RetrogeneDB ID: retro_ogar_3388

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873814.1:442031..442758(-)
• Located in intron of: ENSOGAG00000016652

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_3388
ATTGCTATCAGAGAGTCAGCAAAAGTAGTTGACCGAGTACAGTGAAAAGTGTTGAGGGGAGTTGATGACCTTGACTTTTT
CATAGGGATGAAGCTACTGATAAACCTATGTATGCTACAAAATGGCCAATCCGACATGGAATCACTGAAGACTGGGATCT
TATGGAAAGGTTTATGGAGCGGGTAGTTTTTAAGTATCTTCGAGCTGAACCTGAGGACCATTATTTTTTAACGACAGAAC
CTCCACTGAATACACCAGAAAACAGAGAATATCTTACAGAAATTATGTTTGAATCGTTCAATGTACCAGGACTTTACATT
GCAGTTCAGGCAGTGCTGGCCTTAGCAGCATGATGGACATCAAGACAAGTTGGTGAATGTACATTAACAGGGATAGACAT
TGACAGTGGAGATGGAGTTACCCATGTTATCCCAGTGGCCAAAGGTTATGTAATTGGAAGCTGCATCAAACACATCCTGA
TTGCAGGTAGAGATATTACGTATTTCATTCAACAGCTGCTAAGGGAGAGGGAGGTGGGAATCCCTCCTGAGCAATCACTG
AAGACCACAAAATTCATTAAGGAAAAATACTATTACATTTACCCTGATACACTCAAGGAATTTGCTAAGTATGACATGGA
TCCCTGGAAATGGATAAAACAGTATATGAGTATCAGTGCATCAACCAGAAGAAGTTCATTATAGACGCTGGTTACAAAAA
GTTTCTG

Alignment

ORF - retro_ogar_3388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.94 %
• Parental protein coverage: 63.28 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IAIRESAKVVDQAQRRVLRGVDDLDFFIG-DEAIDKPTYATKWPIRHGIIEDWDLMERFMEQVVFKYLRA
          IAIRESAKVVD..Q..VLRGVDDLDFFIG.DEA.DKP.YATKWPIRHGI.EDWDLMERFME.VVFKYLRA
Retrocopy IAIRESAKVVDRVQ*KVLRGVDDLDFFIG<DEATDKPMYATKWPIRHGITEDWDLMERFMERVVFKYLRA

Parental  EPEDHYFLMTEPPLNTPENREYLAEIMFESFNVPGLYIAVQAVLALAASWTSRQVGERTLTGIVIDSGDG
          EPEDHYFL.TEPPLNTPENREYL.EIMFESFNVPGLYIAVQAVLALAA.WTSRQVGE.TLTGI.IDSGDG
Retrocopy EPEDHYFLTTEPPLNTPENREYLTEIMFESFNVPGLYIAVQAVLALAA*WTSRQVGECTLTGIDIDSGDG

Parental  VTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQLLREREVGIPPEQSLETAKAIKEKYCYICPDIVKEFA
          VTHVIPVA.GYVIGSCIKHI.IAGRDITYFIQQLLREREVGIPPEQSL.T.K.IKEKY.YI.PD..KEFA
Retrocopy VTHVIPVAKGYVIGSCIKHILIAGRDITYFIQQLLREREVGIPPEQSLKTTKFIKEKYYYIYPDTLKEFA

Parental  KYDVDPRKWIKQYTGINA-INQKKFIIDVGYERFL
          KYD.DP.KWIKQY..I.A.INQKKFIID.GY..FL
Retrocopy KYDMDPWKWIKQYMSISA<INQKKFIIDAGYKKFL

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_3388 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 ,