RetrogeneDB ID: retro_tbel_2337

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_109198:46475..46990(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CARKD
• Ensembl ID: ENSTBEG00000007624
• Aliases: None
• Description: carbohydrate kinase domain containing [Source:HGNC Symbol;Acc:25576]

Sequence

>retro_tbel_2337
CACATAGTACAGGGTATGGAGAATACCTTTCGGCTGATGGGGAATCTCCTCCCTCACTAACTGCCAAGAAGCCTATGGGG
CAAGACAGGAAATAGGTGGAGTGGAGACTATTGGGGATATACTGGAGTCCCAAAATTTGTGGCAATCTCAGCTCTCAAAG
TGGGTGCAGATTTGTCCCATGTGTCCTGTGCCAGGCAGGCTGCACTTGTGAGCAAGTCCGACAGCCTGGAGCTGAGCTTC
CACCCAGTTCTTGACAGCCCTCATGCCTTTCTTGAGATGGGAAAGTGGCTACCATACTGCATGCCCTTGTCATTGGGCCC
GGGTTAGGTGGAGAAGACATCCTTCTTAAAAATATGTCGTGAACATTTTGGAAGTCAAAGGCCTAGGACATCCACGTTGT
CATCGAAGCAGGTGGCCTGGGACTGGTGGTTCAGCTTTCGGCCCTCATGTAGGGCTACCAGAAAGCTGTTCTCACCCCCA
ACCACATGGAGTTCGGCAGACTCTACGAAGCTGTG

Alignment

ORF - retro_tbel_2337 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.41 %
• Parental protein coverage: 50.44 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  HSVQDMEDTFQLVRSVIP-PLTATKHKGQDGR-IGVV-GGCQEYTGAPYFAAISALKVGADLSHVFCARE
          H.VQ.ME.TF.L.....P..LTA.K..GQD...IG.V.G....YTG.P.F.AISALKVGADLSHV.CAR.
Retrocopy HIVQGMENTFRLMGNLLP<SLTAKKPMGQDRK<IGGV<GDYWGYTGVPKFVAISALKVGADLSHVSCARQ

Parental  AALVIKSYSPELIVHPVLDSPNAALEVQKWLPR-LHALVVGPGLGRDDALLKTVVDILEVSKARDIPIVI
          AALV.KS.S.EL..HPVLDSP.A.LE..KWLP..LHALV.GPGLG..D.LLK........SKA.DI..VI
Retrocopy AALVSKSDSLELSFHPVLDSPHAFLEMGKWLPY<LHALVIGPGLGGEDILLKNMS*TFWKSKA*DIHVVI

Parental  DADGLWLVAQQPALVQGYQKAVLTPNHMEFSRLYEAV
          .A.GL.LV.Q..AL..GYQKAVLTPNHMEF.RLYEAV
Retrocopy EAGGLGLVVQLSALM*GYQKAVLTPNHMEFGRLYEAV

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_2337 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2337 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Tupaia belangeri	ENSTBEG00000007624	1 retrocopy	retro_tbel_2337 ,