RetrogeneDB ID: retro_tbel_3390

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_139137:171610..172314(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FUCA1
• Ensembl ID: ENSTBEG00000013160
• Aliases: None
• Description: fucosidase, alpha-L- 1, tissue [Source:HGNC Symbol;Acc:4006]

Sequence

>retro_tbel_3390
TGGGTACCTCCACTTTACTATTTATAAGGAAAAAAATGGCTTTAAAACTCAGCATTTTGCTAGTGTGAAAACAATGCCAG
AACTATAGAACCTTGTTAATAGGGGAAGACCTGATCTTATTTGGTCTGATGGGATATGCAAATATCCTGATACTAATTGA
ACCTTAAGAGGCTTTTTTCCCCCCTCATGTCTGCTCAATAATAGACCCATTAAGGATGAGGTGGTGTTAAATAGCCAATG
GGGTTGAAAATACTCCTGTCGTCATGGGTGGATGCTACAGTTGTCAAGATAAACTCAAGCCTGGGAAATTGCCAGGGCAC
AAGTGGGAGTGTGTTCCACCATCAACAAGAAATCTTAGGGCATCTTTGCAGCATGGTGATATCTAACATTGCAGGTGAGT
CTGACATCATTTTGGAGCTAACTCAGACAGTGAGTTTGGGAAGGGACTATCTTCTCAACATGAAACCAACTAAAGGTAAA
TGGATTGTTCCATCTTTCAAGAAAGACTTCTTGCTGTTGAGAAGGTGACTAGCATCAATGGGGAGACTATCTGTACCTTT
AAACCATGGAGGGTGAAATTAGAAAAGAACTGGGTATCTGTATAGCAGACCTCAGAAGGATCACCTGCTTAAGCCATTTT
ACTACACTGGCCAAGATAGAGAGTAGTGACCCTTGAGTACCCCATAACTACATTGAATACAAAG

Alignment

ORF - retro_tbel_3390 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.0 %
• Parental protein coverage: 55.21 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  WFHPLYLL-DKKNGFKTQNFVSAKTMPELYDLVTRYKPDLIWSDGEWESPDTYWNSTEFL--SWLYNDSP
          W..PLY.L...KNGFKTQ.F.S.KTMPEL..LV.R..PDLIWSDG....PDT......F...S.L.N..P
Retrocopy WVPPLYYL>KEKNGFKTQHFASVKTMPEL*NLVNRGRPDLIWSDGICKYPDTN*TLRGFFPPSCLLNNRP

Parental  VKDKVVVNDRWGQNCPCHHG-GYYNCQDKFKPESLPDHKWE-MCTSIDKMS-WGYRRDMTVSHIMNESEI
          .KD.VV.N..WG....C.HG.G.Y.CQDK.KP..LP.HKWE..C..I.K.S..G....M..S.I..ES.I
Retrocopy IKDEVVLNSQWG*KYSCRHG>GCYSCQDKLKPGKLPGHKWE<VCSTINKKS<LGHLCSMVISNIAGESDI

Parental  ISELVQTVSLGGNYLLNIGPTKDGLIVP-IFQERLLAVGKWLSVSGEAIYASRPWRVQKENNTKAVWYTS
          I.EL.QTVSLG..YLLN..PTK...IVP.IFQERLLAV.K..S..GE.I....PWRV..E.N...V..TS
Retrocopy ILELTQTVSLGRDYLLNMKPTKGKWIVP<IFQERLLAVEKVTSINGETICTFKPWRVKLEKNWVSV*QTS

Parental  KGPAVYAIFMHWPENGVLTLEAPITTSTTK
          .G....AI..HWP...V.TLE.PITT..TK
Retrocopy EGSPA*AILLHWPR*RVVTLEYPITTLNTK

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_3390 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3390 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
Choloepus hoffmanni	ENSCHOG00000012304	2 retrocopies	retro_chof_1090, retro_chof_542,
Equus caballus	ENSECAG00000024652	1 retrocopy	retro_ecab_450,
Loxodonta africana	ENSLAFG00000015305	1 retrocopy	retro_lafr_252,
Microcebus murinus	ENSMICG00000007213	1 retrocopy	retro_mmur_542,
Tupaia belangeri	ENSTBEG00000013160	1 retrocopy	retro_tbel_3390 ,