RetrogeneDB ID: retro_tbel_4170

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_69872:4746..5042(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000006575
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC31A1
• Ensembl ID: ENSTBEG00000009011
• Aliases: None
• Description: solute carrier family 31 (copper transporter), member 1 [Source:HGNC Symbol;Acc:11016]

Sequence

>retro_tbel_4170
CATCACCTGGCCACCACAGCCTCACATTCTCATGGGAGAGGAGACATGATGATAATGATTTATGACCTTCTACTTTGACT
TTAAGAATGCAGAACTATTATTTTCCGGTTTAGGGATGAATACAGCTGGAGAAATGCCTGGAGCTTTTGTGGCAGTGTTT
TCAGTAGCAATATTCTATAAAGGGCTCAAGGTAGCTGGGGAAAGCCTGCCGCGAAAGCAACAATTCGGTGTTCACTACAG
TTCCATGCCTGTCCCAGGACAAATGGAACCATCCTAGGGAGACACACACCATTGTC

Alignment

ORF - retro_tbel_4170 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.9 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HHPATT-SHSHGGGDMMMMMP-MTFYFGFKNVELLFSGLVINTAGEMAGAFVAVFLLAMFYEGLKIARES
          HH.ATT.SHSHG.GDM.M.M..MTFYF.FKN.ELLFSGL..NTAGEM.GAFVAVF..A.FY.GLK.A.ES
Retrocopy HHLATTASHSHGRGDM-MIMI>MTFYFDFKNAELLFSGLGMNTAGEMPGAFVAVFSVAIFYKGLKVAGES

Parental  LLRKSQVSIRYNSMPVPG-PNGTIL-METHKTV
          L.RK.Q....Y.SMPVPG..NGTIL..ETH..V
Retrocopy LPRKQQFGVHYSSMPVPG<TNGTIL<RETHTIV

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_4170 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4170 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 9 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011908	5 retrocopies	retro_chof_1186, retro_chof_1646, retro_chof_1661, retro_chof_644, retro_chof_776,
Felis catus	ENSFCAG00000005512	1 retrocopy	retro_fcat_425,
Macropus eugenii	ENSMEUG00000015425	2 retrocopies	retro_meug_1049, retro_meug_1533,
Microcebus murinus	ENSMICG00000015008	2 retrocopies	retro_mmur_1465, retro_mmur_46,
Myotis lucifugus	ENSMLUG00000015299	1 retrocopy	retro_mluc_2,
Nomascus leucogenys	ENSNLEG00000016636	1 retrocopy	retro_nleu_622,
Pongo abelii	ENSPPYG00000019514	3 retrocopies	retro_pabe_2386, retro_pabe_3548, retro_pabe_847,
Sorex araneus	ENSSARG00000012787	7 retrocopies	retro_sara_101, retro_sara_326, retro_sara_497, retro_sara_584, retro_sara_585, retro_sara_586, retro_sara_730,
Tupaia belangeri	ENSTBEG00000009011	2 retrocopies	retro_tbel_3123, retro_tbel_4170 ,