RetrogeneDB ID: retro_tbel_3488

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_142409:171521..172504(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000011602
• Aliases: None
• Description: None

Sequence

>retro_tbel_3488
AATGTACTGATCTTAACTTGGGAGGTAGCACTTTTGATGTATCCATCCTCACTGTTGAGGATGGAATTTTTGAGGTCATA
TCTACAGCTGGAGAGACACACTTGGGCGGAGAAGACTTTGACAATCATATGATCAACATTTCATCGCAAAGCTTAAGTGC
AAGTATAAGAAGGATATCAGTGAGAGCGAGAGAGCTGTCCAGCACCTGTGTACTGCTCATGAATGTACTAAGCATGCCCT
TCCCTCTCGCACCCAGGACAGTATTGAAATCAATTCCCTCTATGAAGGAATCGACTTTTATACCTCCATTACCTGTCCCA
GTTTGAAGCATTGAACACAGACTTACTCTGTGTCACCCTGGACCCTGTAGTGAAAGTCCTTCAGAACACCAAACTAGACA
AGTCACAGATCAATGACATCATCCTGGTGGACGGGTCTACTTGTCTCCCCAAGATCCAGAAGCTGCTGCAAGACTTCTTC
AATGGGAAGAAACTGACTAAGAGCATCAACCCTGATAAGGCTGTTGCTTACAGCGTAGCTGTTCAGGCAGCCATCTCATC
AGGAGACAAATCTGAAAGTGCTCAGGATTTGCTGCTCTGGGATGTCCCTCTTCTTTCCCTTGGCATTGAAACTACTGGTG
GAGTCATGACTGTCCTCATCAAGTGTAATACCACCATTCCTACCAAGCAGACACAGCCTTCACTACAGACTCCAACAACC
AACCTGGCGTGCTCATTCAGGTTTATGAAGGTGAGTATGCCATGACCAAGGACAACAACCTGCGGGGCATGTTTGAACTC
ACAGGCATGACTCCTGCACCCCATAGTGTTCCTCAGATCAAAGTCACTTTTGATATTGATGCCAATAGAATCTTGAACAT
TTCTACTGTGGATAAGAGTACAGGTAAAGAGAACAAGATTGCTATCATTGACAATAAGGGTCATTTGAGCAAGGAAGACA
ATGGGCTCATGGTCCAGGAGGCT

Alignment

ORF - retro_tbel_3488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.08 %
• Parental protein coverage: 56.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NVLIF-DLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVN-HFIAEFKRKHKKDISENKRAVR
          NVLI...LGG.TFDVSILT.EDGIFEV.STAG.THLGGEDFDN.M.N.HFIA..K.K.KKDISE..RAV.
Retrocopy NVLIL<NLGGSTFDVSILTVEDGIFEVISTAGETHLGGEDFDNHMIN<HFIAKLKCKYKKDISESERAVQ

Parental  RLRTACERAKRTLSSSTQASIEIDSLYEGIDFYTSIT-RARFEELNADLFRGTLDPVEKALRDAKLDKSQ
          .L.TA.E..K..L.S.TQ.SIEI.SLYEGIDFYTSIT....FE.LN.DL...TLDPV.K.L...KLDKSQ
Retrocopy HLCTAHECTKHALPSRTQDSIEINSLYEGIDFYTSIT<LSQFEALNTDLLCVTLDPVVKVLQNTKLDKSQ

Parental  IHDIVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLS
          I.DI.LV.GST..PKIQKLLQDFFNGK.L.KSINPD.AVAY..AVQAAI.SGDKSE..QDLLL.DV..LS
Retrocopy INDIILVDGSTCLPKIQKLLQDFFNGKKLTKSINPDKAVAYSVAVQAAISSGDKSESAQDLLLWDVPLLS

Parental  LGIETAGGVMTVLIKRNTTIPTKQTQ-TFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPR
          LGIET.GGVMTVLIK.NTTIPTKQTQ..FTT.S.NQPGVLIQVYEGE.AMTKDNNL.G.FELTG..PAP.
Retrocopy LGIETTGGVMTVLIKCNTTIPTKQTQ<AFTTDSNNQPGVLIQVYEGEYAMTKDNNLRGMFELTGMTPAPH

Parental  GVPQIEVTFDIDANGILNVSAVDKSTGKENKITITNDKGRLSKEDIERMVQEA
          .VPQI.VTFDIDAN.ILN.S.VDKSTGKENKI.I...KG.LSKED...MVQEA
Retrocopy SVPQIKVTFDIDANRILNISTVDKSTGKENKIAIIDNKGHLSKEDNGLMVQEA

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_3488 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3488 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000012704	1 retrocopy	retro_eeur_8,
Microcebus murinus	ENSMICG00000004702	1 retrocopy	retro_mmur_7,
Sorex araneus	ENSSARG00000000161	1 retrocopy	retro_sara_31,
Tupaia belangeri	ENSTBEG00000011602	8 retrocopies	retro_tbel_1764, retro_tbel_344, retro_tbel_3488 , retro_tbel_3524, retro_tbel_4348, retro_tbel_4412, retro_tbel_4490, retro_tbel_471,