RetrogeneDB ID: retro_tbel_531

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_2356:74211..74883(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC35C2
• Ensembl ID: ENSTBEG00000005486
• Aliases: None
• Description: solute carrier family 35 (GDP-fucose transporter), member C2 [Source:HGNC Symbol;Acc:17117]

Sequence

>retro_tbel_531
CGTGCTGCCCTGGTCCTGGTGTTCCTCCTCATCCCTGGGGGCCTCTTCCTGTTCACCTGCAAGTCCACGCAGTTCAACAT
GGAGGGCTTCACCTTGGTGCTGGGGACTTCCTTCATCAGTGGCATTTGTTGGACCCTACCCAGAAGCTCTTGCAGAAGGC
TGAACTCAGCCTCCAGAATCAATACCATGTCCCACTTGCAACCACTCATGTTCCTGGAGCTCTTCCCTTTCTTTGTTGTG
TTTGAAGGTGTCCATTTGTCCACATATGAGAAAATCTTCCATTTCCAGAATGCAAGGTTGCTCCTTGAATCCTTGGGAAC
CACTTCCTTGGAGGGACTCTCACCTTTGGTTTGGGTTTCTCTGAGTTCCTCCTAGTCTCCAGGACCTCCAGCCTCACTCT
CTCCACAGCTGGCACCTTTAAGAAAGTCTGCACTTTGCTGTTGGCAGTTCATCTGCTGGGCGATCAGATCAGCCTCCTGA
AATGGCTTGGCTTTGCCCTCCATCTCTCTGGAATATCCCTGCATGTCACCCTCAAAGCCCTGCACCCCAGAGGTGAGGCC
CAAAACCCTTGAAAGGGATGGGCTCCAGCCTGGACCTGGAGCTGCTGTTCCAGATCAGCCAATAAGAGGATGATGACAAT
GAGGAGAAGTACTTTAAGGCCCAGGACAGCAG

Alignment

ORF - retro_tbel_531 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.13 %
• Parental protein coverage: 63.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RAALVLVVLLIAGGLFMFTYKSTQFNLEGFALVLGASFIGGIRWTLTQMLLQKAELGLQNPIDTMFHLQP
          RAALVLV.LLI.GGLF.FT.KSTQFN.EGF.LVLG.SFI.GI.WTL.........L.....I.TM.HLQP
Retrocopy RAALVLVFLLIPGGLFLFTCKSTQFNMEGFTLVLGTSFISGICWTLPRSSCRR--LNSASRINTMSHLQP

Parental  LMFLGLFPLFAVFEGLHLSTSEKIFRFQDAGLLLR-VLGSLFLGGILAFGLGFSEFLLVSGTSSLTLXXX
          LMFL.LFP.F.VFEG.HLST.EKIF.FQ.A.LLL...LG..FLGG.L.FGLGFSEFLLVS.TSSLTL...
Retrocopy LMFLELFPFFVVFEGVHLSTYEKIFHFQNARLLLE<ILGNHFLGGTLTFGLGFSEFLLVSRTSSLTLSTA

Parental  XXXXEVCTLLLAAHLLGDQISLLNWLGFALCLSGISLHIALKALHSKGDS-PKPLKGMGSSPDLELLLRS
          .....VCTLLLA.HLLGDQISLL.WLGFAL.LSGISLH..LKALH..G...PKPLKGMGSS.DLELL...
Retrocopy GTFKKVCTLLLAVHLLGDQISLLKWLGFALHLSGISLHVTLKALHPRGEA<PKPLKGMGSSLDLELLFQI

Parental  SQQDDEDNEEEKYFVAQ-GQQ
          SQ..D.DN.EEKYF.AQ.GQQ
Retrocopy SQ*EDDDN-EEKYFKAQ<GQQ

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_531 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_531 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011583	2 retrocopies	retro_chof_2686, retro_chof_952,
Callithrix jacchus	ENSCJAG00000017091	1 retrocopy	retro_cjac_4140,
Homo sapiens	ENSG00000080189	1 retrocopy	retro_hsap_4789,
Gorilla gorilla	ENSGGOG00000014052	1 retrocopy	retro_ggor_2982,
Nomascus leucogenys	ENSNLEG00000006880	1 retrocopy	retro_nleu_1104,
Pongo abelii	ENSPPYG00000011091	1 retrocopy	retro_pabe_3726,
Pan troglodytes	ENSPTRG00000013582	1 retrocopy	retro_ptro_3186,
Tupaia belangeri	ENSTBEG00000005486	1 retrocopy	retro_tbel_531 ,