RetrogeneDB ID: retro_ogar_2328

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873612.1:150070..150625(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF9
• Ensembl ID: ENSOGAG00000003852
• Aliases: None
• Description: serine/arginine-rich splicing factor 9 [Source:HGNC Symbol;Acc:10791]

Sequence

>retro_ogar_2328
GAGAAAGACTTGGCAGGTCCCTTCTATGAGTACGACCATGTCCGCGAGACCGAGCTCAAGAACCCGCATGGCCTCATGCC
CTTCACGTTCATGCGCTTCGAGGACCCCCCGAGAGGCTGAGGGTGCAATTTTTGGAAGGAATGGTTATGATTATGGCCGG
TGGGGCTTCGCGTGGAGTTCCCCACGACTTACAGAGGTCGGGGTGGGTGGCCCCGTAGTAGAAGGATGGACTTCTTACGA
GAAGATCTGATTTCGGAGTTCTTGTTACAAGACTTCTTTCATCAGGCAGCTGGCCAAGACCTGAAGAGTCACCCGCGAGA
AGCTGGGGGTGTCTGTAATCCAGATGTGCAGAAGGATGGAATGGGGATGGCTGAGTATCTCAAAAAAGAAGACGTGGAAT
ATGCCCCGCGTAAACTGAACGGTAGCCAGTTCCGCCCTCATGGGGGTGACACTTCCAACATCAGAGTTTGTCCTGAGAGA
AGCACCAGCTATGTCTACCCGCAGTCTCAGGCTGGGCCAAGGGGCGGTGACTCTCCTTAACAAAGCAGGGGTTCC

Alignment

ORF - retro_ogar_2328 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.72 %
• Parental protein coverage: 83.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EKDLEDLFYKYGRIREIELKNRHGLVPFAFVRFEDP-RDAEDAIYGRNGYDYGQ-CRLRVEFPRTYGGQG
          EKDL...FY.Y...RE.ELKN.HGL.PF.F.RFEDP.R.AE.AI.GRNGYDYG....LRVEFP.TY.G.G
Retrocopy EKDLAGPFYEYDHVRETELKNPHGLMPFTFMRFEDP>REAEGAIFGRNGYDYGR<VGLRVEFPTTYRGRG

Parental  GWPRGGR-NGPPTRRSDFRVLVSGLPPSGSW-QDLKDHMREAGDVCYADVQKDGMGMVEYLRKEDMEYAL
          GWPR..R..G..TRRSDF.VLV..L..SGSW.QDLK.H.REAG.VC..DVQKDGMGM.EYL.KED.EYA.
Retrocopy GWPRSRR<DGLLTRRSDFGVLVTRLLSSGSW>QDLKSHPREAGGVCNPDVQKDGMGMAEYLKKEDVEYAP

Parental  RKLDDTKFRSHEGETSYIRVYPERSTSYGYSRSRSGSRGRDSPYQSRGS
          RKL....FR.H.G.TS.IRV.PERSTSY.Y..S..G.RG.DSP.QSRGS
Retrocopy RKLNGSQFRPHGGDTSNIRVCPERSTSYVYPQSQAGPRGGDSP*QSRGS

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_2328 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 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012792	1 retrocopy	retro_btau_837,
Choloepus hoffmanni	ENSCHOG00000009241	1 retrocopy	retro_chof_1119,
Callithrix jacchus	ENSCJAG00000001187	1 retrocopy	retro_cjac_442,
Dasypus novemcinctus	ENSDNOG00000012598	2 retrocopies	retro_dnov_1555, retro_dnov_2648,
Homo sapiens	ENSG00000111786	1 retrocopy	retro_hsap_2530,
Macaca mulatta	ENSMMUG00000016494	1 retrocopy	retro_mmul_2154,
Nomascus leucogenys	ENSNLEG00000015661	1 retrocopy	retro_nleu_1931,
Otolemur garnettii	ENSOGAG00000000502	6 retrocopies	retro_ogar_1850, retro_ogar_1959, retro_ogar_2131, retro_ogar_2783, retro_ogar_597, retro_ogar_803,
Otolemur garnettii	ENSOGAG00000003852	1 retrocopy	retro_ogar_2328 ,
Otolemur garnettii	ENSOGAG00000010169	2 retrocopies	retro_ogar_3467, retro_ogar_3481,
Otolemur garnettii	ENSOGAG00000015515	1 retrocopy	retro_ogar_2205,
Otolemur garnettii	ENSOGAG00000025950	1 retrocopy	retro_ogar_2848,
Ochotona princeps	ENSOPRG00000004234	1 retrocopy	retro_opri_878,
Pongo abelii	ENSPPYG00000005031	1 retrocopy	retro_pabe_119,
Sarcophilus harrisii	ENSSHAG00000005685	1 retrocopy	retro_shar_598,
Sus scrofa	ENSSSCG00000009906	1 retrocopy	retro_sscr_745,
Tupaia belangeri	ENSTBEG00000008499	1 retrocopy	retro_tbel_2602,
Tarsius syrichta	ENSTSYG00000006848	4 retrocopies	retro_tsyr_1432, retro_tsyr_1648, retro_tsyr_585, retro_tsyr_891,