RetrogeneDB ID: retro_ogar_3139

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873727.1:2441922..2442574(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000025935
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RRP36
• Ensembl ID: ENSOGAG00000012699
• Aliases: None
• Description: ribosomal RNA processing 36 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:21374]

Sequence

>retro_ogar_3139
CAGTTCGGTACATGGAACATGTCATTTGAGTACTTTTTGGAATTACAGAGCCAAGCGGGCACTAAGACATAGAAACAGTT
GGTAGCTGCAAACAGCTCTAAGAAACAGGTTTCTAGACCACCTGCCCAAAGCCCAGGTGTTGCAGATAAGCACAGGTCTT
TGGAAATGTCAGCCAAGATCCAAGTACCATTTTTACGGCAGGTTGTCCCCCTCTGTAAAACGGTAGCCCGGGAACCCCGC
TTTAATGATCTGTCAGGGGAATATAATCCTGAGGTGTTTGACAAAACATACCAATTCTTGGATAACATCTGACCCAAGGA
AAAAGAGCTTGTGAAAAAGCAGTTGAAGAAGCACGTTCAGGGGAGCAGCATGAGAAGCTGCAGCAGCTGCTTCGGAAAAT
GGAGCGGCAAGAAAAGGCACAGCAGGAAGGAAAGCTGCAGCGGGAGTTGCGCCTGGCCCTGAAGCATGGACCGCGGGCTC
AGGCCCAGGAGGCCCATCGGCCTTACTTCCTAAAGAAATCTGAGCAGCGCAGTTGGCCCTAGCTGAGAAGTTCAAAGAGC
TGAGACGCAGAAGGAAGCTGGAGAGCTTCTTGAAAAGAAAGAGGCTCTGAAATGCAGACAAGGACAAGAGATAGCTCCCT
TTGAGCAAAGAG

Alignment

ORF - retro_ogar_3139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.64 %
• Parental protein coverage: 94.78 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QRGISNMSFEELLELQSQVGTKTYKQFVTANSTKKQVSRPPIQSPGVADKHRPLEMSAKIRVPFLRQVVP
          Q.G..NMSFE..LELQSQ.GTKT.KQ.V.ANS.KKQVSRPP.QSPGVADKHR.LEMSAKI.VPFLRQVVP
Retrocopy QFGTWNMSFEYFLELQSQAGTKT*KQLVAANSSKKQVSRPPAQSPGVADKHRSLEMSAKIQVPFLRQVVP

Parental  ICKKVARDPRFDDLSGEYNPEVFDKTYQFLDDIRAKEKELVKKQLKKH-RSGEQHEKLQQLLQRMERQEM
          .CK.VAR.PRF.DLSGEYNPEVFDKTYQFLD.I..KEKELVKKQLKKH.RSGEQHEKLQQLL..MERQE.
Retrocopy LCKTVAREPRFNDLSGEYNPEVFDKTYQFLDNI*PKEKELVKKQLKKH<RSGEQHEKLQQLLRKMERQEK

Parental  AQQERKRQQELRLALKHERRAQAQEGHRPYFLKKSEQR-QLALAEKFKELRRRRKLESFLSRKRRRNAGK
          AQQE.K.Q.ELRLALKH..RAQAQE.HRPYFLKKSEQR.QLALAEKFKELRRRRKLESFL.RKR..NA.K
Retrocopy AQQEGKLQRELRLALKHGPRAQAQEAHRPYFLKKSEQR<QLALAEKFKELRRRRKLESFLKRKRL*NADK

Parental  DKRQLPLSKE
          DKR.LPLSKE
Retrocopy DKR*LPLSKE

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_3139 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012525	1 retrocopy	retro_chof_160,
Otolemur garnettii	ENSOGAG00000012699	1 retrocopy	retro_ogar_3139 ,
Ictidomys tridecemlineatus	ENSSTOG00000009511	1 retrocopy	retro_itri_1520,