RetrogeneDB ID: retro_tbel_1340

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4435:181883..183384(+)
• Located in intron of: ENSTBEG00000007366

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000016563
• Aliases: None
• Description: None

Sequence

>retro_tbel_1340
GAGAACTGTGATGACCTGCACAAAATCCCTGCTTCCCCAGTTGTCCACATCAGGGGTCTGATTGATGGCGTGGTGGAAGC
TGACCTCGTAGAAGCCTTAAAGGACTTTGCACCCATCAGCTATGTGGTGGTAATGCCTAAAAAGAGACAAGCACTGGTGG
AGTTTGAAGATGTGTCGGGGGCTTGCAATGCAGTGAACTATGCAGCAGACAACCAGATCTATATTGCTGGTCACGCAGCA
TTTGTCAGCTACTCTACTAGCCAAAAGATCTTCCGCCCTGGGGACTCAGATGACTTCCGGAGGGTCAATAGTGTGCTTCT
CTTTACCATACTGAACCCCATCTATTCCATTACAACGGATGTTCTTTACACTGTCTGTAATCCTTGTGGCCCTGTTCAGA
GAATTGTCATTTTCCGGAAGAATGGAGTCCAGGCCATGGTGGAATTTGACTCTCTGCAAAGTGCCCAGCGGGCCAAGGCC
TCGCTCAATGGGGCTGACATTTACTCTGGCTGTTGTACTCTGAAGATTGAATATGCAAAGCCTACACGCTTGAATGTGTT
CAAGAACGATCAGGATACTTGGGACTATACAAATCCCAACCTCAGTGAACAAGGTGACCCTGGCAGCAATACCAGCAAAT
ACCAGAGGCAGCCCCCTCTCCTGGGAGATCATCCCACAGAATATGGAGGGCCTCACGGTGGATACCACAGCCATTACCGT
GATGAGGGCTATGGCTCTCCCCCACCTCATTACGAAGAGAGAAGGATGGGCCCACTAGTGGGGGGTCACCGTCGGGGCCC
AAGCCACTGCAGCCCCCAATATGGGTATCCCCCACCCACTCCCCCACCACCTGAGTACAGCCCCCACAGTGACAGCCCTG
TGCTCATGGTCTATGGCTTGGATAAATCTAAGATGAATTGTGACAGAGTCTTCAATGTCTTCTGCTTATATGGCAATGTG
GAGAAGGGTAAAATTCATGAAAAGCAAACCTGGGGCTGCCATGGTAGAAATGGCTGATAGCTATGCTGTGGACCAGGCCG
TTACCCACCTCAACAACAACTTCATGTTTCGGCAAAAGCTGACTGTCTGTGTCTCCAAGCAACCAGCCATCATTCCTGGA
CAGTCATACAGGCTGGAAGACGGGTCCCGCAGTTACAAAGACTTCGGCGAGTCGAGGAACAATCGGTTTTCCACTCCAGA
GCAGGCAGCCAAGAACCGCATCCAGCACCCTAGCAATGTGCTGCATTTCTTCAATGCCCCTCTGGAGGTGACTGAGGAGA
ACTTCTTTGAGATCTGCGATGAGCTAGGAGTGAAGCGGCCGTCTTCTGTGAAAGTATTCTCAGGCAAGAGTGAACGTAGC
TCCTCTGGGCTGTTGGTGTGGGAGTCCAAGAGCGATGCCCTGGAGACTTTGGGCTTCCTCAACCATTACCAGATGAAAAC
CCCAAATGGCTCATACTGGTACACTCTGAAGTTGTGTTTCTTCACCGCTCAGCACGCCTCC

Alignment

ORF - retro_tbel_1340 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.43 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAAD
          EN.DD.HK.PASPVVHIRGLIDGVVEADLVEAL..F.PISYVVVMPKKRQALVEFEDV.GACNAVNYAAD
Retrocopy ENCDDLHKIPASPVVHIRGLIDGVVEADLVEALKDFAPISYVVVMPKKRQALVEFEDVSGACNAVNYAAD

