RetrogeneDB ID: retro_ogar_2555

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873634.1:5127823..5128157(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LMO1
• Ensembl ID: ENSOGAG00000013163
• Aliases: None
• Description: LIM domain only 1 (rhombotin 1) [Source:HGNC Symbol;Acc:6641]

Sequence

>retro_ogar_2555
CACGAAGATGCCTCAAGTGTGCCTGCTGTGACTGCCGCCTGGGCGAGGTGGGCTCTACCCTCGACATCAAGGACAATCTC
ATCCTGTGCTGACTCGACCACCTGAGGCTCTTCGGCACCACAGGAAACTGCACTGTTGCAGCAAGCTGATCCCAGCCTTC
CAGATGGTGACGTGGGCCCAGGACAATGTGTATCACCTTGACTGCTTCGCTTGCCAGCTCTGCAACCAGAGATGTTGCGT
GGGAGACAAATTCTTCCTGAAGAACAACATGATCTTGTATCAGATGGACTATGAGGCGGGCCAGTTCAATGGCACCTTTG
AATCCCAGGTTCAG

Alignment

ORF - retro_ogar_2555 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.21 %
• Parental protein coverage: 71.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HED-CLKCACCDCRLGEVGSTLYTKANLILCRRDYLRLFGTTGNCAA-CSKLIPAFEMVMRARDNVYHLD
          HED.CLKCACCDCRLGEVGSTL..K.NLILC..D.LRLFGTTGNC...CSKLIPAF.MV..A.DNVYHLD
Retrocopy HED<CLKCACCDCRLGEVGSTLDIKDNLILC*LDHLRLFGTTGNCTV<CSKLIPAFQMVTWAQDNVYHLD

Parental  CFACQLCNQRFCVGDKFFLKNNMILCQMDYEEGQLNGTFESQVQ
          CFACQLCNQR.CVGDKFFLKNNMIL.QMDYE.GQ.NGTFESQVQ
Retrocopy CFACQLCNQRCCVGDKFFLKNNMILYQMDYEAGQFNGTFESQVQ

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_2555 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000002475	1 retrocopy	retro_eeur_650,
Otolemur garnettii	ENSOGAG00000013163	1 retrocopy	retro_ogar_2555 ,