RetrogeneDB ID: retro_tbel_4529

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_88453:484..812(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAPPC6B
• Ensembl ID: ENSTBEG00000003331
• Aliases: None
• Description: trafficking protein particle complex 6B [Source:HGNC Symbol;Acc:23066]

Sequence

>retro_tbel_4529
AGGTTTACAAAAGATACTGCAAGGTTCAAGGATGAGTTAGATTATCTTGAAGCTCATTTGTAAAGATTTTTGGACTACAG
TATTCAAGAAACAGATTGACAATCTAAGGACAAATCATCAGGGCATCTATATACTTCAGGACAACAAATTTCATCTGCTT
ACTCAGATATATGCAGGAGAGCAGTATTTAGAACATGCATCTAAGTACTTAGCATTTACATACAGTTTAATCAGATGAGG
CTTATCAAACTTGGGGAAAAAAAGTATTGTTACTGCTGCAGTATCTTCTATGCTTGCCTGCAAATTTCAGGTGATGATAC
AGAAGCTG

Alignment

ORF - retro_tbel_4529 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.36 %
• Parental protein coverage: 68.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RFTKDTARFKDELD-IMKFICKDFWTTVFKKQIDNLRTDHQGIYVLQDNKFRLLTQMSAGKQYLEHASKY
          RFTKDTARFKDELD.I.K.ICKDFWTTVFKKQIDNLRT.HQGIY.LQDNKF.LLTQ..AG.QYLEHASKY
Retrocopy RFTKDTARFKDELD>ILKLICKDFWTTVFKKQIDNLRTNHQGIYILQDNKFHLLTQIYAGEQYLEHASKY

Parental  LAFTCGLIRGGLSNLGIKSIVTAEVSSMPACKFQVMIQKL
          LAFT..LIR.GLSNLG.KSIVTA.VSSM.ACKFQVMIQKL
Retrocopy LAFTYSLIR*GLSNLGKKSIVTAAVSSMLACKFQVMIQKL

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_4529 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4529 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000013828	1 retrocopy	retro_etel_1104,
Myotis lucifugus	ENSMLUG00000002627	2 retrocopies	retro_mluc_1179, retro_mluc_663,
Mus musculus	ENSMUSG00000020993	2 retrocopies	retro_mmus_1734, retro_mmus_2069,
Oryctolagus cuniculus	ENSOCUG00000002171	1 retrocopy	retro_ocun_813,
Sarcophilus harrisii	ENSSHAG00000001400	1 retrocopy	retro_shar_235,
Ictidomys tridecemlineatus	ENSSTOG00000002897	2 retrocopies	retro_itri_476, retro_itri_795,
Tupaia belangeri	ENSTBEG00000003331	1 retrocopy	retro_tbel_4529 ,