RetrogeneDB ID: retro_ogar_2077

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873588.1:4572602..4572965(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPD3
• Ensembl ID: ENSOGAG00000012708
• Aliases: None
• Description: small nuclear ribonucleoprotein D3 polypeptide 18kDa [Source:HGNC Symbol;Acc:11160]

Sequence

>retro_ogar_2077
GTGCCGATTAAAGTCCTGCACAAGGCTGAAGGCCACATCGTAACAAGTGAGACAAACCCCGGGGAGATATATCGGGGCAG
CTCATTGAAGCTGAAGGCAAAATGAACGGCCAGATGTCCAATGTCATGGTCACGTACACAGACGGCCGTGTGGCCCAGCT
GGAGCAAGTACACATCATGGCAGCAAGATTCACTTTCTGATTTTGCCCTACATGCTGAAAAATGCACCCATATTACAGAC
CATGAAAAATAACAATCAAGGCTCAGTGGCTGGCCGGGGGAAGGCTGCTATTCTGAAGGCCTGTGTGGCTGCGAGAGGAA
GAGGATGTGGACTGGACATGGAAACATCTTCCAGAAGCAAAGA

Alignment

ORF - retro_ogar_2077 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.6 %
• Parental protein coverage: 96.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VPIKVLHEAEGHIVTCETNTGEVYRG-KLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYI-RGSKIRFLI
          VPIKVLH.AEGHIVT.ETN.GE.YRG..LIEAE..MN.QMSN..VTY.DGRVAQLEQV.I..GSKI.FLI
Retrocopy VPIKVLHKAEGHIVTSETNPGEIYRG<QLIEAEGKMNGQMSNVMVTYTDGRVAQLEQVHI<HGSKIHFLI

Parental  LPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVAARGRGRGM-GRGNIFQKRR
          LP.MLKNAP.L..MKN.NQGS.AGRGKAAILKA.VAARGRG.G..G.GNIFQK.R
Retrocopy LPYMLKNAPILQTMKNNNQGSVAGRGKAAILKACVAARGRGCGL<GHGNIFQKQR

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_2077 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013864	1 retrocopy	retro_cfam_173,
Cavia porcellus	ENSCPOG00000012304	1 retrocopy	retro_cpor_297,
Dipodomys ordii	ENSDORG00000005801	1 retrocopy	retro_dord_791,
Otolemur garnettii	ENSOGAG00000012708	3 retrocopies	retro_ogar_1209, retro_ogar_2077 , retro_ogar_2235,
Rattus norvegicus	ENSRNOG00000050410	1 retrocopy	retro_rnor_232,