RetrogeneDB ID: retro_tbel_3402

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_139383:13100..13521(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DPCD
• Ensembl ID: ENSTBEG00000006817
• Aliases: None
• Description: deleted in primary ciliary dyskinesia homolog (mouse) [Source:HGNC Symbol;Acc:24542]

Sequence

>retro_tbel_3402
AGGAAGGGCACTTACATGTTCCCAAACAGGAAGGAAATGGCACAAGAATATGATGAGAACATGAGTGAACTACTTGTGAG
AAAGTAGCATGTCAAGAGTGCCCTGGGAGCCTTGGGCCTCTGGCAGCTCAAAGTGGGAGAGCCTGTACCCCTGGGAGCAG
AGAGCCTGGGGCCTGAACTCATCAAGGAAAGCAACACCAATCTCATTTTCGTGTGCTAGGACGCCAAGATGAATTTCCAG
TGACGAGCTGGAAACCTCCCTTACCCTAAAGATGTCTACAGTGTTCTGTTTGAACCAGAGAGAGCAGTGAGTCATTGTCA
GAATAACCAAGAAAGAGTACTACAAGAAGTTCTCCATTCCCAACTTAGACAGATAACAGCTGCCTCTGGTTGATTCCTCA
GTGAGCTTTGCTCATGCTAAC

Alignment

ORF - retro_tbel_3402 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.63 %
• Parental protein coverage: 77.35 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RKVHYLFPDGKEMAEEYDEKTSELLVRKWRVKSALGALGQWQLEVGEPAPPGAGSLGPELIKESNANPIF
          RK..Y.FP..KEMA.EYDE..SELLVRK..VKSALGALG.WQL.VGEP.P.GA.SLGPELIKESN.N.IF
Retrocopy RKGTYMFPNRKEMAQEYDENMSELLVRK*HVKSALGALGLWQLKVGEPVPLGAESLGPELIKESNTNLIF

Parental  MRKDTKMSFQWRIRNLPYPKDVYSV-CVDQKERCIIVRTTNKKYYKKFSIPDLDRHRLPLDDSSLSFAHA
          ...D.KM.FQ.R..NLPYPKDVYSV.C..Q.E...IVR.T.K.YYKKFSIP.LDR..LPL.DSS.SFAHA
Retrocopy VC*DAKMNFQ*RAGNLPYPKDVYSV>CLNQREQ*VIVRITKKEYYKKFSIPNLDR*QLPLVDSSVSFAHA

Parental  N
          N
Retrocopy N

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_3402 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3402 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
Procavia capensis	ENSPCAG00000004838	1 retrocopy	retro_pcap_147,
Tupaia belangeri	ENSTBEG00000006817	1 retrocopy	retro_tbel_3402 ,