RetrogeneDB ID: retro_ogar_2054

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873585.1:2259299..2259911(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ASF1A
• Ensembl ID: ENSOGAG00000034346
• Aliases: None
• Description: anti-silencing function 1A histone chaperone [Source:HGNC Symbol;Acc:20995]

Sequence

>retro_ogar_2054
ATGGCAAAGGTTCAGATGCACAATGTAGTGGTTCTAGATAACCCTTCTCCTTTCTACAACCCATTCCAGTTTGAGATCAC
CTTCAAGTGCACTGAGGACCTGTCTGAGGACTCAGAGTGGAAGATTATCTTACGTGGGCTCTGCAGACAGTGGAGAATAT
GGTCAAGGTTTAGACTCCATGTTAGGGGCCCTGTTCCTGCAGGAAGGCACATGTTTGTACTTCAGGCTGATGCCCCCGAT
CCAGGACTCCGTACAGAAGCAGGTGCCGCAGGTATAACAGTTGTACTAATTTCCTGCACCTATCAGGGTCAAGAATTTAT
TAGATTTGGCTGTTGCGTAAATAATGAACACACTGAGACAGAATTAAGAGAAAATCCACCGGTAAAGCCAGACTTTTCTA
AGTTTCAGAGGAACACTTTGCCATCTAATCCCAGGGTCATAAGATTCCACATTCATTGGGAAGATAACACAGGACAACTG
GAAGACTCAGAGAGCAGTGGTCCCAACCCACAGTCACGTCTCTCAACAGATGAGTTACCTTCAGCTCCAAAGGGGTGGTC
CACGCCAGAAAACTCACTAAATGTCTCGCAAGGATCCCACATGGACTGCATG

Alignment

ORF - retro_ogar_2054 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.64 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAKVQVNNVVVLDNPSPFYNPFQFEITFECIEDLSEDLEWKII-YVGSAESEEYDQVLDSVL-VGPVPAG
          MAKVQ..NVVVLDNPSPFYNPFQFEITF.C.EDLSED.EWKII.YVGSA.S.EY.Q.LDS.L..GPVPAG
Retrocopy MAKVQMHNVVVLDNPSPFYNPFQFEITFKCTEDLSEDSEWKII>YVGSADSGEYGQGLDSML<RGPVPAG

Parental  RHMFVFQADAPNPGLIPDADAVGVTVVLITCTYRGQEFIRVGYYVNNEYTETELRENPPVKPDFSKLQRN
          RHMFV.QADAP.PGL...A.A.G.TVVLI.CTY.GQEFIR.G..VNNE.TETELRENPPVKPDFSK.QRN
Retrocopy RHMFVLQADAPDPGLRTEAGAAGITVVLISCTYQGQEFIRFGCCVNNEHTETELRENPPVKPDFSKFQRN

Parental  ILASNPRVTRFHINWEDNTEKLEDAESSNPNLQSLLSTDALPSASKGWSTSENSLNVMLESHMDCM
          .L.SNPRV.RFHI.WEDNT..LED.ESS.PN.QS.LSTD.LPSA.KGWST.ENSLNV...SHMDCM
Retrocopy TLPSNPRVIRFHIHWEDNTGQLEDSESSGPNPQSRLSTDELPSAPKGWSTPENSLNVSQGSHMDCM

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_2054 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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.

---

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,