RetrogeneDB ID: retro_ogar_3505

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873995.1:44746..45156(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPA
• Ensembl ID: ENSOGAG00000024154
• Aliases: None
• Description: centromere protein A [Source:HGNC Symbol;Acc:1851]

Sequence

>retro_ogar_3505
ATTGGCACGCACCAGAGACGCAAGTCCGAGGCCCTAACGAGGCACAGCCCAAGCCCGAGCCCTGGCCCCTTGAGGTGGGG
TCCTTCCCTAGGCACCTCCTCCCATCAATATAATTAGACAAGACTTTTGTGGTTAAAGGAGATCCGAAAACTTCAGAAGA
GCACAAACCACTTGTTAAGGAAAACCCTGTCAGCCACCTGGCAAGAGAAATATGTAGTAAATTCGCTCCTGGTGTGGACT
TCAATTGGCAAGCCCAGGCCCAGTTGGCCCTACAAGAGGCAGAAGAAGCATTTCTAGTTCATGTCTTTGAAGATGCTTAT
CTTCTCACCTTACATGCTGGCCCAGTTACTGTTTTCCCAAAGGATGTGCAACTGTTGAGAAGGATCTGAGGCATTCAGGA
AGGGCTCGGC

Alignment

ORF - retro_ogar_3505 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.91 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGPRRRRKPETPTRRPASPSPGPSRRGPSLGTSSRGHGQRRPLWLKEIRKLQKSTNLLLRKA-PFSRLTR
          .G...RRK.E..TR...SPSPGP.R.GPSLGTSS......R.LWLKEIRKLQKSTN.LLRK..P.S.L.R
Retrocopy IGTHQRRKSEALTRHSPSPSPGPLRWGPSLGTSSHQYN*TRLLWLKEIRKLQKSTNHLLRKT<PVSHLAR

Parental  EICGKFTRGVDYNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIRGIQEGLG
          EIC.KF..GVD.NWQAQA.LALQEA.EAFLVH.FEDAYLLTLHAG.VT.FPKDVQL.RRI.GIQEGLG
Retrocopy EICSKFAPGVDFNWQAQAQLALQEAEEAFLVHVFEDAYLLTLHAGPVTVFPKDVQLLRRI*GIQEGLG

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_3505 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.

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023938	1 retrocopy	retro_btau_947,
Choloepus hoffmanni	ENSCHOG00000004496	3 retrocopies	retro_chof_2096, retro_chof_2448, retro_chof_4,
Ornithorhynchus anatinus	ENSOANG00000000516	1 retrocopy	retro_oana_72,
Otolemur garnettii	ENSOGAG00000024154	2 retrocopies	retro_ogar_3405, retro_ogar_3505 ,
Ictidomys tridecemlineatus	ENSSTOG00000025168	2 retrocopies	retro_itri_835, retro_itri_994,
Tarsius syrichta	ENSTSYG00000010334	1 retrocopy	retro_tsyr_2007,
Tursiops truncatus	ENSTTRG00000010278	2 retrocopies	retro_ttru_590, retro_ttru_784,