RetrogeneDB ID: retro_ogar_2116

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873592.1:3774165..3774647(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VDAC2
• Ensembl ID: ENSOGAG00000030039
• Aliases: None
• Description: voltage-dependent anion channel 2 [Source:HGNC Symbol;Acc:12672]

Sequence

>retro_ogar_2116
AATGTGAAAACAGAGTCATGCAGGGGTGTGGAATTCTCAACATCTGCTTCATCAAACACATCTAACTTTAATTGGTACAG
TCACTGGTACCTTGGAGACCAAATAGAAATGATGTGAGTGTAGTCTGACTTTCACAGAAAAATGGAAACATACAATACCC
TGGGAACAAAAATCTCAATTGAAGGACAGATTTATCACAGTCTGAAGCTGACACATGATACTGCCTTCTCACCGAACATG
GGGAAGGAAAGTAGCAAACTCTAGACCTCTTCTAAGAAGGAGTGTATTCATCCTGGCTGGGATGCTGGCTTTGATTCTGC
TGAACCAATACCTGCTGGTTTTGGTCGTGAGGCCTGTCTTGCTGGTTCCCAGGTGGCTGTTGACAATGCCAAGTCACAGC
TGACCAGGGATAACTTTGCAGTGGGATTAAGACTGGGGTCTTCCAGCTGCATACCAATGTCAATGAGGGGACAGGATTTG
GA

Alignment

ORF - retro_ogar_2116 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.48 %
• Parental protein coverage: 55.1 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DVKTKSCSGVEF--STSGSSN-TDTGKVTGTLETKYKWCEYGLTFTEKWN-TDNTLGTEIAIEDQICQGL
          .VKT.SC.GVEF..S.S.....T..G.VTGTLETK.K.CE..LTFTEKW..T.NTLGT.I.IE.QI...L
Retrocopy NVKTESCRGVEFSTSASSNTS>TLIGTVTGTLETK*K*CECSLTFTEKWK<TYNTLGTKISIEGQIYHSL

Parental  KLTFDTTFSPNTGKKSGKIKSSYRRECINLGCDVDFDFAGPAIHGSAVFGYEGWLAGYQMTFDSAKSKLT
          KLT.DT.FSPN.GK.S.K...S...ECI..G.D..FD.A.P...G...FG.E..LAG.Q...D.AKS.LT
Retrocopy KLTHDTAFSPNMGKESSKL*TSSKKECIHPGWDAGFDSAEPIPAG---FGREACLAGSQVAVDNAKSQLT

Parental  RNNFAVGYR-TGDFQLHTNVNDGTEFG
          R.NFAVG.R.TG.FQLHTNVN.GT.FG
Retrocopy RDNFAVGLR<TGVFQLHTNVNEGTGFG

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_2116 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 18 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012975	2 retrocopies	retro_btau_1252, retro_btau_1389,
Canis familiaris	ENSCAFG00000015398	1 retrocopy	retro_cfam_376,
Callithrix jacchus	ENSCJAG00000001145	1 retrocopy	retro_cjac_2385,
Felis catus	ENSFCAG00000026943	3 retrocopies	retro_fcat_1385, retro_fcat_804, retro_fcat_815,
Homo sapiens	ENSG00000165637	1 retrocopy	retro_hsap_2114,
Gorilla gorilla	ENSGGOG00000005861	5 retrocopies	retro_ggor_1677, retro_ggor_1949, retro_ggor_2934, retro_ggor_3036, retro_ggor_425,
Macropus eugenii	ENSMEUG00000012995	1 retrocopy	retro_meug_30,
Myotis lucifugus	ENSMLUG00000007500	2 retrocopies	retro_mluc_1710, retro_mluc_2252,
Mustela putorius furo	ENSMPUG00000003268	1 retrocopy	retro_mputfur_354,
Mus musculus	ENSMUSG00000021771	1 retrocopy	retro_mmus_2667,
Otolemur garnettii	ENSOGAG00000016163	4 retrocopies	retro_ogar_2770, retro_ogar_2870, retro_ogar_589, retro_ogar_995,
Otolemur garnettii	ENSOGAG00000030039	1 retrocopy	retro_ogar_2116 ,
Otolemur garnettii	ENSOGAG00000030742	2 retrocopies	retro_ogar_1197, retro_ogar_2876,
Rattus norvegicus	ENSRNOG00000013505	1 retrocopy	retro_rnor_2652,
Sarcophilus harrisii	ENSSHAG00000012048	1 retrocopy	retro_shar_325,
Tupaia belangeri	ENSTBEG00000001946	4 retrocopies	retro_tbel_1504, retro_tbel_1541, retro_tbel_1885, retro_tbel_4597,
Tarsius syrichta	ENSTSYG00000004764	1 retrocopy	retro_tsyr_14,
Vicugna pacos	ENSVPAG00000008068	1 retrocopy	retro_vpac_156,