCCACGGGGCAGGC
AGAGGGCTTCTACTACAGCTTCCTGGAGCAGCTGCGCACGATGTACCCGCGGAGCTCATGGAAGATGGCAAGGTTGGGGC
CTACACGCAAGCGCACAGAACCACGGACCATAGAATTGGAGTCCCGGCTCCGGGTGCTGCGACCCCTGACCCAAAGCTGC
TCTCAAAGCTTGAAAACCAGCAGCAGAGGAAAGAAAAGACCAGAGCTAGGGGGCCTTCTGAATCAAGCAAAGAAAGAAAC
GCTCCCCGAAAAGAAGACGGCTATGCCAGTAGAGGGGCAGAAGGTGACACGTCTTCTGAACGGGAG

Alignment

ORF - retro_tbel_3434 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.37 %
• Parental protein coverage: 63.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CVSQFTLQCVLKGNKPDFHLAMPTEQAEGFYNSFLEQLRKSY-RPELIKDGKFGAYMQVHIQNDGPVTIE
          CVSQFTLQCVL.GNKPDFHLAMPT.QAEGFY.SFLEQLR..Y...EL..DGK.GAY.Q.H...D......
Retrocopy CVSQFTLQCVLTGNKPDFHLAMPTGQAEGFYYSFLEQLRTMY<PAELMEDGKVGAYTQAHRTTDHRIGV-

Parental  LESPAPGAATSDPKQLSKLEKQQQRKEKTRAKGPSESSKERNAPRKEDRSASSGAEGDVSSERE
          ...PAPGAAT.DPK.LSKLE.QQQRKEKTRA.GPSESSKERNAPRKED..AS.GAEGD.SSERE
Retrocopy ---PAPGAATPDPKLLSKLENQQQRKEKTRARGPSESSKERNAPRKEDGYASRGAEGDTSSERE

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_3434 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3434 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008964	1 retrocopy	retro_btau_767,
Macropus eugenii	ENSMEUG00000009170	2 retrocopies	retro_meug_137, retro_meug_1809,
Macaca mulatta	ENSMMUG00000012880	1 retrocopy	retro_mmul_217,
Monodelphis domestica	ENSMODG00000005696	1 retrocopy	retro_mdom_509,
Mus musculus	ENSMUSG00000027430	1 retrocopy	retro_mmus_2774,
Oryctolagus cuniculus	ENSOCUG00000010988	1 retrocopy	retro_ocun_1357,
Tupaia belangeri	ENSTBEG00000000242	1 retrocopy	retro_tbel_3434 ,