RetrogeneDB ID: retro_tbel_1468

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_482:58937..59801(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDE1
• Ensembl ID: ENSTBEG00000005260
• Aliases: None
• Description: nudE nuclear distribution E homolog 1 (A. nidulans) [Source:HGNC Symbol;Acc:17619]

Sequence

>retro_tbel_1468
GCAGAGAATACACAGGAGGAACTTAGAGAATTCCAGAAGGGAAGCCAAGAATATGAAGCTGAATTGGAGACGCAGTTGCA
ACAGATTGAAATCAGGAACAGAGACCTCATTTCAGAAAATAACCGCCTTCGCATGGAGCTGGAAACCATCAAGGAGAAGT
TTGAGATGCAGCATTCCGAGGGTTACTGGCAGATCTCAGCTTTAGAAGATGACCTTGCCCAGACAAAAGCGATTAAAGAT
CAACTGCAGAAATACATCCGAGAGCTGGAGCAAGCCAATGATGACTTGGAAAGGGCCAAACGAGCCATGATCATGTCTCT
GGAAGACTTTGAGCAGCGCCTGAATCAAGCCATCGAAAGAAATGCCTTCCTGGAAAGCGAGCTTGACGAGAAGGAGAATC
TCCTGGAATCTGTGCAGCGATTGAAGGATGAAGCCAGAGATTTGCGGCAGGAGCTGGCGGTGCAGCAGAAGCAGGACAAA
CCCCGGACCCCCATAGCCAGCTCAGCAGCCACTGAACGGACAGACACAGCTGTACAAGACACTGGCTCCATGCCTTCCAC
TCCCATAGCTCATCGAGGACCTGGCTCTAGTTTAAACACACCAGGCACATTCAGACGTGGTCTAGACGACTCCACAGGCG
GGACCCCCCCTCACGCCTGTGGCCCGAATATCTGCGCTCAACATCATGGGTGACCTGCTGCGGAAGTAGGGGCACTGGAA
TCCAAATTGGCATCCTGCCAGAACTTCGTATAAGATCTGTCCCCAAACCAAACGAGTGGCCCAAACCCGGGACGAGCGAA
CAAGAACTGAGACAGCAGTGACAGGCGGCTGAGCGGCACCAGCGTGCCCTTGGGCGATAAAGGG

Alignment

ORF - retro_tbel_1468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.07 %
• Parental protein coverage: 93.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AENTQEELREFQEGSREYEAELETQLQQIETRNRDLLSENNRLRMELETIKEKFEMQHSEGYRQISALED
          AENTQEELREFQ.GS.EYEAELETQLQQIE.RNRDL.SENNRLRMELETIKEKFEMQHSEGY.QISALED
Retrocopy AENTQEELREFQKGSQEYEAELETQLQQIEIRNRDLISENNRLRMELETIKEKFEMQHSEGYWQISALED

Parental  DLAQTKAIKDQLQKYIRELEQANDDLERAKRATIMSLEDFEQRLNQAIERNAFLESELDEKENLLESVQR
          DLAQTKAIKDQLQKYIRELEQANDDLERAKRA.IMSLEDFEQRLNQAIERNAFLESELDEKENLLESVQR
Retrocopy DLAQTKAIKDQLQKYIRELEQANDDLERAKRAMIMSLEDFEQRLNQAIERNAFLESELDEKENLLESVQR

Parental  LKDEARDLRQELAVQQKQDKPRTPMPSSAATERTDTAVQATGSVPSTPIAHRGPGSSLNTPGTFRRGLDD
          LKDEARDLRQELAVQQKQDKPRTP..SSAATERTDTAVQ.TGS.PSTPIAHRGPGSSLNTPGTFRRGLDD
Retrocopy LKDEARDLRQELAVQQKQDKPRTPIASSAATERTDTAVQDTGSMPSTPIAHRGPGSSLNTPGTFRRGLDD

Parental  STGGT-PLTPAARISALNIVGDLLRK-VGALESKLASCRNFVYDQSPNRTSGLNPGRANKNRDSGDRWQS
          STGGT.PLTP.ARISALNI.GDLLRK.VGALESKLASC.NFV.D.SPN.TSG.NPGRANKN.DS.DR..S
Retrocopy STGGT>PLTPVARISALNIMGDLLRK<VGALESKLASCQNFV*DLSPNQTSGPNPGRANKN*DSSDRRLS

Parental  GTSVPLGDKG
          GTSVPLGDKG
Retrocopy GTSVPLGDKG

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_1468 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1468 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
Ailuropoda melanoleuca	ENSAMEG00000009557	1 retrocopy	retro_amel_104,
Canis familiaris	ENSCAFG00000018722	1 retrocopy	retro_cfam_1579,
Choloepus hoffmanni	ENSCHOG00000006004	1 retrocopy	retro_chof_1270,
Cavia porcellus	ENSCPOG00000019614	2 retrocopies	retro_cpor_875, retro_cpor_876,
Ictidomys tridecemlineatus	ENSSTOG00000019896	1 retrocopy	retro_itri_1101,
Tupaia belangeri	ENSTBEG00000005260	1 retrocopy	retro_tbel_1468 ,