RetrogeneDB ID: retro_tbel_2900

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_122979:73300..73713(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ASF1A
• Ensembl ID: ENSTBEG00000000592
• Aliases: None
• Description: anti-silencing function 1A histone chaperone [Source:HGNC Symbol;Acc:20995]

Sequence

>retro_tbel_2900
GACTTGGAATGGTAAATTATCTACATGAACTCTGCAGAAAGTGAGGATATGATCAAGTTTTAGACTCTATCTTAAGTGGG
TCCTGTTCTGGCAGGAAGGCATATGTTTGTATTTCAGGCTGATGTACCTAATCCAGGACTCGTTTCAGATGCAAATTCAG
TAGATATAACAGTTGTGCTAACAATTTGCACCTATTGAAGCCAAGAATTTATTAGAGTTGGCTATTGTGTAAATAATGAA
TATACTGGGACAGAATTAAGTAAAAACAATCTACCTATAAATCGGACTTTTCTAAACTTCAGAGGAAAATTTTGGCATCT
AATCCAAGGGAGGTCACTAGCACTAGATTCCACATTAATTGGAATGATAATACAGAAAAGCTGAAAGATGCAGAGAGCAG
TAATCCAAACCTA

Alignment

ORF - retro_tbel_2900 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.18 %
• Parental protein coverage: 79.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DLEWKIIYVGSAESEE-YDQVLDSVL-VGPVPAGRHMFVFQADAPNPGLIPDADAVGVTVVLITCTYRGQ
          DLEW.IIY..SAESE..YDQVLDS.L.VGPV.AGRHMFVFQAD.PNPGL..DA..V..TVVL..CTY..Q
Retrocopy DLEW*IIYMNSAESED<YDQVLDSIL>VGPVLAGRHMFVFQADVPNPGLVSDANSVDITVVLTICTY*SQ

Parental  EFIRVGYYVNNEYTETEL-RENPPV-KPDFSKLQRNILASNPR---VTRFHINWEDNTEKLEDAESSNPN
          EFIRVGY.VNNEYT.TEL...N.P..K.DFSKLQR.ILASNPR....TRFHINW.DNTEKL.DAESSNPN
Retrocopy EFIRVGYCVNNEYTGTELSKNNLPI<KSDFSKLQRKILASNPREVTSTRFHINWNDNTEKLKDAESSNPN

Parental  L
          L
Retrocopy L

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_2900 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2900 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013007	1 retrocopy	retro_chof_496,
Felis catus	ENSFCAG00000023561	1 retrocopy	retro_fcat_1357,
Myotis lucifugus	ENSMLUG00000013053	1 retrocopy	retro_mluc_1410,
Otolemur garnettii	ENSOGAG00000034346	1 retrocopy	retro_ogar_2054,
Ochotona princeps	ENSOPRG00000004979	1 retrocopy	retro_opri_416,
Tupaia belangeri	ENSTBEG00000000592	2 retrocopies	retro_tbel_2900 , retro_tbel_4175,