RetrogeneDB ID: retro_tbel_3503

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_142955:376..809(+)
• 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_3503
GACACCCGGTGCCTGATCATCAAGCCACGGAATCTGAATGATGCCTACGGCCTCCAAACAACTTCCTCAAGATCAACATG
AGCAACCCTCAGATGGTGGAGGTCGGCCGGGCTCCTTCACCACCTATGAAATCAGGGACAAAGACAAATCTTCCTATTTT
CAAGCTGAAAGAATCCACTGTTAGAAGAAAATACAGTGACTTTGAATGGCTGCAAAATGAATTAGAGAGAGCAAGGTTGT
AGTTCTTCCACTCCCTGGAAAAGCGTTTTTATGTCAACTATCTTTTAGAGGCAATGATGGAATATTTGATGACAATTTCA
TTGAGGAAAGGAAGCAAGGGCTGGAGCAATTTATAAACAAGGTTGTTGGTCATCCTCTGGCACAAAATGAATGTTGTCTT
CACATGTTTTTACAGGGTGAAATAATAAATAAA

Alignment

ORF - retro_tbel_3503 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78. %
• Parental protein coverage: 90.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DTRRLITKPQNLNDGYG-PPSNFLEIDVSNSQTVGVGR-GRFTTYEIR-VKTNLPIFKLKESTVRRRYSD
          DTR.LI.KP.NLND.YG.PP.NFL.I..SN.Q.V.VGR.G.FTTYEIR..KTNLPIFKLKESTVRR.YSD
Retrocopy DTRCLIIKPRNLNDAYG<PPNNFLKINMSNPQMVEVGR<GSFTTYEIR>TKTNLPIFKLKESTVRRKYSD

Parental  FEWLRSELER-ESKVVVPPLPGKAFLRQLPFRGDDGIFDDSFIEERKQGLEQFINKVAGHPLAQNERCLH
          FEWL..ELER....VV.P.LPGKAFL.QL.FRG.DGIFDD.FIEERKQGLEQFINKV.GHPLAQNE.CLH
Retrocopy FEWLQNELER<SKVVVLP-LPGKAFLCQLSFRGNDGIFDDNFIEERKQGLEQFINKVVGHPLAQNECCLH

Parental  MFLQDEIIDK
          MFLQ.EII.K
Retrocopy MFLQGEIINK

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_3503 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3503 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 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,