RetrogeneDB ID: retro_tbel_2171

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_103408:20806..21125(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL21
• Ensembl ID: ENSTBEG00000017030
• Aliases: None
• Description: mitochondrial ribosomal protein L21 [Source:HGNC Symbol;Acc:14479]

Sequence

>retro_tbel_2171
CACCCCTCCCATTGTCCGAATGAAATAAATAAGCTGTTCGCTTCGGTGCTGTACGCAGCTTCTTTGATTTTGTAATTACG
ACAACACCTGTGAAGGGTGACAGTTGAAGTCTTATTTTTAATCCAAAATGAGCTAGATATGGCATGCGGAGAGAGGATTC
AGTTGGAGAATGTCCTACTGGTGGGGCAGACAATTTCACGGTACTTGGAAAGCCACTCCGGGAAAGGATCTTGTTTGAGT
AGAAGCCACAGTTATTGAAAAGACAGAGTCATGGCCAAGAGTCAATATGAAATTTAAGAAAAGGAAAAACTTCAGGAAG

Alignment

ORF - retro_tbel_2171 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.36 %
• Parental protein coverage: 58.38 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HHTEVVKKVNELIASGQYGRLFAVVHFASHQWKVTAEDLILIENELDVACGERIQLEKVLLVG-ADNFTL
          H........N.L.AS..Y...........H...VT.E.L.LI.NELD.ACGERIQLE.VLLVG.ADNFT.
Retrocopy HPSHCPNEINKLFASVLYAASL-IL*LRQHL*RVTVEVLFLIQNELDMACGERIQLENVLLVG<ADNFTV

Parental  LGKPLL-GKDLVRVEATVIEKTESWPRVNMKFKKRKNFRK
          LGKPL..GKDLV.VEATVIEKTESWPRVNMKFKKRKNFRK
Retrocopy LGKPLR<GKDLV*VEATVIEKTESWPRVNMKFKKRKNFRK

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_2171 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2171 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000010124	1 retrocopy	retro_mmul_815,
Mus musculus	ENSMUSG00000024829	1 retrocopy	retro_mmus_3280,
Tupaia belangeri	ENSTBEG00000017030	1 retrocopy	retro_tbel_2171 ,