RetrogeneDB ID: retro_ogar_2205

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873601.1:1836561..1837396(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF4
• Ensembl ID: ENSOGAG00000015515
• Aliases: None
• Description: serine/arginine-rich splicing factor 4 [Source:HGNC Symbol;Acc:10786]

Sequence

>retro_ogar_2205
GATGGCAGTTACAGTCTGGACACAGGGAATATGGTTATTGAAGAAGTGGCCAAGATAAATATGGCTCTCCTACCTGCACA
AAGTACAGGCTTATTGTGGAGAATTTGTCAAGTCGGTGCAGCTGGCAAGACTTGAAGGATTATATGCATCGGGCAGGAGA
AGTGACTTAAGCAGATACTCACAAGGGACACAAAAATGAAGTGATTGAATTTGTATCTTATTCTGATATGAAAAGAGCTT
TGGAAAAGATGGGTGGAACTGAAGTCAAGGGCAGGAAAATCAGATTAGTTGAAGACAAGCCGGGTTCCAGATGACGCCGA
TCCTACTCCAGGAGCTGGAGCCATTCAAGGCCTTGCCCTCAAAGCAGACACTCCTGTAAAAGCAGAAGCCAAAGCAGCAG
CAGCAAAAGTGGTCATTCTAAGAGCAGATCCCCGTCCAGGTCAGGCTCCCACTCACGGAGCAAGAGCTGCAGCCGGAGCA
AGAGTGAGAGGAGCAGGAAGTGGGGCAGCAAGTGAGACAGCAAGACAGGTAGCAGAAGAAGGAAGACACAGACAGCTCAC
AGTCGCGGTGGCCCTCCTGCTCAGTGTCAAAGGACCGTGAACACACCAAGTCCAAATCTGGCCAGAGGGAAGGCCGAGGG
GAGAGCGAGGATGCTGGCACCAATCAGGAGACCCAGCCTAGGTCAGGATCGAATTCCAAATCGAAACCAAACTGTCTGTC
AGAATCACGCTCCAGATCAAAGTCAGCTTCAAAAACCTGATCTCGGTCCAAGTCTCCATCCAGGTCTGCTTCCAGATCAG
CCTCCCCGGCTAGATCTAGGTCCCACTCAAGGTCC

Alignment

ORF - retro_ogar_2205 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.74 %
• Parental protein coverage: 57.61 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DGSYG-SGRSGYGYRRSGRDKYGPPTRTEYRLIVENLSSRCSWQDLKDYMRQAGEVTYADAHKGRKNEGV
          DGSY..SG...YGY.RSG.DKYG.PT.T.YRLIVENLSSRCSWQDLKDYM..AGEVT.AD.HKG.KNE.V
Retrocopy DGSYS<SGHREYGY*RSGQDKYGSPTCTKYRLIVENLSSRCSWQDLKDYMHRAGEVT*ADTHKGHKNE-V

Parental  IEFVSYSDMKRALEKLDGTEVNGRKIRLVEDKPGSRRRRSYSRSRSHSRSRSRSRHSRKSRSRSGSSKSS
          IEFVSYSDMKRALEK..GTEV.GRKIRLVEDKPGSR.RRSYSRS.SHSR....SRHS.KSRS.S.SSKS.
Retrocopy IEFVSYSDMKRALEKMGGTEVKGRKIRLVEDKPGSR*RRSYSRSWSHSRPCPQSRHSCKSRSQSSSSKSG

Parental  HSKSRSRSRSGSHSRSKSRSRSQSRSRSKKEKSRSPSKDNKSRSRSRSLGKSHSKNKDQAEEKIQNN-NS
          HSKSRS.SRSGSHSRSKS.SRS.S..RS.K..S...SK.....SR.R.....HS.....A......N...
Retrocopy HSKSRSPSRSGSHSRSKSCSRSKS-ERSRKWGSK*DSK---TGSRRRKTQTAHSRGGPPAQCQRTVN<HT

Parental  TGKSKSRSPSRHKSKSKSRSRSQERRAEEEKRGSVSRSRSQEKSRNQDHSRSRSRGGSRSRSRSKSKDKS
          ..KS..R...............Q.R.....K......S.S...S.......SRS...SRS.SRS.S...S
Retrocopy KSKSGQREGRGESEDAGTNQETQPRSGSNSKSKPNCLSESRSRSKSASKT*SRSKSPSRSASRSASPARS

Parental  KSRKRS
          .S..RS
Retrocopy RSHSRS

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_2205 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 8 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013858	1 retrocopy	retro_chof_1058,
Callithrix jacchus	ENSCJAG00000009971	3 retrocopies	retro_cjac_3688, retro_cjac_3883, retro_cjac_3899,
Microcebus murinus	ENSMICG00000008965	1 retrocopy	retro_mmur_1597,
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,