RetrogeneDB ID: retro_ogar_3085

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873711.1:2114228..2114564(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPD1
• Ensembl ID: ENSOGAG00000007833
• Aliases: None
• Description: small nuclear ribonucleoprotein D1 polypeptide 16kDa [Source:HGNC Symbol;Acc:11158]

Sequence

>retro_ogar_3085
AGACTTTTGATGAAATTGAGTCATTTGCCAGTAACTGTTGAATTGCAGAGTGGATCAGAGGGCCATGGAACAATCACAGG
TGTAGATATCAGCATATTCATTTCACATCTTAAAGCTATGAAAATGACCCTGAAGGACAGAGCCCTTGTACAGCTAAAAA
CACTGAGTATTCAAGGAAATAACTTTTGATATTCTATTCTACCAGACAGCTTACCTCTGAATACACTACTTGTGGATGTT
GAACCTAAGGTGAAATTTAAGAAAAATGAAACTATTGCAAGAAGAAGCCAAGGTCGAGGCAGAGGAAGTAGATGTGGCCA
TGACAGGAAGAAGGGG

Alignment

ORF - retro_ogar_3085 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.07 %
• Parental protein coverage: 93.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RFLMKLSHETVTIELKNGTQVHGTITGVDVSMN-THLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDS
          R.LMKLSH..VT.EL..G...HGTITGVD.S....HLKA.KMTLK.R..VQL.TLSI.GNN..Y.ILPDS
Retrocopy RLLMKLSHLPVTVELQSGSEGHGTITGVDISIFISHLKAMKMTLKDRALVQLKTLSIQGNNF*YSILPDS

Parental  LPLDTLLVDVEPKVKSKKREAVAGRGRGRGRGRGRGRGRGRG
          LPL.TLLVDVEPKVK.KK.E..A.R..GRGRG...G..R..G
Retrocopy LPLNTLLVDVEPKVKFKKNETIARRSQGRGRGSRCGHDRKKG

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_3085 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002576	1 retrocopy	retro_amel_1905,
Bos taurus	ENSBTAG00000008292	3 retrocopies	retro_btau_144, retro_btau_706, retro_btau_84,
Mustela putorius furo	ENSMPUG00000005567	1 retrocopy	retro_mputfur_185,
Nomascus leucogenys	ENSNLEG00000006822	2 retrocopies	retro_nleu_2824, retro_nleu_945,
Oryctolagus cuniculus	ENSOCUG00000023761	1 retrocopy	retro_ocun_224,
Otolemur garnettii	ENSOGAG00000007833	1 retrocopy	retro_ogar_3085 ,