RetrogeneDB ID: retro_ogar_645

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873524.1:46460316..46460744(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIN28B
• Ensembl ID: ENSOGAG00000011042
• Aliases: None
• Description: lin-28 homolog B (C. elegans) [Source:HGNC Symbol;Acc:32207]

Sequence

>retro_ogar_645
GGCAGGAGGAGCAAAGGTGGTGGAGAAGACTCACCTTCTTCTCCTGTCTGAGCAGCAGAGGAAGAATCCTCCCAGGTTTT
GCATGGGGCTGGCCACGGCAGGTGGTTCATCGTGCCCAAGGCATTTGGATTCATCTCCATGGTAAACTGACAGTGATGCC
CCTTGAACACTCCAGTGGGTGTATTTGCACACCAAAGCAAACTATTCATGGAAGTATTTAGGGGCCTAAAAGAAGGAAAA
CCAGTGGAATTCACGTTTAAAAAATCTTGCAAAATTCTTGAATCAATTCAGGTAACAGGACCTGGTGGGAGCCCTTGCTG
AGGAAGTGAAAGACCCAAAGGGAAGACGTTACAAAGAAGAAAACCAAGTAGATGTGGCCCTGTGGTGGCCTTGATCATCA
CGCTTAGGAATGTAGCCTCCCCAGCCAA

Alignment

ORF - retro_ogar_645 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.75 %
• Parental protein coverage: 58. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGASKGGGED-PGKLSEPAEEEPSQVLHGTGHCKWFNVRMGFGFISMINREGSPLDIPVDVFVHQSKLFM
          G..SKGGGED.P......AEEE.SQVLHG.GH..WF.V...FGFISM.N....PL..PV.VF.HQSKLFM
Retrocopy GRRSKGGGEDSPSSPV*AAEEESSQVLHGAGHGRWFIVPKAFGFISMVN*Q*CPLNTPVGVFAHQSKLFM

Parental  EGFRSLKEGEPVEFTFKKSSKGLESIRVTGPGGSPCLGSERRPKGKTLQKRKPKGDRC-YNCGGLDHHAK
          E.FR.LKEG.PVEFTFKKS.K.LESI.VTGPGGSPC.GSE.RPKGKTLQ.RKP...RC...CGGLDHHA.
Retrocopy EVFRGLKEGKPVEFTFKKSCKILESIQVTGPGGSPC*GSE-RPKGKTLQRRKP--SRC<WPCGGLDHHA*

Parental  ECSLPPQ
          ECSLP.Q
Retrocopy ECSLPSQ

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_645 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000015340	1 retrocopy	retro_etel_1927,
Microcebus murinus	ENSMICG00000002297	4 retrocopies	retro_mmur_1377, retro_mmur_1390, retro_mmur_660, retro_mmur_800,
Oryctolagus cuniculus	ENSOCUG00000017850	1 retrocopy	retro_ocun_532,
Otolemur garnettii	ENSOGAG00000003971	1 retrocopy	retro_ogar_481,
Otolemur garnettii	ENSOGAG00000011042	1 retrocopy	retro_ogar_645 ,
Sorex araneus	ENSSARG00000008374	2 retrocopies	retro_sara_121, retro_sara_746,
Tarsius syrichta	ENSTSYG00000006480	1 retrocopy	retro_tsyr_1815,