RetrogeneDB ID: retro_tbel_3201

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_13375:48211..49315(-)
• 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_3201
AATAAATTTATCCAATGAGATGACACTAGAAGATTTTATATTCTGAACACACTGTTCAACCTACCAGAGACCTACCGATT
GGCCTGTCTAGTAATTTTATTTTTCCTAATTGTCCAAGATATACCAGCTGTGAAACAGAATTTAAAGATGGGGACCTCTT
CATGTCCTACTGGAGTATGTTCCAGGTTGTAGATATGCTGTTGACTGGGTTCATGACAAGGGTTCTCTTGAGGAAAAAAA
AACAGTTGAAAATCTTGAGAAGTGTGTAGTCAAAGATGGAAAATTGCCTTTGCTTCTGAGCCAGATGAAGGAAATAGGGA
AAGTATTTCTTGCCACCAACAGTGACTAAATGTACAGGTAAAATTAGGACTTACCTGTTTGATTTCCCACATGGCTCCAA
GCCTGGTAGCTCCCATCAACCATGGCAGTCCTACTTTGACCTGATTTTGGTGGATGTCCAGAAACTCTTTTTTTTTTTTT
GAGAAGGCACAGTACTTCATCAAGTGCATACTAAAACTGGCAAGCTGAAAATTGGTACCTACACAGACCCCCTACAGCAT
GGCATTGTGTGCTCAGGAGGTTCATCTGATGACCTGTGATCTCTTGGGAACCAAGGGCAAAGACATTTTGTATATTGGAG
ATCACATTTTTGGAGACATTTTAAAATCAAAGAAATGGCAAGGGTGGTGAACTATCTTGGTAATTCCTGAACTTGCACAA
GAGCTACACATCTGGACAGACAAGAGCGCCCTTTTGGAAGAGCTTCAGAGGTTGGAGGTGTTCTTGGTGGAACTTTATAA
GCACCTGGATAGCAGTAGTAATGAGTGCCTGGACATTGCTTTAATCCAAAGACATATTAAGAAAGTCACTCATGACATGG
GACATGTGCTATAGGATGACAGGAGTCTGTTCTGCAGTGGCCTCCCTGCAGACCCTGGTTTGCCAGGTCAAGTGGATGTG
ATATGATGATCTCAACACGGCACCTGTCATCACCTTGCTGTATTACCCATTTCAGCTACCTCTTCAGAGTGCCAACGTCC
TGGAGGCTTCATGAAATCATGGGGGATCACACCAACCGTGGATTTCATTGAAGAGGAAGAACCC

Alignment

ORF - retro_tbel_3201 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.6 %
• Parental protein coverage: 69.2 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  NKFIQRDDTERFYILNTLFNLPETYLLACLV-NF-FTNCPRYTSCETGFKDGDLFMSYRSMFQDV-RDAV
          NKFIQ.DDT.RFYILNTLFNLPETY.LACLV.NF.F.NCPRYTSCET.FKDGDLFMSY.SMFQ.V.R.AV
Retrocopy NKFIQ*DDTRRFYILNTLFNLPETYRLACLV<NFIFPNCPRYTSCETEFKDGDLFMSYWSMFQVV<RYAV

Parental  DWVHYKGSLKEKT-VENLEKYVVKDG--PLL--SMK-VGKVFLANSD-YKYTDKIMTYLFDFPHGPKPGS
          DWVH.KGSL.....VENLEK.VVKDG..PLL...MK..GKVFLA.....K.T.KI.TYLFDFPHG.KPGS
Retrocopy DWVHDKGSLEXXXXVENLEKCVVKDGKLPLLLSQMKEIGKVFLATNS>TKCTGKIRTYLFDFPHGSKPGS

Parental  SHRPWQSYFDLILVDARK-PLFFGEGTVLRQVDTKTGKLKIGTYTGPLQHGIVYSGGSSDT-ICDLLG-K
          SH.PWQSYFDLILVD..K......EGTVL.QV.TKTGKLKIGTYT.PLQHGIV.S.G.S....CDLLG.K
Retrocopy SHQPWQSYFDLILVDVQKLXXXXXEGTVLHQVHTKTGKLKIGTYTDPLQHGIVCS-GGSSD>TCDLLGTK

Parental  GKDILYIGDHID---IKSKKRQGWRTFLVIPELAQELHVWTDKSALFEELQSLDIFLAELYKHLDSSSNE
          GKDILYIGDHI.....KSKK.QGW.T.LVIPELAQELH.WTDKSAL.EELQ.L..FL.ELYKHLDSSSNE
Retrocopy GKDILYIGDHIFGDILKSKKWQGW*TILVIPELAQELHIWTDKSALLEELQRLEVFLVELYKHLDSSSNE

Parental  RPDISSIQRRIKKVTHDM-DMCYGMMGSLFRSGSRQTLFAS-QVMRYADLYAASFINLLYYP-FSYLFRA
          ..DI..IQR.IKKVTHDM.DMCY.M.G......S.QTL......M.Y.DL..A..I.LLYYP.FSYLFR.
Retrocopy CLDIALIQRHIKKVTHDM>DMCYRMTGVCSAVASLQTLVCQVKWM*YDDLNTAPVITLLYYP>FSYLFRV

Parental  AHVLMPHESTVEHTH-VDINEMESP
          ......HE....HT..VD..E.E.P
Retrocopy PTSWRLHEIMGDHTN>VDFIEEEEP

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_3201 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3201 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,