RetrogeneDB ID: retro_ogar_2848

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873672.1:1282425..1283164(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF1
• Ensembl ID: ENSOGAG00000025950
• Aliases: None
• Description: serine/arginine-rich splicing factor 1 [Source:HGNC Symbol;Acc:10780]

Sequence

>retro_ogar_2848
GGAGGTGGTGTGATTCATGGCCCATCGTGGAACAATGATTGCAGCATCTTCGTGGGTAACTTACCTCCAGACATGCGAAC
CAAGGACATTGAGGACATGTTCTTCAAATAGAGCTCTATGGGAGACATCAACCTCAAGAATTGACATGGGGTATCACCTT
GAGCTTCGGTTGAATTTGAGGACCCGCAAGATGCTGAGGACGCAGGGTACGGTTGTGAGGACTATGATTATGGTGGATCC
CGTCTGTGTGTGGAGTTTCCTGCAAGACGCCCTGGTACAGGCTGAGGCAGCGATGAGGCATAGAGCTGGTGGAGCTCCCT
GAGGCAGCTATAGCCTCCCTTCTAGGCGGTCTGAAAACAGAGTGGTTGTCTCTGTACTGCCTCCAAGTGGAAGCTGGCAG
GATTTAAAGGATCACCCGAGGGAAGCAGGTGATGTATGTTATGCTGATATTTACCAAGATACCACTAGTGTTGTGGAGTT
TGTACAGAAAGAAGATATAACCTATGCCATTGAAGAACTGGATAACACTAAGTTTAGATCTCATGAGGGAGAAACTGCCT
ACATCCAGGTTAACGTTGATGGGCCTAGAAGTCCAAGTTATGGAAGATCTCCATCCCAAAGCCATAGTAGTAGCAGAAGT
GGTAGCAGAGGCAACAGCAAGAGTCCCAGTTATGCCCCAAGGAGAAGCAGAGCATCACCACGTTATTCTCCCCATCATGG
CAGATCTTGCTCTCATACA

Alignment

ORF - retro_ogar_2848 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.26 %
• Parental protein coverage: 99.19 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVY
          GGGVI.GP..NNDC.I.VGNLPPD.RTKDIED.F.K.....DI.LKN..G..P.A.VEFEDP.DAEDA.Y
Retrocopy GGGVIHGPSWNNDCSIFVGNLPPDMRTKDIEDMFFK*SSMGDINLKN*HGVSP*ASVEFEDPQDAEDAGY

Parental  GRDGYDYDGYRLRVEFPRSGRGTGRGGGGG-GGGGAPRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHM
          G...YDY.G.RL.VEFP....GTG.G.......GGAP.G.Y..PSRRSENRVVVS.LPPSGSWQDLKDH.
Retrocopy GCEDYDYGGSRLCVEFPARRPGTG*GSDEA>RAGGAP*GSYSLPSRRSENRVVVSVLPPSGSWQDLKDHP

Parental  REAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRSRS
          REAGDVCYAD.Y.D.T.VVEFV.KED.TYA...LDNTKFRSHEGETAYI.V.VDGPRSPSYGRS.S.S.S
Retrocopy REAGDVCYADIYQDTTSVVEFVQKEDITYAIEELDNTKFRSHEGETAYIQVNVDGPRSPSYGRSPSQSHS

Parental  RSRSRSRSNSRSRSYSPRRSRGSPRYSPRHSRSRSRT
          .SRS.SR.NS.S.SY.PRRSR.SPRYSP.H.RS.S.T
Retrocopy SSRSGSRGNSKSPSYAPRRSRASPRYSPHHGRSCSHT

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_2848 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 7 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000011040	1 retrocopy	retro_mluc_307,
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	ENSOPRG00000001234	2 retrocopies	retro_opri_335, retro_opri_625,