RetrogeneDB ID: retro_tbel_3666

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_148113:24035..24802(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PARPBP
• Ensembl ID: ENSTBEG00000013476
• Aliases: None
• Description: PARP1 binding protein [Source:HGNC Symbol;Acc:26074]

Sequence

>retro_tbel_3666
GTAGATGATGAAACTGATCTTATGTACCAGCATCACCAATAACTAAACACAACCGGGATGATGAAAAGGTACAGGTACTA
GCAAAGAAAATTTTTCTTTCCTATTTAAGCCTAATGGTGAATTCAAAGAATGACCTGGCTCTGGCTCATATTCCCAATAT
TCCTGATAGAGGAGTTGGGAAAGAAACCTTCACGGTTTTGAAACACACTGCTCGAGAGAAACAGACGTCTATCTTTTTGG
TGGCTGCATCATTTATTAGAACAATTGAGCTTGGAGGGAAAGGATATACACCATCACCATGTGATCCGTTAAGGGCACAT
ATAAAGGGACTGTCTAATTGTATTAATGTCATTGATGAATTAGATGAGACTCTTGGAGAAATACCAAATCCAAGCATTGC
AGGGGTTCGGATACTGTCAGTGATAAAGATGCAGCTAATTAAAGGCCAGAACAACAGGGATCCTTTTTATAAAGCAGTAG
AGGAAGTTGCTTAAGATTTGGATTTGAGGATTAAAAATCTCATCAGTTATCAAAAAGGAGAGGTAGCCATTAGCACCACT
GAGATCAGTCCTGCACTGCCAAAATCTTATACCATAAACCATGGTACTGCATACTGTGGCAGAGATACTGTGAAAATGCT
ACTTCATCTTTTGGATGAAGCAGCAGCCAGTGTTCCTACCAAAAACAAAGCAGAGCTTTTATATGATGATGAAAACACAA
TTCAAAATGGCACTTCTATTCTTATACCTTTTAGATCTCCCACACAA

Alignment

ORF - retro_tbel_3666 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.27 %
• Parental protein coverage: 58.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VNDETDL-YVPTSPMTKHNQDNEKVQVLAKKIILSYLSLIVNSKNDLALAHILNIPDRGLGKEAFTDLKH
          V.DETDL.YVP.SP.TKHN.D.EKVQVLAKKI.LSYLSL.VNSKNDLALAHI.NIPDRG.GKE.FT.LKH
Retrocopy VDDETDL<YVPASPITKHNRDDEKVQVLAKKIFLSYLSLMVNSKNDLALAHIPNIPDRGVGKETFTVLKH

Parental  AAREKQLSLFLVATSFIRTIQLGGKGYAPSPSDPLRAHVKGLSNFINFIDKLDEILGDIPNPSIAGGRIL
          .AREKQ.S.FLVA.SFIRTI.LGGKGY.PSP.DPLRAH.KGLSN.IN.ID.LDE.LG.IPNPSIAG.RIL
Retrocopy TAREKQTSIFLVAASFIRTIELGGKGYTPSPCDPLRAHIKGLSNCINVIDELDETLGEIPNPSIAGVRIL

Parental  SVIKMQLIKGQNNGDPFYKAVEEVAQDLDLRIKNLFNSQQGEVAVNNTDISPARPKSYTINHGTAYCGRD
          SVIKMQLIKGQNN.DPFYKAVEEVA.DLDLRIKNL...Q.GEVA...T.ISPA.PKSYTINHGTAYCGRD
Retrocopy SVIKMQLIKGQNNRDPFYKAVEEVA*DLDLRIKNLISYQKGEVAISTTEISPALPKSYTINHGTAYCGRD

Parental  TVKILLYLLDEEAASVPTKNKAELLYDDENTIYNGTSILTLFRSPTQ
          TVK.LL.LLDE.AASVPTKNKAELLYDDENTI.NGTSIL..FRSPTQ
Retrocopy TVKMLLHLLDEAAASVPTKNKAELLYDDENTIQNGTSILIPFRSPTQ

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_3666 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3666 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011914	1 retrocopy	retro_chof_1428,
Tupaia belangeri	ENSTBEG00000013476	1 retrocopy	retro_tbel_3666 ,