RetrogeneDB ID: retro_tbel_1158

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3962:153116..154723(-)
• Located in intron of: ENSTBEG00000000880

Retrocopy information

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

Parental gene information

• Parental gene symbol: TDP1
• Ensembl ID: ENSTBEG00000002578
• Aliases: None
• Description: tyrosyl-DNA phosphodiesterase 1 [Source:HGNC Symbol;Acc:18884]

Sequence

>retro_tbel_1158
TCGAGTAGTGATGAAAGTGAGGAAGAAAAGCCTAAAGCGGACAAGTCATCTACCTCTTCTCTCCCTCACGCTAGCACTGA
GTGGCAGCTGAGCCCGGGTGCACCTGCTCCGAAGCTCCTCGGAAAGCCGCACACAGGAGGAAGATATCCCCGGTGAGGTG
CAGCAACACAGATTCAGTTTCACCTCTCAAAAGACAGAAAAGCGGCTCCCAGGATGACCTAGGCTGGTGTCTGTCCAGCA
GCGATGATAAGTCACCACCAGAAACGCAGCATAAACAGGCTGAGTAAGCGATGGTCAGAGGAGAAAGACATCTCTCCTCC
CAAAGATGGTGCTGCCCAAAGAACTGGAAATCATGGGCCGCCCGCCAGCTACAGACTCAAAGAGGAGGACGAAGATGAAT
ATGAGACGTCTGGGGAAGGCCAGGATGTTTGGGACATGCTGAGTAAAGGGAACCCCTTCCAGTTTTACCTCACCAGAGTC
AAGGGAATTAAGCCAAAGTACAACTCTGGAGCCCTCCACATCAAGGATATTTTATCTCCTCTATTTGGAACGCTTGTTTC
TTCAGCTCAGTTTAACTACTGCTTTGACGACTGGCTCGTAAAACAGTATCCACCAGAATTCAGGAAGAAACTAATCCTGC
TTGTGCATGGGGATAAGTGAGAAGCTAAGGCTCACTTACACGCGCGGGCGAAGCCTTACGAGAACATTTCCCTCTGCCAG
GCAAAGCTGGATATCACATTTGGAACACATCACACGAAAATGATGCTGTTGCTCTATGAAGAAGGCCCCTGGGTTGTCAT
ACACACCTCCCACCTCATCCATGAGGACTGGTACCAGAAAACTCAGGGAATATGGTTGAGCCCCTGTACCCACGGATCGT
CCACGGAACCCCCAGATCTGGAGAATCAACAACACATTTTAAAGCTGATCTCATCAGTTACTTGACGGCTTACAATGCTC
CGTCTCTCAAAGAGTGGATAGACACCGTCCACGAGCATGACCTCTCTGAAACAAATGTTTACCTTATTGGTTCAACTCCA
GGATGCTTTCAAGGAAGCCAGAAAGATAACTGGGGACATTTCAGGCTCAGGAAGCTCCTGAGAGAACATGCCTCGTCCAC
CCCCAAAACAGAGCCCTGGCCCCTGGTAGGTCAGTTCTCAAGCATTGGCTCCTTGGGGGCTGATGAGTCAAAATGGTTAT
GTTCTGAGTTTAAAGAGAGCTTGCTGACACTGGGGACGGATAGCAAGAGTCCTGGAAAACGCGCCGCGCCTCTTCATTTG
ATCTATCCTTCTGTGGAGAACGTGCGGACCAGCTTAGAAGGCTATCCTGCCGGGGGTTCTCTTCCCTGCAGCATCCAGAC
AGCTGAAAAACAGAACTGGCTGCATTCCTATTTTCACAAATGGTCAGCCGAGACTTCTGGCCGCAGCAATGCCATGCCAC
ATATCAAGACATACATGAGGCCCTCTCCAGACTTCAGTGAAATTGCTTGGTTCCTTGTCACAAGCGCGAATCTGTCCAAA
GCCACCTGGGGAGCTCTGGAGAAGAATGGCACTCAGCTGATGATCCACTCCTACAAGCTTGGGGTCCTTTTCCTGCCTTC
AGCATTT

