RetrogeneDB ID: retro_tbel_344

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_1807:104963..106070(+)
• Located in intron of: ENSTBEG00000000337

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_344
AACGTGCTTATCTTCAACTTGGGAGGTGGTACTTTTGATGTGTCCATCCTCACTATTGAGGATGGGAGTTTTGAGGTCAG
ATCTACAGCTGGAGATACACACTTGGGCAGAGAAGACTTCAACAATCGCATGGTCATCGCCGAGTTTAAGTTCAAGCATA
AGAAGGACATCAGTGAGAACAAGAGAGCTGTCCGCCACCTTCGCACTGCTTGTGAACGGGCTAAGCACACCCACTCCTCC
AGCACCCAAGCCAGTATTGAGATCGACTCCCTCTATGAAGGAATCGATTTCTATACCTCCATTACCTGTTGCCCGATTTG
AAGAGTTGAATGCAGACCTGTTCCGTCGGACCCTGGACCCTGTAGAGAAAGCTCTTCAGGACGCCAGACTAGACAAGTCA
CAGATCCATGACATTGTCCTGGTGGGTGGCTCTACTTGTGTCCCCAAGATTCAGAAGCTGCTACAAGACTTTTTCAATGG
GAAGGAACTGAGTAAGAGCATCAACCCTGATGAGGCTGTTGCTTATGGTGCAGCTGTCCAGGCAGCCATCTTATCCAGAG
ACAAGTCTGAGAACATCCAGGACCTGCTACTCTTGGGTGTCACGTCTCTGTCCCTGGGCATCAAAACTGCTGGCGGGGTC
ATGACTGTCCTCATCAAGCAGAACACCACCATTCCCACCAAGCAGACGCAGACCTTCACCACCTACTCCGACAACCAACC
CAGGGTGCTCATCCAGGTTTATGAAGGTGAGCACACCATGACCAAGAATAACAATTTGCTGGTCAAGTTTGAGCTCACAG
GCATATCTCTTGCACCCTGTGGTATTCCTCAGATTGAAGTCACTTTCAATATTGATGCCAGTGGCAGCCTGAACATCTCT
GCTGTGAATAAGAACACTGAGAAAGAGAACAGAATCACCATCATCAACGATAAGGGTTGTCTGAGCAAGGAGGACATGGA
GCACATGGTCCAGGAAGCTGAGAAGTACAAGGCTAAGGACAAGAAGCAGAGGGACAAGTGTCTTCCAAGAACTCCCTGGA
ATCCTACGTGTTCAACATGAAAGCCACGGTGGAGGAGGAGAAACTCCAAGGCAAGGTCAACAATGAG

Alignment

ORF - retro_tbel_344 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.56 %
• Parental protein coverage: 63.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRL
          NVLIF.LGGGTFDVSILTIEDG.FEV.STAGDTHLG.EDF.NRMV...IAEFK.KHKKDISENKRAVR.L
Retrocopy NVLIFNLGGGTFDVSILTIEDGSFEVRSTAGDTHLGREDFNNRMV---IAEFKFKHKKDISENKRAVRHL

Parental  RTACERAKRTLSSSTQASIEIDSLYEGIDFYTSITR-ARFEELNADLFRGTLDPVEKALRDAKLDKSQIH
          RTACERAK.T.SSSTQASIEIDSLYEGIDFYTSIT..ARFEELNADLFR.TLDPVEKAL.DA.LDKSQIH
Retrocopy RTACERAKHTHSSSTQASIEIDSLYEGIDFYTSITC>ARFEELNADLFRRTLDPVEKALQDARLDKSQIH

Parental  DIVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLG
          DIVLVGGST..PKIQKLLQDFFNGKEL.KSINPDEAVAYGAAVQAAILS.DKSEN.QDLLLL.VT.LSLG
Retrocopy DIVLVGGSTCVPKIQKLLQDFFNGKELSKSINPDEAVAYGAAVQAAILSRDKSENIQDLLLLGVTSLSLG

Parental  IETAGGVMTVLIKRNTTIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVP
          I.TAGGVMTVLIK.NTTIPTKQTQTFTTYSDNQP.VLIQVYEGE..MTK.NNLL.KFELTGI..AP.G.P
Retrocopy IKTAGGVMTVLIKQNTTIPTKQTQTFTTYSDNQPRVLIQVYEGEHTMTKNNNLLVKFELTGISLAPCGIP

Parental  QIEVTFDIDANGILNVSAVDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDK-VSSKNS
          QIEVTF.IDA.G.LN.SAV.K.T.KEN.ITI.NDKG.LSKED.E.MVQEAEKYKA.D.KQRDK.VSSKNS
Retrocopy QIEVTFNIDASGSLNISAVNKNTEKENRITIINDKGCLSKEDMEHMVQEAEKYKAKDKKQRDK<VSSKNS

Parental  LESYAFNMKATVEDEKLQGKINDE
          LESY.FNMKATVE.EKLQGK.N.E
Retrocopy LESYVFNMKATVEEEKLQGKVNNE

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_344 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_344 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,