RetrogeneDB ID: retro_mmur_1597

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_8952:20092..21198(+)
• Located in intron of: ENSMICG00000009998

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF4
• Ensembl ID: ENSMICG00000008965
• Aliases: None
• Description: serine/arginine-rich splicing factor 4 [Source:HGNC Symbol;Acc:10786]

Sequence

>retro_mmur_1597
TATGGCTTTGTGGAGTCTGATGATCTGTGTGATGCAGATGCTGTTTATGAACTGAACGGCAAAGACCTCTGTGGTGAGCG
AGTAATTGTTGAGCATGCCTGCGGCCCACATGAGATGGCAGTTACAGTTCTGGAGGCAATGGATATGGTTATAGAAGAAG
TGACCGAGATAAATATAGCCCTCCTACCTGTACAGAGTACAGACTTATTGCGGAGAATGTGTCAAGTCAGTGCAGCTATC
AAGACCTAAAGGATTATATGCATCAGATAGGAGAAGTGACTTATGCAGCTCCTCATAAGGGACGAAAAAACGAAGGGGTG
ACTGAATTTGTATCTTATTCTGATATGAAAAGAGCTTTGGAAAAGTTAGATGGAACTGAAGTCAATGGCAGAAAAATCAG
ATTAGTTAAAGACAAGTCAGGTTCCTGACCACGCCAGTCCTAATCCAGGAGCCAGAGCCATTCAAGGTCTCACTCTCAAA
GCAGACATTTCTGTAAGAGCAAAGCTAAAGTGGCAGCAGCAAAAGCAGTCATTCTAAGAGTAGATCCCTATCCAGGCTGG
GCTCCTACTCCCAAAGCAAGAGCCGCAGCCGTAGCCAGAGCTGGAGTCAAAGCAAGAAAAAGAAAAGCAGGCGCCCAGCA
AGGACAAGAGCCACAGATGCAGCGCAGGCAAAAGCCACAGCAAAAGCAAAGCCCAAGCTGAAGAGAAGATCCAGAGCAAT
GACAGTGCTGGGACATCCAAGAGCCAGAGGCCCAGCAGGCATAAAAGTAAAAGGATGAGTCAGAGCAGGAGTCAGCAGAG
GACAGTGGAGGAGAAGCAAGGGAGTGTGAGCGGGAGCTGGAGCCAGAAGGGCCTCCTCAAGAGTCGCAGCCACAACTACA
GCAGAGGGGCAGCAGGAGCCACAGAAAGAGCAAGGGCAGGATGAGAAGCAGGGAAGAGAGCTGGAGCAAGAGTGAGAGGA
ACAGAAGCTGAGGCAGTGATTAAGACAGCAAGGCAGGCAGCAGCAAGAAAAAGGAGGAAGACACTGACTACTCCCAGTCC
CAATCACAGTCCCGCACAGAGTCAAAGGAGCAGGCACTTGCCAAATCCTAGTCTGGCTGGAGGGAA

Alignment

ORF - retro_mmur_1597 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.75 %
• Parental protein coverage: 82.93 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  YGFVEFDDLRDADDAVYELNGKDLCGERVIVEHARGPRR-DGXXXXXXXGYGYRRSGRDKYGPPTRTEYR
          YGFVE.DDL.DAD.AVYELNGKDLCGERVIVEHA.GP...DG.......GYGYRRS.RDKY.PPT.TEYR
Retrocopy YGFVESDDLCDAD-AVYELNGKDLCGERVIVEHACGPHE<DGSYSSGGNGYGYRRSDRDKYSPPTCTEYR

Parental  LIVENLSSRCSWQDLKDYMRQAGEVTYADAHKGRKNEGVIEFVSYSDMKRALEKLDGTEVNGRKIRLVED
          LI.EN.SS.CS.QDLKDYM.Q.GEVTYA..HKGRKNEGV.EFVSYSDMKRALEKLDGTEVNGRKIRLV.D
Retrocopy LIAENVSSQCSYQDLKDYMHQIGEVTYAAPHKGRKNEGVTEFVSYSDMKRALEKLDGTEVNGRKIRLVKD

Parental  KPGSRRRRSYSRSRSHSRSRSRSRHSRKSRSR-SGSSKSSHSKSRSRSRSGSHSRSKSRSRSQSRSRSKK
          K.GS..R.S.SRS.SHSRS.S.SRH..KS....SGSSKSSHSKSRS.SR.GS.S.SKSRSRSQS.S.SKK
Retrocopy KSGS*PRQS*SRSQSHSRSHSQSRHFCKSKAK<SGSSKSSHSKSRSLSRLGSYSQSKSRSRSQSWSQSKK

Parental  EKSR-SPSKDNKSRSRSRSAGKSRSKSKDQAEEKIQNNDSAGKSKSRSPSRHKSKSKSRSRSQERRAEEE
          .KSR..PSKD...R....SAGKS.SKSK.QAEEKIQ.NDSAG.SKS..PSRHKSK..S.SRSQ.R...EE
Retrocopy KKSR<APSKDKSHRC---SAGKSHSKSKAQAEEKIQSNDSAGTSKSQRPSRHKSKRMSQSRSQQRTV-EE

Parental  KRGSVSRGRSQEKGLLKSRSHSRSRG-GSRSRSRSKSKDKSKGRKRSREESRSRSRSRSKSERSRKRGSK
          K.GSVS.G....KGLLKSRSH..SRG.GSRS...SK....S.....S..E...R.RS......S....SK
Retrocopy KQGSVS-GSWSQKGLLKSRSHNYSRG<GSRSHRKSKGRMRSREESWSKSE---RNRS*GSD*DSKAGSSK

Parental  RDSKAGSSKKKKKEDTDRSQSRSPSRSVSKERE
          ..................S.......S.S..RE
Retrocopy KKEEDTDYSQSQSQSRTESKEQALAKS*SGWRE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Microcebus murinus was not studied using RNA-Seq expression data.

ChIP-Seq

Microcebus murinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmur_1597 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1597 was not experimentally validated.

Homology

Retrocopy orthology:

Microcebus murinus 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 11 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	ENSMICG00000004674	5 retrocopies	retro_mmur_1090, retro_mmur_160, retro_mmur_287, retro_mmur_710, retro_mmur_916,
Microcebus murinus	ENSMICG00000008965	1 retrocopy	retro_mmur_1597 ,
Otolemur garnettii	ENSOGAG00000015515	1 retrocopy	retro_ogar_2205,