RetrogeneDB ID: retro_tbel_596

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_2527:17653..18048(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL11
• Ensembl ID: ENSTBEG00000007838
• Aliases: None
• Description: ribosomal protein L11 [Source:HGNC Symbol;Acc:10301]

Sequence

>retro_tbel_596
ATGGCACAAGATCAGGGTGAAAAGAAGAACCCCACACAGGAAGTTATTTCCATAAGCTGTACCTCAACATCTGTGTGGGG
GAGAGTGAAGCCAGACTGCCCTGAGCAGCCAAAGTGCTGGAGCAGCTCACAGGCCAGAGCCCTGAGTTTTCCAAAGTTAC
ATACACTGTCAGATCCTTTGGCATTAGGAGATATGAGAAGATTGCTGTCCACTGCCCAGTCTGTGGGGCCAAGGCAGAAG
AAATTCTGGAAAAAGGTTTAAGGGTATGGGATTATGAGTTATGAAACAATAACTTCTGAGATACTGGAAACTTTGGTTTT
GGGATCCAGGAACACATCGATCTGGGGATCGAATATACCCCAAGCATTGGTAGCTACGGCCTGGGTTTCTATGTG

Alignment

ORF - retro_tbel_596 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.69 %
• Parental protein coverage: 74.16 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAQDHGEKENPMREL-RIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSFGIRRNEKIA
          MAQD.GEK.NP..E.....KL.LNICVGES..RL..AAKVLEQLTGQ.P.FSK..YTVRSFGIRR.EKIA
Retrocopy MAQDQGEKKNPTQEV<YFHKLYLNICVGESEARLP*AAKVLEQLTGQSPEFSKVTYTVRSFGIRRYEKIA

Parental  VHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYDPSIGIYGLDFYV
          VHC.V.GAKAEEILEKGL.V..YEL..NNF.DTGNFGFGIQEHIDLGI.Y.PSIG.YGL.FYV
Retrocopy VHCPVCGAKAEEILEKGLRVWDYEL*NNNF*DTGNFGFGIQEHIDLGIEYTPSIGSYGLGFYV

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_596 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_596 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 6 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013232	2 retrocopies	retro_cfam_1059, retro_cfam_543,
Gorilla gorilla	ENSGGOG00000014628	6 retrocopies	retro_ggor_1192, retro_ggor_1325, retro_ggor_1690, retro_ggor_2204, retro_ggor_533, retro_ggor_603,
Macaca mulatta	ENSMMUG00000002445	3 retrocopies	retro_mmul_2039, retro_mmul_2415, retro_mmul_2462,
Mus musculus	ENSMUSG00000059291	3 retrocopies	retro_mmus_144, retro_mmus_146, retro_mmus_78,
Rattus norvegicus	ENSRNOG00000026260	9 retrocopies	retro_rnor_1735, retro_rnor_2287, retro_rnor_2314, retro_rnor_2690, retro_rnor_271, retro_rnor_2725, retro_rnor_668, retro_rnor_795, retro_rnor_919,
Tupaia belangeri	ENSTBEG00000007838	5 retrocopies	retro_tbel_2850, retro_tbel_3023, retro_tbel_3273, retro_tbel_4736, retro_tbel_596 ,