RetrogeneDB ID: retro_tbel_4636

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_9494:53331..54711(-)
• Located in intron of: None

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_4636
TCGAGTAGTGATGAAAGTGAGGATGAAAAGCCTAAAGCGGACAAGCCATCTACCTCTTCTCTCCCTCACGCTGGGCACGG
AGCGGCAGCTGAGCCCGGGTGCACCTGCTCTAGGCTCAGAAAGCCGCACACAGGAGGAAGATGTCCCCGGTGAGGTGCAG
CAACACAGATTCAGTTTCACCTCTCAAAAGACAGAAAAGTGGCTCCCAGGATGACCTAGGCTGGTGTCTGTCCAGCAGCG
ATGATGAGTCGCCACCAGAAACGCAGCATGCACAGGCTGAGAAAGCGACGGTCAAAGAGGAGAAAGACATCCCTCCTCCC
AAAGATGGTGCTGCCCAAAGAGCTGGAAACCATAGGCCACCCGCCAGCCACAGACTCAAAGAGGAGGAAGAAGATGAATA
TGAGACGTCAGGGTAAGGCCAGGATGTTTGGGACATGCTGAGTAAAGGGAACCCCTTCCAGTTTTACCTCACCAGAGTCA
AGGGAATTAAGCCAAAGTACAACTCTGGAGCCCTCCACATCAAGGGTATTTTATCTCCTCTATTTGGAACGCTTGTTTCT
TCAGCTCAGTTTAACTATTGCTTTGACGTGGACTGGCCCGTAAAACTGTATCCACCCGAATTCAGGAAGAAACCAATCCC
GCTTGTGCACGGTGATAAGTGAGAAGCTAAGGCTCACTTACACGCCCGGGTGAAGCCTTACCAGAACATTTTCCTCTGCC
AGGCAAAGTTGGATATCGCATTTGGAACACATCACACGAAAATGATGCTGTTGCTCTATGAAGAAGGCCTCCGGGTTGTC
ATACACGCCTCCAAACTCATTCATGAGGACTGGTACCAGAAAACTCGGAATATGGTTGAGCCCCTTGTACCCACAGATCG
TCCATGGAACCCCCAGATCTGGAGAATCAACAACACTTTTTAAAGCTGATCTCATCAGTTACTTGACGGCTTACAATGCT
CCGTCTCTCAAAGAGTGGATAGACACCATCTACGAGCATGACCTCTCTGAAACAAATGTTTACCTTATTGGTTCAACTCC
AGGATGCTTTCAAGGAAATCAGAAAGATAACTGGGGACATTTCAGGCTCAGGAAGCTCCTGAGAGAACATGCCTCGTCCA
CACCCAAAACAGAGCCCTGGCCCCTGGTAGGTCAGTTCTCAAGCATTGACTTCTTAGGGGCTGATGAGTCAAAATGGTTA
TGTTCTGAGTTTAAAGAGAGCTTGCTGACACTGCGGAGGGATAGCAAGAGTCCTGGAAAACGCGCCGCGCCTCTTCATTT
GATCTATCCTTCTGTGGAGAACGTGCGGACCAGCTTAGAAGGCTATCCTGCCGGGGGTTCTCTTCCCTGCAGCATCCAGA
CAGCTGAAAAACAGAACTGG

Alignment

ORF - retro_tbel_4636 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.93 %
• Parental protein coverage: 77.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSSDESEDE-PKADKPSTSSLPHAGHGAATEPGYTCSE-ARKAAHRRKMSPVRCSNTDSVSPLKRQKSGS
          SSSDESEDE.PKADKPSTSSLPHAGHGAA.EPG.TCS..A.KAAHRRKMSPVRCSNTDSVSPLKRQKSGS
Retrocopy SSSDESEDEKPKADKPSTSSLPHAGHGAAAEPGCTCSR<AQKAAHRRKMSPVRCSNTDSVSPLKRQKSGS

Parental  QDDLGWCLSSSDDESPPETQHKQAEEATVKEEKDIPPPKDGAAQRARNHGPPASHRLKEEEEDEYETSGE
          QDDLGWCLSSSDDESPPETQH.QAE.ATVKEEKDIPPPKDGAAQRA.NH.PPASHRLKEEEEDEYETSG.
Retrocopy QDDLGWCLSSSDDESPPETQHAQAEKATVKEEKDIPPPKDGAAQRAGNHRPPASHRLKEEEEDEYETSG*

Parental  GQDVWDMLSKGNPFQFYLTRVKGIKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFR
          GQDVWDMLSKGNPFQFYLTRVKGIKPKYNSGALHIK.ILSPLFGTLVSSAQFNYCFDVDW.VK.YPPEFR
Retrocopy GQDVWDMLSKGNPFQFYLTRVKGIKPKYNSGALHIKGILSPLFGTLVSSAQFNYCFDVDWPVKLYPPEFR

Parental  KKPILLVHGDKREAKAHLHARAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHEDWY
          KKPI.LVHGDK.EAKAHLHAR.KPY.NI.LCQAKLDIAFGTHHTKMMLLLYEEGLRVVIH.S.LIHEDWY
Retrocopy KKPIPLVHGDK*EAKAHLHARVKPYQNIFLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHASKLIHEDWY

Parental  QKTQGIWLSP-LYPRIVHGTPRSGESTTHFKADLISYLTAYNAPSLKEWIDTIHEHDLSETNVYLIGSTP
          QKT......P.LYP.IVHGTPRSGESTT.FKADLISYLTAYNAPSLKEWIDTI.EHDLSETNVYLIGSTP
Retrocopy QKTRNM-VEP>LYPQIVHGTPRSGESTTLFKADLISYLTAYNAPSLKEWIDTIYEHDLSETNVYLIGSTP

Parental  GRFQGSQKDNWGHFRLRKLLREHASSTPKTEPWPLVGQFSSIGSLGTDESKWLCSEFKESLLTLGRDSKI
          G.FQG.QKDNWGHFRLRKLLREHASSTPKTEPWPLVGQFSSI..LG.DESKWLCSEFKESLLTL.RDSK.
Retrocopy GCFQGNQKDNWGHFRLRKLLREHASSTPKTEPWPLVGQFSSIDFLGADESKWLCSEFKESLLTLRRDSKS

Parental  PGKSTVPLHLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNW
          PGK...PLHLIYPSVENVRTSLEGYPAGGSLP.SIQTAEKQNW
Retrocopy PGKRAAPLHLIYPSVENVRTSLEGYPAGGSLPCSIQTAEKQNW

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_4636 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4636 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 ,