RetrogeneDB ID: retro_tbel_3929

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_40438:580..900(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX3
• Ensembl ID: ENSTBEG00000011755
• Aliases: None
• Description: sorting nexin 3 [Source:HGNC Symbol;Acc:11174]

Sequence

>retro_tbel_3929
TCACTGTATCTGTTCACACATATGTCTTCAACACGTGTTCAAAATAACAGTGACTTTGAAGCGCTGCAAAGTGAATTAGA
AAAAGAGAGTAAGGTTGTAGTCCCCCGCTCCCTGGGAAAGCTTTCTTATGTCAAATTCCTTTTAGAGGAGAGGATGGAAT
ATCTGTTGATAATTTTACTGAGGAAAGGAAGCAAAGGCTGGAGCAATTTATAAACAAGGTCGCTGGTCATTCTTTGGCAC
AAAACGAATGTTGTCTTCACTTGTTTTTACAGGATGAGATAATAGATAAAAGCTATATTCCATCCAAAATAAGACATGCC

Alignment

ORF - retro_tbel_3929 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.07 %
• Parental protein coverage: 66.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NLPIFKLKESTVRRRYSDFEWLRSELERESKVVVP-PLPGKAFLRQLPFRGDDGIFDDSFIEERKQGLEQ
          .L..F....ST.....SDFE.L.SELE.ESKVVVP.PLPGKAFL.Q.PFRG.DGI..D.F.EERKQ.LEQ
Retrocopy SLYLFTHMSSTRVQNNSDFEALQSELEKESKVVVP<PLPGKAFLCQIPFRGEDGISVDNFTEERKQRLEQ

Parental  FINKVAGHPLAQNERCLHMFLQDEIIDKSYTPSKIRHA
          FINKVAGH.LAQNE.CLH.FLQDEIIDKSY.PSKIRHA
Retrocopy FINKVAGHSLAQNECCLHLFLQDEIIDKSYIPSKIRHA

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_3929 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3929 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000015256	1 retrocopy	retro_eeur_525,
Echinops telfairi	ENSETEG00000003537	3 retrocopies	retro_etel_1331, retro_etel_645, retro_etel_924,
Felis catus	ENSFCAG00000024997	1 retrocopy	retro_fcat_1705,
Loxodonta africana	ENSLAFG00000018131	1 retrocopy	retro_lafr_579,
Oryctolagus cuniculus	ENSOCUG00000005858	2 retrocopies	retro_ocun_1022, retro_ocun_750,
Tupaia belangeri	ENSTBEG00000011755	3 retrocopies	retro_tbel_2964, retro_tbel_3503, retro_tbel_3929 ,
Tursiops truncatus	ENSTTRG00000008868	2 retrocopies	retro_ttru_1028, retro_ttru_1103,