RetrogeneDB ID: retro_ogar_3249

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873756.1:192462..193327(+)
• Located in intron of: ENSOGAG00000000362

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPG21
• Ensembl ID: ENSOGAG00000010385
• Aliases: None
• Description: spastic paraplegia 21 (autosomal recessive, Mast syndrome) [Source:HGNC Symbol;Acc:20373]

Sequence

>retro_ogar_3249
ATTATTGTAGATGATGATGACAGTAAGAGATGGTTGCTGTATGATACGGGCCCCAGAAGCATCAGGTGTCCCCTCATATC
CCCCTCCACTCCCCCTCCCCTGTCAGTGGAACTACAGATGTATTTTTCCGGCAGATTTTGGCTTTGACTGGATGGGGGTT
ACCTTGTTATAGCTTTGCAGTATCCAGTTTACTGGTACCATCTTGAATTCTGTGATGGATTCAGAAAACTTTTAGATCAT
TTACAATTGGATAAAGTTCATCTTTTTGGGGCTTCTTTGGGAGGCTTTTTGGCCCCCAAATTTGCTGAATGCACTCATAA
ATCTCCTAGAGTTCATTCCCTCATCCTTTGCAATTTCTTCAGTGATACCTCTATCTTTAACCAAACTTGGACTGCAAACA
GCTTTTGGCTAATGCCAGGATTTATGCTCCTAAAAATAGTTCTTGGAAATTTCTCATCTGGCCCAGTGGACCCTGTGATG
GCTGATGCCATTGATTTCGTGGTGGATAGGTTGGAAAGTTTGGGTCAGAGTGAACTGGCTTCGAGACTTACCCTGAATTG
TCAAAATTCTTATGTGGAACCTCATAAAATTCGGGACATCCCTCTAACCATTACGGATGTGTTTGACCAGAGTACATGTC
AACTGAAGCTGAAGAAGAAATGTACAAGCTGTTATCTCAATGCCCAAAGAGCTCACCTTAAAACAGGAGGCAATTTCCTA
TACCTGTGCAGAAGTGAATCTTTATGTCCAGATACATTTGCTACAATTACAGGGAACCAAATACGTAGCTATTGACCCAT
CGATGATCAGTGCTGAGGAGCTTGAGGTGCATAAAGGCAACCTCAGCATCAGCCAGGAGGAGCAG

Alignment

ORF - retro_ogar_3249 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.51 %
• Parental protein coverage: 93.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  IIVDDDDSKIWSLYDA-GPR----SIRCPLIFLPPVSGTADVFFRQILALTGWG-YRVIALQYPVYWDHL
          IIVDDDDSK.W.LYD..GP.....S...PL....PVSGT.DVFFRQILALTGWG.Y.VIALQYPVYW.HL
Retrocopy IIVDDDDSKRWLLYDT<GPQKHQVSPHIPLHSPSPVSGTTDVFFRQILALTGWG>YLVIALQYPVYWYHL

Parental  EFCDGFRKLLDHLQLDKVHLFGASLGGFLAQKFAEYTHKSPRVHSLILCNSFSDTSIFNQTWTANSFWLM
          EFCDGFRKLLDHLQLDKVHLFGASLGGFLA.KFAE.THKSPRVHSLILCN.FSDTSIFNQTWTANSFWLM
Retrocopy EFCDGFRKLLDHLQLDKVHLFGASLGGFLAPKFAECTHKSPRVHSLILCNFFSDTSIFNQTWTANSFWLM

Parental  PAFMLKKIVLGNFSSGPVDPVMADAIDFMVDRLESLGQSELASRLTLNCQNSYVEPHKIRDIPVTIMDVF
          P.FML.KIVLGNFSSGPVDPVMADAIDF.VDRLESLGQSELASRLTLNCQNSYVEPHKIRDIP.TI.DVF
Retrocopy PGFMLLKIVLGNFSSGPVDPVMADAIDFVVDRLESLGQSELASRLTLNCQNSYVEPHKIRDIPLTITDVF

Parental  DQSA-LSTEAKEEMYKL-YPNARRAHLKTGGN-FP-YLCRSAEVNLYVQIHLLQFHGTKYAAIDPSMVSA
          DQS...STEA.EEMYKL.Y.NA.RAHLKTGGN.FP.Y.C..AEVNLYVQIHLLQ..GTKY.AIDPSM.SA
Retrocopy DQST<MSTEAEEEMYKL>YLNAQRAHLKTGGN<FP<YTC--AEVNLYVQIHLLQLQGTKYVAIDPSMISA

Parental  EELEVQKGNLSVSQEEQ
          EELEV.KGNLS.SQEEQ
Retrocopy EELEVHKGNLSISQEEQ

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_3249 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005282	1 retrocopy	retro_cjac_67,
Macropus eugenii	ENSMEUG00000013791	1 retrocopy	retro_meug_116,
Oryctolagus cuniculus	ENSOCUG00000016136	1 retrocopy	retro_ocun_204,
Otolemur garnettii	ENSOGAG00000010385	1 retrocopy	retro_ogar_3249 ,
Ictidomys tridecemlineatus	ENSSTOG00000010101	1 retrocopy	retro_itri_1397,