RetrogeneDB ID: retro_tbel_2188

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_104016:5513..6406(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5C2
• Ensembl ID: ENSTBEG00000017707
• Aliases: None
• Description: 5'-nucleotidase, cytosolic II [Source:HGNC Symbol;Acc:8022]

Sequence

>retro_tbel_2188
ACTAATTGTCCAAGATATACCAGCTGTGAAACAGGGTTTAAAGATGGGGACTTCTTCATGTCCTACTGGAGTATGTTCTA
GGATGTAGAGATGCTGTTGACTAGGTTTATGACAAGAGTTCTCTTAAAGAAAAAAAAGTTGAAAATCTTGAGAAGTATGT
AGTCAAAGATGGAAAATTTCCTTTGCTTCTGAGCCAGATGAAGGAAGTATGGAAAGTATTTCCTGCCACCAACAGTGACT
ATAAATGTACAGATAAAATTATTACTTACCTGTTTGATTTCCCATGTGGCTTTAAGCCTGGTAGCTCCCATTGACCATGG
CTTTCCTACTTTGACTAGATTTTGGTGGATGCCTGGAAACTCCTTTTTTGGAGAGGCACAGTACTGCATCAAGTGGATAC
TAAAATTGGCAAGCTGAGACTTGGTACTTACACAGGCCCCCTACAGCATGGCATTGTGTACTCAGGAGGCTCATGTGATG
CAATCTGTGATCTCTTGGGAGTCAAGGGCAAAGACATATTGTACATTGGAGATCACATTTTTGGGGACATTTTAAAATCA
AAGAAATGGCAAGGGTGGCAAACTTTCTTGGTGATTCCTGAACTTGCACAAGAGCTGCATATCTGGACAGACAAGAGTTC
CCTTTTTGAAGAGCTTCAGAGGTTGGATGTTTTCTTGGTGGAACATTATAAGCACCTCGATAGCAGTAGTAATGAGTGCC
CAGACATTAATTCCATCCAGAGATATATTAAGAAATTCACTCATGACATGGACATGTGCTACAGGATGATGGGAAGCCTG
ATCCACAGCAGCTCCCGGCAGACCCTGTTTGCCAGTCAAGTGATGTGATATGCCAACCTCTACACAGCATCATTCATCAA
CCTGTTGTATTAC

Alignment

ORF - retro_tbel_2188 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.0 %
• Parental protein coverage: 56.34 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TNCPRYTSCETGFKDGDLFMSYRSMFQDV-RDAVDWVHYKGSLKEKTVENLEKYVVKDG--PLL--SMK-
          TNCPRYTSCETGFKDGD.FMSY.SMF.DV.RDAVD.V..K.SLK...VENLEKYVVKDG..PLL...MK.
Retrocopy TNCPRYTSCETGFKDGDFFMSYWSMF*DV<RDAVD*VYDKSSLKXXXVENLEKYVVKDGKFPLLLSQMKE

Parental  VGKVFLA-NSDYKYTDKIMTYLFDFPHGPKPGSSHRPWQSYFDLILVDARKPLFFGEGTVLRQVDTKTGK
          V.KVF.A.NSDYK.TDKI.TYLFDFP.G.KPGSSH.PW.SYFD.ILVDA.K.LF...GTVL.QVDTK.GK
Retrocopy VWKVFPATNSDYKCTDKIITYLFDFPCGFKPGSSH*PWLSYFD*ILVDAWKLLFW-RGTVLHQVDTKIGK

Parental  LKIGTYTGPLQHGIVYSGGSSDTICDLLG-KGKDILYIGDHID---IKSKKRQGWRTFLVIPELAQELHV
          L..GTYTGPLQHGIVYSGGS.D.ICDLLG.KGKDILYIGDHI.....KSKK.QGW.TFLVIPELAQELH.
Retrocopy LRLGTYTGPLQHGIVYSGGSCDAICDLLGVKGKDILYIGDHIFGDILKSKKWQGWQTFLVIPELAQELHI

Parental  WTDKSALFEELQSLDIFLAELYKHLDSSSNERPDISSIQRRIKKVTHDMDMCYGMMGSLFRSGSRQTLFA
          WTDKS.LFEELQ.LD.FL.E.YKHLDSSSNE.PDI.SIQR.IKK.THDMDMCY.MMGSL..S.SRQTLFA
Retrocopy WTDKSSLFEELQRLDVFLVEHYKHLDSSSNECPDINSIQRYIKKFTHDMDMCYRMMGSLIHSSSRQTLFA

Parental  SQVMRYADLYAASFINLLYY
          SQVM.YA.LY.ASFINLLYY
Retrocopy SQVM*YANLYTASFINLLYY

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_2188 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2188 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010354	1 retrocopy	retro_cfam_684,
Choloepus hoffmanni	ENSCHOG00000004098	1 retrocopy	retro_chof_280,
Microcebus murinus	ENSMICG00000012316	1 retrocopy	retro_mmur_1476,
Rattus norvegicus	ENSRNOG00000020179	1 retrocopy	retro_rnor_430,
Tupaia belangeri	ENSTBEG00000017707	4 retrocopies	retro_tbel_2188 , retro_tbel_3201, retro_tbel_3465, retro_tbel_3467,