RetrogeneDB ID: retro_tbel_923

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3313:447501..447924(+)
• Located in intron of: ENSTBEG00000007639

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRNAU1AP
• Ensembl ID: ENSTBEG00000008049
• Aliases: None
• Description: tRNA selenocysteine 1 associated protein 1 [Source:HGNC Symbol;Acc:30813]

Sequence

>retro_tbel_923
GAGTACTTGCTCTTTGTAGGGGATCTGACCCTAGACATGGATGACAGCAGGCTGTATCAGTTTTTTGTCAAGGTCTATCC
CACTTGTCCCGGAAGCAAGGTGATTTTAGACCAGACAGGCATGTCTAAGGGTTATGGTTTTGTGAAATTCACGGATGAAC
TGGGATAGAAGCGAGCCCTGACGGAGTGCCAGGGAGCAGTAGGTCTGGTGTCCAAGCCCGTGCGTCTTAGCGTGGCAATT
CTCAAAGCGAGCTGTGTGAAGCCAGTGGAATACAGTCAGATGTACAGCTACAGCTACCACCAGCACTACCAGCAGTACCA
GAACTATTCCCAGTGGGACTACGACCAGAACACCAACAGCGACAGCTACCTGCAATACGGCTACACGCAGAGCACCATGC
ATATGTACAAAGCTCTGGAAGAC

Alignment

ORF - retro_tbel_923 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.69 %
• Parental protein coverage: 58.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EYSLFVGDLTPDVDDGVLYEFFVKVYPSC-GGKVILDQAGVSKGYGFVKFTDELEQKRALTECQGAVGLG
          EY.LFVGDLT.D.DD..LY.FFVKVYP.C.G.KVILDQ.G.SKGYGFVKFTDEL..KRALTECQGAVGL.
Retrocopy EYLLFVGDLTLDMDDSRLYQFFVKVYPTCPGSKVILDQTGMSKGYGFVKFTDELG*KRALTECQGAVGLV

Parental  SKPVRLSVAIPKASRVKPVEYSQMYSYSYSQYYQHCQSYYAQWGYDQNTGSYSYSYPQYGYTQSTMQTYE
          SKPVRLSVAI.KAS.VKPVEYSQMYSYSY.Q.YQ..Q..Y.QW.YDQNT.S.SY...QYGYTQSTM..Y.
Retrocopy SKPVRLSVAILKASCVKPVEYSQMYSYSYHQHYQQYQN-YSQWDYDQNTNSDSYL--QYGYTQSTMHMYK

Parental  EVGD
          ...D
Retrocopy ALED

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_923 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_923 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011367	1 retrocopy	retro_amel_1782,
Callithrix jacchus	ENSCJAG00000009717	1 retrocopy	retro_cjac_3928,
Equus caballus	ENSECAG00000012980	1 retrocopy	retro_ecab_452,
Mustela putorius furo	ENSMPUG00000015511	2 retrocopies	retro_mputfur_1185, retro_mputfur_856,
Pelodiscus sinensis	ENSPSIG00000006864	1 retrocopy	retro_psin_41,
Tupaia belangeri	ENSTBEG00000008049	1 retrocopy	retro_tbel_923 ,