RetrogeneDB ID: retro_ogar_2447

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873624.1:4258344..4258820(+)
• Located in intron of: ENSOGAG00000007251

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM12
• Ensembl ID: ENSOGAG00000010489
• Aliases: None
• Description: LSM12 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:26407]

Sequence

>retro_ogar_2447
CGGCTGCTCTCCCAAGATGGCAGCTCCTCCAGTGGAAAGCCCAATCACGCAGACATCCTGCTTATAAACTTAGAGTATGT
TTCAGAAGTGGAAATAATTAATGACCGAACAGAAACCCCTCCTCCCCTAGCTTCACTCAATGTTAGTAAGCTTGCCAGCA
AAGCACGGACGGAGAAAGAGGAGAAGCTGAGCCAGGCCTATGCAATCAGTGCTGGTGTCTCTCTAGAGGGCCAGCACTCT
TCCAGACCATTCACAAGACCATTAAAGACTGTAAATGGCAAGAAAAAAACATTGTAGTCATGGAAGAAGTTGTTATTACA
CCCCCATATCAAGTGGAAAATTGTAAAGGCAAAGAGGGGAGTGCACTGAGCCATGTACGCAAAATAGTTGAAAAACATTT
TAGAGATGTGGAAAGCCAAAAGATACTGCAACGTTCACAAGCCCAGCAACCACAGAAGGAGGCTACCCTGTCATCC

Alignment

ORF - retro_ogar_2447 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.75 %
• Parental protein coverage: 81.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KMLALKCPSSSGKPNHADILLINLQYVSEVEIINDRTETPPPLASLNVSKLASKARTEKEEKLSQAYAIS
          ..L.....SSSGKPNHADILLINL.YVSEVEIINDRTETPPPLASLNVSKLASKARTEKEEKLSQAYAIS
Retrocopy RLLSQDGSSSSGKPNHADILLINLEYVSEVEIINDRTETPPPLASLNVSKLASKARTEKEEKLSQAYAIS

Parental  AGVSLEGQQ-LFQTIHKTIKDCKWQEKNIVVMEEVVITPPYQVENCKGKEGSALSHVRKIVEKHFRDVES
          AGVSLEGQ..LFQTIHKTIKDCKWQEKNIVVMEEVVITPPYQVENCKGKEGSALSHVRKIVEKHFRDVES
Retrocopy AGVSLEGQH<LFQTIHKTIKDCKWQEKNIVVMEEVVITPPYQVENCKGKEGSALSHVRKIVEKHFRDVES

Parental  QKILQRSQAQQPQKEATLSS
          QKILQRSQAQQPQKEATLSS
Retrocopy QKILQRSQAQQPQKEATLSS

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_2447 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 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014379	2 retrocopies	retro_cfam_1843, retro_cfam_312,
Echinops telfairi	ENSETEG00000008374	1 retrocopy	retro_etel_21,
Felis catus	ENSFCAG00000029083	1 retrocopy	retro_fcat_787,
Homo sapiens	ENSG00000161654	1 retrocopy	retro_hsap_4041,
Loxodonta africana	ENSLAFG00000005202	1 retrocopy	retro_lafr_906,
Macropus eugenii	ENSMEUG00000007501	1 retrocopy	retro_meug_1462,
Macaca mulatta	ENSMMUG00000006804	1 retrocopy	retro_mmul_3,
Mus musculus	ENSMUSG00000020922	1 retrocopy	retro_mmus_2683,
Otolemur garnettii	ENSOGAG00000010489	2 retrocopies	retro_ogar_1771, retro_ogar_2447 ,
Oryzias latipes	ENSORLG00000011310	1 retrocopy	retro_olat_12,
Rattus norvegicus	ENSRNOG00000020894	1 retrocopy	retro_rnor_2845,
Tupaia belangeri	ENSTBEG00000012523	2 retrocopies	retro_tbel_3062, retro_tbel_60,
Vicugna pacos	ENSVPAG00000011145	1 retrocopy	retro_vpac_627,