RetrogeneDB ID: retro_tbel_2134

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_101629:4441..5300(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000017599
• Aliases: None
• Description: None

Sequence

>retro_tbel_2134
CCTAGAGTCATTTCATTTGAGGATCAGGTTGCTTCCATAAGACAACATCTTGCATCCATATATGGGAAAGAAGAAGACTG
GAGAAATGCAGCCCAAGTGTTGGTGGGAATTCCTTTGGAAACAAGACAAGAATAGTATAATGTAGATTATAAACTGGACA
CTTACTTGAACATTGCTAGGTTATATCTGGAGGATGATGATGCTGTCCAGGCAGAGGTTTACATAAATCGAACATCATTG
CTTCAGAATGAATCAACAAATGAACGGTTACATATACATTATAAGGTATTCTATGTACGTGTTGTTGATTAAAGACAAAA
CTTCATTGAAGCTGCACAGCAGTACAAAGAGCTCTCGTACAAGATGATAGTCCATGAAAGTGAAAGACTAGAGGCCTTAA
AACATGCTTCGGACTGTACCATCTTAGCGTCAGCAGGACAGCAGCATTCTTGGATGCTGGCTACTCTTTTTAAGAATGAA
TGGTACCAGCAACTTGCTGCTTACAGGATCCTAGAGAAAATGTACCTAGACACGGATCCATCAGGAGGAAATCAGCTCCA
AGAATTTGCTGCCCATGTTGATGCCTCAACAAAAATGCACTATGACTGATGGTTCTAGCATCTTGGACAGAGCTGTTATT
GAATACAATTTGTTGTCTGCAAGCAAATTATATAATAATATCACCTTTGAAGAACTTGGAGCTCTTTTAGAGATTCCTGT
AGCTAAGATGGAAAAGAGATCATATCAAATGAGAACAGAAGGACGTATGAATAGATTCATTGACCAGATTGATGGAACAG
TTCATTTTGAAACACAAGAAGCACTGCCAACGTGGGACAAGCAGATCCAATCACGTTGT

Alignment

ORF - retro_tbel_2134 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.23 %
• Parental protein coverage: 75.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PRVISFEEQVASIRQHLASIYEKEEDWRNAAQVLVGIPLETGQKQYNVDYKLETYLKIARLYLEDDDPVQ
          PRVISFE.QVASIRQHLASIY.KEEDWRNAAQVLVGIPLET.Q..YNVDYKL.TYL.IARLYLEDDD.VQ
Retrocopy PRVISFEDQVASIRQHLASIYGKEEDWRNAAQVLVGIPLETRQE*YNVDYKLDTYLNIARLYLEDDDAVQ

Parental  AEAYINRASLLQNESTNEQLQIHYKVCYARVLDYRRKFIEAAQRYNELSYKTIVHESERLEALKHALHCT
          AE.YINR.SLLQNESTNE.L.IHYKV.Y.RV.D.R..FIEAAQ.Y.ELSYK.IVHESERLEALKHA..CT
Retrocopy AEVYINRTSLLQNESTNERLHIHYKVFYVRVVD*RQNFIEAAQQYKELSYKMIVHESERLEALKHASDCT

Parental  ILASAGQQRSRMLATLFKDERCQQLAAYGILEKMYLDRIIRG-NQLQEFAA-MLMPHQKATTADGSSILD
          ILASAGQQ.S.MLATLFK.E..QQLAAY.ILEKMYLD....G.NQLQEFAA.MLMP.QK.T..DGSSILD
Retrocopy ILASAGQQHSWMLATLFKNEWYQQLAAYRILEKMYLDTDPSGGNQLQEFAA>MLMPQQKCTMTDGSSILD

Parental  RAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVHFETREALPTWD
          RAVIE.NLLSASKLYNNITFEELGALLEIP.AK.EK...QM.TEGRMN.FIDQIDG.VHFET.EALPTWD
Retrocopy RAVIEYNLLSASKLYNNITFEELGALLEIPVAKMEKRSYQMRTEGRMNRFIDQIDGTVHFETQEALPTWD

Parental  -QIQSLC
          .QIQS.C
Retrocopy KQIQSRC

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_2134 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2134 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005067	2 retrocopies	retro_cjac_2148, retro_cjac_2345,
Equus caballus	ENSECAG00000015209	2 retrocopies	retro_ecab_315, retro_ecab_600,
Monodelphis domestica	ENSMODG00000019311	1 retrocopy	retro_mdom_824,
Mustela putorius furo	ENSMPUG00000014708	1 retrocopy	retro_mputfur_1010,
Otolemur garnettii	ENSOGAG00000027198	1 retrocopy	retro_ogar_3514,
Tupaia belangeri	ENSTBEG00000017599	2 retrocopies	retro_tbel_2134 , retro_tbel_53,