RetrogeneDB ID: retro_tbel_4725

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_99106:3484..3839(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL39
• Ensembl ID: ENSTBEG00000006067
• Aliases: None
• Description: mitochondrial ribosomal protein L39 [Source:HGNC Symbol;Acc:14027]

Sequence

>retro_tbel_4725
ATGGAGGCAATGGCTTGGGCTGTTCGGTGTCTGCGGCTTCTGCAGGTAGTCCCTGGCGACGGGGCTGCCTGGAGATTTAT
AGCAACATCATCAGCTTCTCAGCTGTCACCGACCAAATTGACAGAAATGCGGAATGATCTCTTTAATAAAGAGAAAAGCA
GACAGTTATCATTAACTCCACGAACTGAGAAGATTGAAGTTAAACATGTTGGAAAAACTGACCCTGGAACTGTCTTTGTG
ATGAATAAAAGCATTTCAACTCCATATAGTTGTACCATGCATTTGAATGAGTGGTACTACAGGAAATCCATCCTGGCTCT
TGTAGATGGACAGCGCTTGGGACATGTATAAGCCG

Alignment

ORF - retro_tbel_4725 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.76 %
• Parental protein coverage: 60.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEAMARGVRCLRLLQVVPGDGAGWRFIATSAATQLSPSKLTEMRNDLFNKEKSRQLSLTPRTEKIEVKHV
          MEAMA..VRCLRLLQVVPGDGA.WRFIATS.A.QLSP.KLTEMRNDLFNKEKSRQLSLTPRTEKIEVKHV
Retrocopy MEAMAWAVRCLRLLQVVPGDGAAWRFIATSSASQLSPTKLTEMRNDLFNKEKSRQLSLTPRTEKIEVKHV

Parental  GKTDPGTVFVMNKNISTPYSCAMHLNEWYCRKSILALVDGQ-PWDMYKP
          GKTDPGTVFVMNK.ISTPYSC.MHLNEWY.RKSILALVDGQ..WDMYKP
Retrocopy GKTDPGTVFVMNKSISTPYSCTMHLNEWYYRKSILALVDGQ>AWDMYKP

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_4725 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4725 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000022879	2 retrocopies	retro_fcat_1817, retro_fcat_300,
Macropus eugenii	ENSMEUG00000002198	1 retrocopy	retro_meug_682,
Myotis lucifugus	ENSMLUG00000015959	1 retrocopy	retro_mluc_2403,
Tupaia belangeri	ENSTBEG00000006067	2 retrocopies	retro_tbel_2146, retro_tbel_4725 ,