RetrogeneDB ID: retro_tbel_2771

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_118759:84941..85500(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GALM
• Ensembl ID: ENSTBEG00000003695
• Aliases: None
• Description: galactose mutarotase (aldose 1-epimerase) [Source:HGNC Symbol;Acc:24063]

Sequence

>retro_tbel_2771
ACACTGGATGGGAAGGGGTATCACCTGTGCATTAACAAGCAACCTAGTAGTTTGCACGGATGAGTCAGAGGGTTTGATAA
GATCCTCTGAACTTCTTGAGGGCTTTCAAATGGCATCAGACTCCCACACAGAAGTCGAGATATCGAGGAAGGCTACCTTA
GAGAGTTACAAGTCTGAATAACATATACCCTGGATAGCTTGGGGCTCATGGTCAACTCTAAAGCACAAGTCAGTCAAGAC
ACTTCAGTCGATCTGACCAACCATTCCTATTTCAACCTGGTAGGCCATGATTCCCCAAAATACATATGACCATGAGCTGA
CCATAAAAGCTGATGCTTTTTTGCCTGTAGATGAAATCCTGATTCCTATAGGAGAAGTTGCTGCAGTGCAAGGAATTGCA
TTTAACCTGAGAAAGCCAATGGAACTTGAAAAACACCTCTAGGAGTTCTGTGTCAAAGGTTTTGATCACAAATTCTGTCT
GAAGCGATCTGATGAAAAGCATTTTTGTGCAAGGGTGTATTGTTCTGGAAGTGGGCAGTGCTAAACTCTGTACCATACA

Alignment

ORF - retro_tbel_2771 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.31 %
• Parental protein coverage: 54.39 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TLDGKEYHLAINKEPNSLHGGVRGFDKVLWTPQVLSNGVQFSRVSPDGEEGYPGELKVWVTYTLSGGELT
          TLDGK.YHL.INK.P.SLHG.VRGFDK.L.T...LSNG......S.D.EEGY..EL.V..TYTL....L.
Retrocopy TLDGKGYHLCINKQPSSLHG*VRGFDKIL*TS*GLSNGIRLPHRSRDIEEGYLRELQV*ITYTLDSLGLM

Parental  VNYRAQASQTTPVNLTNHSYFNLAGQGSP-NIYDHEVTIEADAFLPVDETLIPTGEVAPVQGTAFDLRKP
          VN..AQ.SQ.T.V.LTNHSYFNL.G..SP.N.YDHE.TI.ADAFLPVDE.LIP.GEVA.VQG.AF.LRKP
Retrocopy VNSKAQVSQDTSVDLTNHSYFNLVGHDSP>NTYDHELTIKADAFLPVDEILIPIGEVAAVQGIAFNLRKP

Parental  VELGKHLQEFRLNGFDHNFCLKGSKEKHFCARVYHAGSGRVLEVYTT
          .EL.KHL.EF...GFDH.FCLK.S.EKHFCARVY..GSG.....Y.T
Retrocopy MELEKHL*EFCVKGFDHKFCLKRSDEKHFCARVYCSGSGQC*TLYHT

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_2771 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2771 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000015006	1 retrocopy	retro_meug_2094,
Macaca mulatta	ENSMMUG00000008248	1 retrocopy	retro_mmul_761,
Oryctolagus cuniculus	ENSOCUG00000006325	1 retrocopy	retro_ocun_1151,
Sus scrofa	ENSSSCG00000008486	1 retrocopy	retro_sscr_147,
Tupaia belangeri	ENSTBEG00000003695	2 retrocopies	retro_tbel_2040, retro_tbel_2771 ,