RetrogeneDB ID: retro_ogar_1307

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873542.1:16603502..16604256(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTR3C
• Ensembl ID: ENSOGAG00000003249
• Aliases: None
• Description: ARP3 actin-related protein 3 homolog C (yeast) [Source:HGNC Symbol;Acc:37282]

Sequence

>retro_ogar_1307
ACGTACGCTACTAAGTGGCCAGTGTGACATGGAATCACTGAAGACTGGGATCTTATGAAAAGGTTTATGGAGCAGGTAGT
TTTTAAATATCTTTGAGCTGAACCTGAGGACAATTACTTTTTAATGGCAGAACCTCCACTGAATACACCAGAAAGCAGAG
AATATCTTGCGGAAATTATGTTTGAATCATTCAATGTCCAGGACTCTACTTTGCACTTTGGGCAGTGCTAGCCTTAGCAG
CATCTTGGGCATTGAGATAAGTTGGTGAATATACACTAACAGGAACAGTCAGTGATAGTGGAGATGGGTTACCCACCTTA
TCCCAGTGGCTAAAGGTTATGTAATCGAAAGCTGCTTCAAACACATCCAGATTTCAGGTAGAGATGTTATGTATCATTCA
ACAGCTGCTAAAGGAGAGGGGGTTGGGAATCCCTCCTGATCAGTCACTAGAGACCACAAAAGACATTAAGAAGAAATAAT
ATTACATTTTCCTGATATAATCAAAGAATTTGCTAAGAATGATGTGGATCCCCGGAAATGGATCAAACAGTATACAGGTG
TCAATGAGATCAACTAGAAGTTCATTATAGACACTGGTTACACAAGGTTCCTGGGTCCTGAAATAGTCTTCCATCCTGAG
TTTGCCCACCCAGACTTTATGGAATCCATCTCAGATGTTGTGGATGAAATAATACAGAATTGTCCCACCAATGTGCATTG
TCCATTGTATAAGAATGTCATTCTTTCAGGAGGC

Alignment

ORF - retro_ogar_1307 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.58 %
• Parental protein coverage: 66.15 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TYATKWPIRHGIIEDWDLMERFMEQVVFKYLRAEPEDHYFLMTEPPLNTPENREYLAEIMFESFNV-PGL
          TYATKWP..HGI.EDWDLM.RFMEQVVFKYL.AEPED.YFLM.EPPLNTPE.REYLAEIMFESFNV.PGL
Retrocopy TYATKWPV*HGITEDWDLMKRFMEQVVFKYL*AEPEDNYFLMAEPPLNTPESREYLAEIMFESFNV<PGL

Parental  YIAVQAVLALAASWTSRQVGERTLTGIVIDSGDG-VTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQLL
          Y.A..AVLALAASW..R.VGE.TLTG.V.DSGDG.VTH.IPVA.GYVI.SC.KHI.I.GRD..Y......
Retrocopy YFALWAVLALAASWALR*VGEYTLTGTVSDSGDG<VTHLIPVAKGYVIESCFKHIQISGRDVMYH-STAA

Parental  REREVGIP-PEQSLETAKAIKEKYCYI-CPDIVKEFAKYDVDPRKWIKQYTGINAINQKKFIIDVGYERF
          ....VG.P.P.QSLET.K.IK.K..YI..PDI.KEFAK.DVDPRKWIKQYTG.N.IN..KFIID.GY.RF
Retrocopy KGEGVGNP>PDQSLETTKDIKKK*YYI<FPDIIKEFAKNDVDPRKWIKQYTGVNEIN-*KFIIDTGYTRF

Parental  LGPEIFFHPEFANPDFMESISDVVDEVIQNCPIDVRRPLYKNVVLSGG
          LGPEI.FHPEFA.PDFMESISDVVDE.IQNCP..V..PLYKNV.LSGG
Retrocopy LGPEIVFHPEFAHPDFMESISDVVDEIIQNCPTNVHCPLYKNVILSGG

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_1307 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 6 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007730	5 retrocopies	retro_chof_1134, retro_chof_1204, retro_chof_1899, retro_chof_208, retro_chof_2171,
Dasypus novemcinctus	ENSDNOG00000019288	2 retrocopies	retro_dnov_1143, retro_dnov_2539,
Homo sapiens	ENSG00000133627	7 retrocopies	retro_hsap_1676, retro_hsap_2126, retro_hsap_2540, retro_hsap_2966, retro_hsap_4334, retro_hsap_4921, retro_hsap_561,
Macropus eugenii	ENSMEUG00000004885	5 retrocopies	retro_meug_1340, retro_meug_1477, retro_meug_2105, retro_meug_330, retro_meug_899,
Oryctolagus cuniculus	ENSOCUG00000000459	1 retrocopy	retro_ocun_320,
Otolemur garnettii	ENSOGAG00000003249	2 retrocopies	retro_ogar_1307 , retro_ogar_3388,