RetrogeneDB ID: retro_tbel_3467

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_141559:12382..13345(-)
• 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_3467
AAGTAGGGAAAGTATTTCCCTGCCACCAACAGTGACTATAAATGTACAGATAAAATTATTACTTACCTGTTTGATTTCCC
ATGTGGCTTTAAGCCTGGTAGCTCCCATTGACCATGGCTTTCCTACTTTGACTAGATTTTGGTGGATGCCTGGAAACTCC
TTTTTTTGGAGAAGGCACAGTACTGCGTCAAGTGGATACTAAAATTGGCAAGCTGAGACTTGGTACTTACACAGGCCCCC
TACAGCATGGCATTGTGTACTCAGGAGGCTCATGTGATGCAATCTGTGATCTCTTGGGAGTCAAGGGCAAAGACATATTG
TACATTGGAGATCACATTTTTGGGGACATTTTAAAATCAAAGAAATGGCAAGGGTGGCAAACTTTCTTGGTGATTCCTGA
ACTTGCACAAGAGCTGCATATCTGGACAGACAAGAGTTCCCTTTTTGAAGAGCTTCAGAGGTTGGATGTTTTCTTGGTGG
AACATTATAAGCACCTCGATAGCAGTAGTAATGAGTGCCCAGACATTAATTCCATCCAGAGATATATTAAGAAATTCACT
CATGACATGAACATGTGCTACAGGATGATGGGAAGCCTGATCCACAGCAGCTCCCGGCAGACCCTGTTTGCCAGTCAAGT
GATGTGATATGCCAACCTCTACACAGCATCATTCATCAACCTGTTGTATTACTCACTCAGCTACTTCCTCAGAGCTGCCC
ACGTCCTCATGCCTCATGAATCAATGGTGGAGCACACATACATGGATATGAAGGAGTTGGAGTCCCCCCTTGCCACCCAG
AACCGCACATCAGTGGATTTTTAAAGACACGGACTACAAGCTGCACCAGTTGACATGGTCAGTTAGCAAGATTAAACACC
CAAACCTCTTCCAATGCCCCCCTTCCCAGGAAATTAGACACTGCCATGATGAAGACGATGATGAAGAGGAAGGAGAGGAG
GAA

Alignment

ORF - retro_tbel_3467 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.95 %
• Parental protein coverage: 61.4 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KVGKVFLA-NSDYKYTDKIMTYLFDFPHGPKPGSSHRPWQSYFDLILVDARKPLF-FGEGTVLRQVDTKT
          K.GK.F.A.NSDYK.TDKI.TYLFDFP.G.KPGSSH.PW.SYFD.ILVDA.K.LF.FGEGTVLRQVDTK.
Retrocopy K*GKYFPATNSDYKCTDKIITYLFDFPCGFKPGSSH*PWLSYFD*ILVDAWKLLF<FGEGTVLRQVDTKI

Parental  GKLKIGTYTGPLQHGIVYSGGSSDTICDLLG-KGKDILYIGDHID---IKSKKRQGWRTFLVIPELAQEL
          GKL..GTYTGPLQHGIVYSGGS.D.ICDLLG.KGKDILYIGDHI.....KSKK.QGW.TFLVIPELAQEL
Retrocopy GKLRLGTYTGPLQHGIVYSGGSCDAICDLLGVKGKDILYIGDHIFGDILKSKKWQGWQTFLVIPELAQEL

Parental  HVWTDKSALFEELQSLDIFLAELYKHLDSSSNERPDISSIQRRIKKVTHDMDMCYGMMGSLFRSGSRQTL
          H.WTDKS.LFEELQ.LD.FL.E.YKHLDSSSNE.PDI.SIQR.IKK.THDM.MCY.MMGSL..S.SRQTL
Retrocopy HIWTDKSSLFEELQRLDVFLVEHYKHLDSSSNECPDINSIQRYIKKFTHDMNMCYRMMGSLIHSSSRQTL

Parental  FASQVMRYADLYAASFINLLYYPFSYLFRAAHVLMPHESTVEHTHVDINEMESPLATRNRTSVD-FKDTD
          FASQVM.YA.LY.ASFINLLYY..SY..RAAHVLMPHES.VEHT..D..E.ESPLAT.NRTSVD.FKDTD
Retrocopy FASQVM*YANLYTASFINLLYYSLSYFLRAAHVLMPHESMVEHTYMDMKELESPLATQNRTSVD>FKDTD

Parental  YKRHQLTRSISEIKPPNLFPLAP-QEITHCHDEDDDEEEEEEE
          YK.HQLT.S.S.IK.PNLF...P.QEI.HCHDEDDDEEE.EEE
Retrocopy YKLHQLTWSVSKIKHPNLFQCPPSQEIRHCHDEDDDEEEGEEE

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_3467 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3467 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 ,