RetrogeneDB ID: retro_tbel_198

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_1430:195695..196472(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC35A3
• Ensembl ID: ENSTBEG00000004128
• Aliases: None
• Description: solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3 [Source:HGNC Symbol;Acc:11023]

Sequence

>retro_tbel_198
AGTGTAAGAGCTCTAAATTGAGTACTGCATGATGAAATTCTTAATAAGCTTCTGGAAACACTTAAACTTGCTATCCCATC
AGAGATATATGCTCTTCAGAATAATTTTCTGAACATGGTGCTCTCCAATCTAGATGCTGCTACTTATCAGGTCACAAATC
AGTTGAAAATTCTTAACGACAGCATTATTTTCTGCATGATGCTTAGTAAAAGTATCAGGGTGTCCCAGTGGCTCTTCCTT
ATAATTTTGATGACAGCAGTTGCTTTCATCCAGTGGTGTTCTGATTCTCAAGAGCTTGATTCTAAGGAGCTAACAGCTGG
CTCTTAATTTGTAGCCCTCATGGCAGTTCTCACAGCATGTTTTTCAAGTGGCTGTGCGGGAGTTTATTTTGAGAAAATTT
TAAAAGAACAAGCAGTCAGTATGGATAAGAAACATTCAGCTTGGTTTCTTTAGGAGTATATTTGGATTAATGGGTGTATA
CAGCTATGATGGTGAATTGGTATTAAAGAATGGATGTTTTCAGGGATATAACTGACTGACCTGGGTAGTTGTTCCTCTTC
AGGCACCTGGAGCTCTTGTAATAACTGCTGTTATTAAGTATGCAGATAATATTTTTAAAGAATTTGCAACTTCTTTATTC
ATAATATTATCAACACTGATTCCTATTTGTGGCTACAAGAGTTTGTGCCACCCACTGTCTTTTTCCTTGGAGACATCCTA
GTAATAACAGTGACTTTCTTACATGGTTATTATCCCAAACCTGCAGGAAATCCCACT

Alignment

ORF - retro_tbel_198 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.05 %
• Parental protein coverage: 70.65 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SLRALNRVLHDEILNKPMETLKLAIPSGIYTLQNNLLYVALSNLDAATYQVTYQLKILTTALFSVSMLSK
          S.RALN.VLHDEILNK..ETLKLAIPS.IY.LQNN.L...LSNLDAATYQVT.QLKIL........MLSK
Retrocopy SVRALN*VLHDEILNKLLETLKLAIPSEIYALQNNFLNMVLSNLDAATYQVTNQLKILNDSIIFCMMLSK

Parental  KLGVYQWLSLIILMTGVAFVQWPSDSQEVDSKELSAGSQFVGLMAVLTACFSSGFA-GVYFEKILKET-K
          ...V.QWL.LIILMT.VAF.QW.SDSQE.DSKEL.AGS.FV.LMAVLTACFSSG.A.G..F....K.T.K
Retrocopy SIRVSQWLFLIILMTAVAFIQWCSDSQELDSKELTAGS*FVALMAVLTACFSSGCA<GSLF*ENFKRT<K

Parental  QSVWIRNIQLGFFGSIFGLMGVYIYDGELVSKNGFFQGYNRLTWIVVILQALGGLVIAAVIKYADNILKG
          QSVWIRNIQLGFF.SIFGLMGVY.YDGELV.KNG.FQGYN.LTW.VV.LQA.G.LVI.AVIKYADNI.K.
Retrocopy QSVWIRNIQLGFFRSIFGLMGVYSYDGELVLKNGCFQGYN*LTWVVVPLQAPGALVITAVIKYADNIFKE

Parental  FATSLSIILSTLI-SYFWLQDFVPTSVFFLGAILVITATFLYGYDPKPAGNPT
          FATSL.IILSTLI.SY.WLQ.FVP..VFFLG.ILVIT.TFL.GY.PKPAGNPT
Retrocopy FATSLFIILSTLI<SYLWLQEFVPPTVFFLGDILVITVTFLHGYYPKPAGNPT

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_198 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_198 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000695	1 retrocopy	retro_chof_37,
Oryctolagus cuniculus	ENSOCUG00000015538	2 retrocopies	retro_ocun_1564, retro_ocun_436,
Tupaia belangeri	ENSTBEG00000004128	1 retrocopy	retro_tbel_198 ,
Vicugna pacos	ENSVPAG00000001029	1 retrocopy	retro_vpac_428,