RetrogeneDB ID: retro_tbel_1871

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_5912:38669..38983(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL52
• Ensembl ID: ENSTBEG00000000986
• Aliases: None
• Description: mitochondrial ribosomal protein L52 [Source:HGNC Symbol;Acc:16655]

Sequence

>retro_tbel_1871
GTCCGGAGGCTGTACTGCAGCACAGCGGCTCAGGCAGGCAGCCGGTGGCAACTCGAGCAGGGTTTGGCCACCAACCCCTC
CGGCTACGGTCCCCTGACGGAGCTCCCAGACTGGTCTTATGTGGATGGCCACCCTGCCCCCCGCAATGAAAGGCCAGCTT
TGAAGAAAAGCCCAGAGAAGTTTGCAAGAAGAGTTGTACTGCTGTCACAGGAAATGGATGCTGGATTACAGGCATGGCAG
CCAGGCAGCAGCAGAAGTTGCAGGAAAAAAGGAAACAAAAAAATGCTCTTAAACTCAAAGGGACTTCACTGCGG

Alignment

ORF - retro_tbel_1871 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.9 %
• Parental protein coverage: 85.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VRRLHCSAAAQAGSRWRLEQGLAANPSGYGPLTELPDWSYADGRPAPPMKGQLRRKAQREKFARRVVLLS
          VRRL.CS.AAQAGSRW.LEQGLA.NPSGYGPLTELPDWSY.DG.PAP........K...EKFARRVVLLS
Retrocopy VRRLYCSTAAQAGSRWQLEQGLATNPSGYGPLTELPDWSYVDGHPAPRNERPALKKSP-EKFARRVVLLS

Parental  QEMDAGLQAWQ-LRQQEKLQEERKQKNALKPKGTSLQ
          QEMDAGLQAWQ..RQQ.KLQ.......ALK.KGTSL.
Retrocopy QEMDAGLQAWQ<ARQQQKLQXXXXXXXALKLKGTSLR

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_1871 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1871 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
Ailuropoda melanoleuca	ENSAMEG00000007264	1 retrocopy	retro_amel_523,
Bos taurus	ENSBTAG00000014822	1 retrocopy	retro_btau_1839,
Felis catus	ENSFCAG00000006625	1 retrocopy	retro_fcat_1224,
Tupaia belangeri	ENSTBEG00000000986	1 retrocopy	retro_tbel_1871 ,