RetrogeneDB ID: retro_tbel_4175

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_70005:4304..4798(+)
• 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_4175
GACTTGGAATGGAAAATTATCTAGGTGGGCTCTGCAGAAAGTGAAGAATACGATCAAGTTTTAGACTCTGTTTAGTGGGT
CCTGTTCCTGCAGGAAGGCATATGTTAGTACTTCAGGCTGATGCACCTAATCCAGGACTCATTCCAGATGCAGATGCAGT
AGGTGTAACAGTTGTGCTAATAACTTGCACCTATCGAGGTCAAGAATTTATTAGAGTTGGCTATTATGTAAATAGTGAAT
ATACTGAGACAGAATTAAGGGAAAATCCACCTGTAAAACCAGACTTTTCTAAGCTTCAAAGAAACATTTTGGCATCTAAT
CCCAGGGTCACAAGATTCCACATTAATTGGGAAGATAACACAGAAAAACTGGAAGATGCAGAAAGCAGGAATCCAAATCT
ACAATCACTTCTTTCGACAGATGCATTACCTTCAGCATCAAAGGGCTGGTCCACGTCAGAAAATGTCATGTTAGAATCCC
ACATGGACTGCATG

Alignment

ORF - retro_tbel_4175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.67 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DLEWKIIYVGSAESEEYDQVLDSV-LVGPVPAGRHMFVFQADAPNPGLIPDADAVGVTVVLITCTYRGQE
          DLEWKII.VGSAESEEYDQVLDSV.LVGPVPAGRHM.V.QADAPNPGLIPDADAVGVTVVLITCTYRGQE
Retrocopy DLEWKII*VGSAESEEYDQVLDSV<LVGPVPAGRHMLVLQADAPNPGLIPDADAVGVTVVLITCTYRGQE

Parental  FIRVGYYVNNEYTETELRENPPVKPDFSKLQRNILASNPRVTRFHINWEDNTEKLEDAESSNPNLQSLLS
          FIRVGYYVN.EYTETELRENPPVKPDFSKLQRNILASNPRVTRFHINWEDNTEKLEDAES.NPNLQSLLS
Retrocopy FIRVGYYVNSEYTETELRENPPVKPDFSKLQRNILASNPRVTRFHINWEDNTEKLEDAESRNPNLQSLLS

Parental  TDALPSASKGWSTSENSLNVMLESHMDCM
          TDALPSASKGWSTSEN...VMLESHMDCM
Retrocopy TDALPSASKGWSTSEN---VMLESHMDCM

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_4175 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4175 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 ,