RetrogeneDB ID: retro_tbel_1224

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4142:947..1816(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNL3
• Ensembl ID: ENSTBEG00000017518
• Aliases: None
• Description: guanine nucleotide binding protein-like 3 (nucleolar) [Source:HGNC Symbol;Acc:29931]

Sequence

>retro_tbel_1224
TTCCCAAATGTGGGGAAAAGCAGCAGCATCAATAGCTTAAAACAAGAAAGGATATGCAATGTTGGTGTATCCATGGGACT
TACAAGGAGCATGCAGGCTGTCCCCTTGGACAAACAGATTACAGTCATAGACAGTCCATGCCTCATTGTCTCTCCACTTA
ACTCTTCCGCTGCACTTGCTCTACGAAGTTCAGCAAGTATTGAAGCAGTAAGGCCAGTAGAGACTGCCAGTGCCATCCTT
TCCCAGGCTGATACTCGACAGGTAGTACTGAAATACAATGGCCCAGACTATAAGGATTCACTGGAGTTTCTCACTATGCT
TGCTCAGAGAAGAGGTCTACACCAAAAAGGGGGAAGCCCAAATGTTAAACATGCTGCTAAACTGCTATGGTCTGAGTGGA
TATGTGCCTCTTTAGGTTACTGTTGCATGCCCCCACATCCTGGACTCCTCCTCCACATCTTAATAAGAGTTTCATGGCAG
ACTTGAAATGGGGCTTTAATCTGGAAGAACTGGAAAACAACAACGCACACAGCAAACAAGCCATCAGCGGTCCTCGTTTA
GCCAATAGCATCCTTTTCCAGTCCTTGGGTCTGACAAACGGGATAACAGAGGAAAAGGATATACCTGAAGGATTGCCAAA
ACAAAAACAGAAGAAACAGGAGGAAAAGGAGGAGGGTGAAGACATGAACAGTGACCAGGAAAGTGTGGATGCAGAAGTGG
ACGAAAGGGCTTCAAACACATCCCCTACAGAAGAGACATGGGTGGCACAGCCTGAAGAGTCCATACCAGGTAACCAGTCT
ACAAGATCTTTTATCTTGGATAAAGTGACTGAAGAGGATGATGTTTATGACTTTAGTACAGATTATGTG

Alignment

ORF - retro_tbel_1224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.75 %
• Parental protein coverage: 54.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FPNVGKSSIINSLKQERICNVGVSMGLTRSMQVVPLDKQITVIDSPCLIVSPLNSSAALALRSPASIEAV
          FPNVGKSS.INSLKQERICNVGVSMGLTRSMQ.VPLDKQITVIDSPCLIVSPLNSSAALALRS.ASIEAV
Retrocopy FPNVGKSSSINSLKQERICNVGVSMGLTRSMQAVPLDKQITVIDSPCLIVSPLNSSAALALRSSASIEAV

Parental  RPVEAASAILSQADTRQVVLKYNVPDYKNSLEFLTMLAQRRGLHQKGGSPNVERAAKLLWSEWTGASLGY
          RPVE.ASAILSQADTRQVVLKYN.PDYK.SLEFLTMLAQRRGLHQKGGSPNV..AAKLLWSEW..ASLGY
Retrocopy RPVETASAILSQADTRQVVLKYNGPDYKDSLEFLTMLAQRRGLHQKGGSPNVKHAAKLLWSEWICASLGY

Parental  YC-HAPTSWTPPPHLNESIMADMKWGFNLEELEKNNAHSIQAIRGPRLANSILFQSLGLTNGVTEEKDIP
          .C.HAPTSWTPPPHLN.S.MAD.KWGFNLEELE.NNAHS.QAI.GPRLANSILFQSLGLTNG.TEEKDIP
Retrocopy CC<HAPTSWTPPPHLNKSFMADLKWGFNLEELENNNAHSKQAISGPRLANSILFQSLGLTNGITEEKDIP

Parental  EGLPKPKQKKQEEKEEDEDMNSDQESVDAEVDERASNTSPAEETWVAQPEESVPGNQSGRSFILDKVTEE
          EGLPK.KQKKQEEKEE.EDMNSDQESVDAEVDERASNTSP.EETWVAQPEES.PGNQS.RSFILDKVTEE
Retrocopy EGLPKQKQKKQEEKEEGEDMNSDQESVDAEVDERASNTSPTEETWVAQPEESIPGNQSTRSFILDKVTEE

Parental  DDVYDFSTDYV
          DDVYDFSTDYV
Retrocopy DDVYDFSTDYV

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

1 EST(s) were mapped to retro_tbel_1224 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CF525768	1211	1480	98.6	265	4	261

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1224 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002726	1 retrocopy	retro_chof_1239,
Tupaia belangeri	ENSTBEG00000017518	1 retrocopy	retro_tbel_1224 ,