RetrogeneDB ID: retro_ogar_3466

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873865.1:107436..107889(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC115
• Ensembl ID: ENSOGAG00000000166
• Aliases: None
• Description: coiled-coil domain containing 115 [Source:HGNC Symbol;Acc:28178]

Sequence

>retro_ogar_3466
GTGTTGAACGCCCGGATAGAGGAGGGATGGCTCTCGCTTGCCAAGGCTCCCTATGCCTTGGGCGCCAAGTCTGTAGGACC
CCTGCAGTATGCTTCCCGTATGGAGCCCCAGGTCTGCATCCATGCCAGTGAGGCCCAGGATGGACTCCAGAAGTTTAGGA
TGGTAAGAGCTGGCGCTCAGACTCCAGAGGGCTTGGGAGCCCCTGAGGAAGGTTTGCATAGGCACAAGGGCCCCACTAAG
ACTCCTGAGCAAAAGTCCTCTGAGGGCCCCCAGGCCCTTCTAAACTAGTTCAGAATCCTGGTTCCTCACAGTCTACAGCT
GGCCCAAGCTAGCTTCTGCTATGGCCTACAGCTGGCATCAGACATAGCCAGTCTTCAGAATTGCATCAACTGGGGGTAAA
GCCAGCTCTGGTGACTCCAGAAGAAACTCAAGCAGCCAGGGCCTGGGGCTGCC

Alignment

ORF - retro_ogar_3466 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.47 %
• Parental protein coverage: 83.89 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLNTRVEEGWLSLAKARYAMGAKSVGPLQYASRMEPQVCVRASEAQDGFQKFRVVRAGVQTPEEVGPREE
          VLN.R.EEGWLSLAKA.YA.GAKSVGPLQYASRMEPQVC..ASEAQDG.QKFR.VRAG.QTPE..G..EE
Retrocopy VLNARIEEGWLSLAKAPYALGAKSVGPLQYASRMEPQVCIHASEAQDGLQKFRMVRAGAQTPEGLGAPEE

Parental  GLRRRKGPTKTPEQESSEGPQDPLNWFGILVPHSLRQAQASFRDGLQLAADIASLQNRINWGQSQLRGLQ
          GL.R.KGPTKTPEQ.SSEGPQ..LN.F.ILVPHSL..AQASF..GLQLA.DIASLQN.INWG.SQL..LQ
Retrocopy GLHRHKGPTKTPEQKSSEGPQALLN*FRILVPHSLQLAQASFCYGLQLASDIASLQNCINWG*SQLW*LQ

Parental  EKLKQPEPGAA
          .KLKQP.PGAA
Retrocopy KKLKQPGPGAA

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_3466 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000010588	2 retrocopies	retro_mdom_200, retro_mdom_435,
Mus musculus	ENSMUSG00000042111	2 retrocopies	retro_mmus_2696, retro_mmus_380,
Oryctolagus cuniculus	ENSOCUG00000005099	1 retrocopy	retro_ocun_1651,
Otolemur garnettii	ENSOGAG00000000166	2 retrocopies	retro_ogar_2849, retro_ogar_3466 ,
Tursiops truncatus	ENSTTRG00000012598	1 retrocopy	retro_ttru_781,