Alignment

ORF - retro_tbel_1158 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.02 %
• Parental protein coverage: 89.93 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SSSDESEDE-PKADKPSTSSLPHAG-HGAATEPGYTCSEA-RKAAHRRKMSPVRCSNTDSVSPLKRQKSG
          SSSDESE.E.PKADK.STSSLPHA..H..A.EPG.TCSEA.RKAAHRRK.SPVRCSNTDSVSPLKRQKSG
Retrocopy SSSDESEEEKPKADKSSTSSLPHAS<H*VAAEPGCTCSEAPRKAAHRRKISPVRCSNTDSVSPLKRQKSG

Parental  SQDDLGWCLSSSDDESPPETQHKQAEEATV-KEEKDIPPPKDGAAQRARNHGPPASHRLKEEEEDEYETS
          SQDDLGWCLSSS.D...P........E.....EEKDI.PPKDGAAQR..NHGPPAS.RLKEE.EDEYETS
Retrocopy SQDDLGWCLSSS-DDKSPPETQHKQAE*AM>SEEKDISPPKDGAAQRTGNHGPPASYRLKEEDEDEYETS

Parental  GEGQDVWDMLSKGNPFQFYLTRVKGIKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPE
          GEGQDVWDMLSKGNPFQFYLTRVKGIKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFD.DWLVKQYPPE
Retrocopy GEGQDVWDMLSKGNPFQFYLTRVKGIKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFD-DWLVKQYPPE

Parental  FRKKPILLVHGDKREAKAHLHARAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHED
          FRKK.ILLVHGDK.EAKAHLHARAKPYENISLCQAKLDI.FGTHHTKMMLLLYEEG..VVIHTS.LIHED
Retrocopy FRKKLILLVHGDK*EAKAHLHARAKPYENISLCQAKLDITFGTHHTKMMLLLYEEGPWVVIHTSHLIHED

Parental  WYQKTQGIWLSP-LYPRIVHGTPRSGESTTHFKADLISYLTAYNAPSLKEWIDTIHEHDLSETNVYLIGS
          WYQKTQGIWLSP.LYPRIVHGTPRSGESTTHFKADLISYLTAYNAPSLKEWIDT.HEHDLSETNVYLIGS
Retrocopy WYQKTQGIWLSP<LYPRIVHGTPRSGESTTHFKADLISYLTAYNAPSLKEWIDTVHEHDLSETNVYLIGS

Parental  TPGRFQGSQKDNWGHFRLRKLLREHASSTPKTEPWPLVGQFSSIGSLGTDESKWLCSEFKESLLTLGRDS
          TPG.FQGSQKDNWGHFRLRKLLREHASSTPKTEPWPLVGQFSSIGSLG.DESKWLCSEFKESLLTLG.DS
Retrocopy TPGCFQGSQKDNWGHFRLRKLLREHASSTPKTEPWPLVGQFSSIGSLGADESKWLCSEFKESLLTLGTDS

Parental  KIPGKSTVPLHLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSSAMPHIKTY
          K.PGK...PLHLIYPSVENVRTSLEGYPAGGSLP.SIQTAEKQNWLHSYFHKWSAETSGRS.AMPHIKTY
Retrocopy KSPGKRAAPLHLIYPSVENVRTSLEGYPAGGSLPCSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTY

Parental  MRPSPDFSEIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSAF
          MRPSPDFSEIAWFLVTSANLSKA.WGALEKNGTQLMI.SY.LGVLFLPSAF
Retrocopy MRPSPDFSEIAWFLVTSANLSKATWGALEKNGTQLMIHSYKLGVLFLPSAF

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_1158 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1158 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001905	1 retrocopy	retro_amel_1840,
Choloepus hoffmanni	ENSCHOG00000005456	1 retrocopy	retro_chof_791,
Tupaia belangeri	ENSTBEG00000002578	2 retrocopies	retro_tbel_1158 , retro_tbel_4636,