RetrogeneDB ID: retro_tbel_1413

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4629:195798..196448(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBXN1
• Ensembl ID: ENSTBEG00000007971
• Aliases: None
• Description: UBX domain protein 1 [Source:HGNC Symbol;Acc:18402]

Sequence

>retro_tbel_1413
GCAGAGCAGGGTGGCCCTGAAGGATCTGGGTCTGCTACTGGATAAGGCAAACCCATTCTGAGTGAAGAGGAAAGATAGGA
ACAGACTAAGAGGATGTTGGAGCTGGTGGTCCAGAAGCAGCGGGAGCGTGAAGAAAGAAAGGAATGAGAGGAACTGGAAT
GGGAACAACAGTATGAAGACAAGGGCAAGAGTTGTCAGCTGCACGCCAGAGGCTACAAGAAGAAGATCTGCACAGGGCTG
TTGAGGAGCTCAGGATGGAGAAGGCTGAAGAGTTAGCAGCCAGCCAGAGGGTTTGAGAAGAGATTGAAAGGGACAAAGCT
GAAAGAACCAAGAAGTATGGTGGTAGTGTGAGTTCTCAGCCAACCCCACCAACAGCAGAGGCAGGTCCTGTTCCCTCTTC
ACCCAGCCAGGAGCCTCCCCTCAAGCGGGAGTATGACCAGTGTCACATACAGGTCAGGCTGCAGGTGGGACCTAACTGAC
CCAGACATTCCAAGGCCCAGGAACAGCTGGCAGCTGTGAGGCTCTATGTGGAACCCCATGGTGGAGAGGAACCTGGAGGG
GGCCAGGACCCTGTGCAGTTACTCAGTGGCTTCCCTAGACGGGTCTTCTCAGAGGCTGACATGGAACGGCCTCTGCAGGA
GTTGGGACTC

Alignment

ORF - retro_tbel_1413 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.27 %
• Parental protein coverage: 70.23 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AEQGGPEGSGSATGEGKPILSEEERQEQTKRMLELVAQKQREREEREEREALERERQRR-RQGQELSAAR
          AEQGGPEGSGSATG.GKPILSEEER.EQTKRMLELV.QKQREREER.E.E.LE.E.Q...RQGQELSAAR
Retrocopy AEQGGPEGSGSATG*GKPILSEEER*EQTKRMLELVVQKQREREERKE*EELEWEQQYE<RQGQELSAAR

Parental  QRLQEDEMRRAAEERRREKAEELAARQRVREKIERDKAERAKKYGGSVSSRPTPPSTEPGPVPSSPSQEP
          QRLQE....RA.EE.R.EKAEELAA.QRV.E.IERDKAER.KKYGGSVSS.PTPP..E.GPVPSSPSQEP
Retrocopy QRLQEEDLHRAVEELRMEKAEELAASQRV*EEIERDKAERTKKYGGSVSSQPTPPTAEAGPVPSSPSQEP

Parental  PTKREYDQCRIQVRLP-DGTSLTQTF-RAREQLAAVRLYVELHRGEEPGGGQDPVQLLSGFPRRAFSEAD
          P.KREYDQC.IQVRL...GT.LTQTF..A.EQLAAVRLYVE.H.GEEPGGGQDPVQLLSGFPRR.FSEAD
Retrocopy PLKREYDQCHIQVRLQ<GGT*LTQTF>KAQEQLAAVRLYVEPHGGEEPGGGQDPVQLLSGFPRRVFSEAD

Parental  MERPLQELGM
          MERPLQELG.
Retrocopy MERPLQELGL

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_1413 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1413 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
Rattus norvegicus	ENSRNOG00000019666	1 retrocopy	retro_rnor_1601,
Sorex araneus	ENSSARG00000008689	1 retrocopy	retro_sara_445,
Tupaia belangeri	ENSTBEG00000007971	1 retrocopy	retro_tbel_1413 ,