Parental  NQIYIAGHPAFVNYSTSQKISRPGDSDDSRSVNSVLLFTILNPIYSITTDVLYTICNPCGPVQRIVIFRK
          NQIYIAGH.AFV.YSTSQKI.RPGDSDD.R.VNSVLLFTILNPIYSITTDVLYT.CNPCGPVQRIVIFRK
Retrocopy NQIYIAGHAAFVSYSTSQKIFRPGDSDDFRRVNSVLLFTILNPIYSITTDVLYTVCNPCGPVQRIVIFRK

Parental  NGVQAMXXXXX--QSQRAKASLNGVDIHSGCCTLKIEYAKPTR-NV-KNDQCTSDYTNHHPSRQGDPGSN
          NGVQAM.........QRAKASLNG.DI.SGCCTLKIEYAKPTR.NV.KNDQ.T.DYTN...S.QGDPGSN
Retrocopy NGVQAMVEFDSLQSAQRAKASLNGADIYSGCCTLKIEYAKPTRLNVFKNDQDTWDYTNPNLSEQGDPGSN

Parental  PNKRQRQPPLLGDHPAEYGGPHGGYHSHYHDEGYGPPPPHYEGRRMGPPVGGHRRGPSRYGPQYGHPPPP
          ..K.QRQPPLLGDHP.EYGGPHGGYHSHY.DEGYG.PPPHYE.RRMGP.VGGHRRGPS...PQYG.PPP.
Retrocopy TSKYQRQPPLLGDHPTEYGGPHGGYHSHYRDEGYGSPPPHYEERRMGPLVGGHRRGPSHCSPQYGYPPPT

Parental  PPPPEYGPHADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEK-VKFMKSKPGAAMVEMADGYAVDRAITH
          PPPPEY.PH.DSPVLMVYGLD.SKMNCDRVFNVFCLYGNVEK.VKFMKSKPGAAMVEMAD.YAVD.A.TH
Retrocopy PPPPEYSPHSDSPVLMVYGLDKSKMNCDRVFNVFCLYGNVEK>VKFMKSKPGAAMVEMADSYAVDQAVTH

Parental  LNNNFMFGQKLNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNA
          LNNNFMF.QKL.VCVSKQPAI.PGQSY.LEDGS.SYKDF.ESRNNRFSTPEQAAKNRIQHPSNVLHFFNA
Retrocopy LNNNFMFRQKLTVCVSKQPAIIPGQSYRLEDGSRSYKDFGESRNNRFSTPEQAAKNRIQHPSNVLHFFNA

Parental  PLEVTEENFFEICDELGVKRPSSVKVFSGKSERSSSGLLEWESKSDALETLGFLNHYQMKNPNGPYPYTL
          PLEVTEENFFEICDELGVKRPSSVKVFSGKSERSSSGLL.WESKSDALETLGFLNHYQMK.PNG.Y.YTL
Retrocopy PLEVTEENFFEICDELGVKRPSSVKVFSGKSERSSSGLLVWESKSDALETLGFLNHYQMKTPNGSYWYTL

Parental  KLCFSTAQHAS
          KLCF.TAQHAS
Retrocopy KLCFFTAQHAS

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_1340 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1340 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000003779	1 retrocopy	retro_etel_886,
Nomascus leucogenys	ENSNLEG00000014696	1 retrocopy	retro_nleu_2327,
Pongo abelii	ENSPPYG00000009945	2 retrocopies	retro_pabe_1282, retro_pabe_3576,
Pan troglodytes	ENSPTRG00000010941	1 retrocopy	retro_ptro_1043,
Tupaia belangeri	ENSTBEG00000010797	1 retrocopy	retro_tbel_570,
Tupaia belangeri	ENSTBEG00000016563	1 retrocopy	retro_tbel_1340 ,