RetrogeneDB ID: retro_mmur_1516

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_73975:3693..4889(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMICG00000014172
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GPATCH4
• Ensembl ID: ENSMICG00000013624
• Aliases: None
• Description: G patch domain containing 4 [Source:HGNC Symbol;Acc:25982]

Sequence

>retro_mmur_1516
CATGGGGTGGGACACGACCCTGCAAGGAGTCACAAACCACGGGTGGAACGAGCTCTTCACAAGACTGCAGCCAACTTGGT
AGTGGAGACTGGACAGGATGGAGGACAGATAAGGCGCCTTTCTACGGAGACCACCTGTCGAAACGTAATCCTCCCAAGCC
CAACTTGCTGTATCAGAAGTTTGCGAAGACGGCTACCCTGACTTCCAGATGGAGGGAAGCCAGACAAAGACATGGAGAGC
TGCAGTGATGATGACAACCAGAGGCCCAACCCCCAAAGATTCTGACGGATGAGATGCTGCTCCAAGCCTGTGAGGGCGAA
CAGCACACAAGGCAGCCGTCTTGGGATTACGATGGAGGCCAGGCTTGCTCGGCTGGAGGCCCAGGAGCAGGCCTTCCTGG
CTCATCTCAAAGGCCAGGCCTCTCAGGCCTCTCAACCACAGTCAGAGAGCAAGCCCCGCAAAAAGAACAAAAAGAAAAGG
AAGCACAAAGAGTAGCCAAGAGGCTACAGCACCTGAAAGGAACGCAGATGAGAAGCAGCCAGAACACACTGACCAGAGCA
CCAGGAAAAGCAAGAAGAAGAAAAGGCAACATCAAGAACGAAAGGTCTCAGATAAGAGAGAGGGAACGACTGTAAGGAAT
GGGGAGGAAGAAGCTGCGGGAACAAGTGAGCTTAGGGAATTGAAGAGCAGAGAGCAAACAGATCAGTCCCCCAGGAAAAG
GAAGAGAAAGAAGAGGCAGCACCATGAAGAGGAGAAGACGGGAGTCTTGGGTGACAGAGGAAGAGGTAAGGAGGCTACAG
GTGCTGTCAGGACAGAGGAGGCAGAGAGCACAGTGTCCACTGACCCGGGCAGCAAAAGCAAGAAGAAACAGCACCATGAG
AAGGATTTGAACCTAGAGGATGAAGAAGTTGAGGAAACCGTTTTAGACGGTGGGACTACGGACACAGAGAACAGAGCATG
CAGTGATGGAGGAAGGAGAAGCAAGAAGAAAACACGGCGACATCGAGAGGAGGAGGAAGTCGTCGATGTAAGGGATGGAA
GAGATGAGGAGGACGGCAGGACTCGGAAAGCAGGGAGCAGAGCACACACTGGCTCACGCAGCAGAGGTGAGAAGAGGAGG
AAACGGCGGTCAGAGGAAGCAAGCTGGAGTTGGCACCGACCAGACAACCAAAAAGAAGAAACAGAGGAAGGGAGAC

Alignment

ORF - retro_mmur_1516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.73 %
• Parental protein coverage: 88.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 10

Retrocopy - Parental Gene Alignment:

Parental  HGVGHD-PAKE-FTNHWWNELF-NKTAANLVVETGQDGVQIRRLSTETTCRNP--PKP-NLLYQKFVKTA
          HGVGHD.P.KE..TNH.WNELF..KTAANLVVETGQDG.QIRRLSTETTCRN...P.P.NLLYQKF.KTA
Retrocopy HGVGHD<PCKE<VTNHGWNELF<HKTAANLVVETGQDGGQIRRLSTETTCRNVILPSP<NLLYQKFAKTA

Parental  TLTS-DGEKPDKDMESCSDDDNQRPN-PPKILTDEMLLQACE-GRTAHKAA-RLGITMKAKLARLEAQEQ
          TLTS.DG.KPDKDMESCSDDDNQRPN.PPKILTDEMLLQACE.GRTAHKAA.RLGITM.A.LARLEAQEQ
Retrocopy TLTS>DGGKPDKDMESCSDDDNQRPN<PPKILTDEMLLQACE<GRTAHKAA<RLGITMEARLARLEAQEQ

Parental  AFLAHLKGQDSQASQPQSESKPPKKKKKKRKHKE-EEEATASERNADEKHPEHTDQSTRKSKKKKRQHQE
          AFLAHLKG.......PQSESKP.KK.KKKRKHKE...EATA.ERNADEK.PEHTDQSTRKSKKKKRQHQE
Retrocopy AFLAHLKGXXXXXXXPQSESKPRKKNKKKRKHKE>SQEATAPERNADEKQPEHTDQSTRKSKKKKRQHQE

Parental  QMVSDKREGTTVGNEEEEATGTSELRELKSREQTDQSPRKRKRKKKQHHGEEKTGVLDEGGRGK-ATGAV
          ..VSDKREGTTV.N.EEEA.GTSELRELKSREQTDQSPRKRKRKK.QHH.EEKTGVL...GRGK.ATGAV
Retrocopy RKVSDKREGTTVRNGEEEAAGTSELRELKSREQTDQSPRKRKRKKRQHHEEEKTGVLGDRGRGKEATGAV

Parental  RTEAVESTVYTDPCSRSKKKRHCEKDLNLEDEEVGETVLDSGTRDTENRACSDGGRRSKKKTRRHREEEE
          RTE..ESTV.TDP.S.SKKK.H.EKDLNLEDEEV.ETVLD.GT.DTENRACSDGGRRSKKKTRRHREEEE
Retrocopy RTEEAESTVSTDPGSKSKKKQHHEKDLNLEDEEVEETVLDGGTTDTENRACSDGGRRSKKKTRRHREEEE

Parental  VVNVGDERDEGDGRTRKAESSAHTGSSSRGKKRRKRQRKKAGVGTDQ-RTKKK-KQKKGD
          VV.V.D.RDE.DGRTRKA.S.AHTGS.SRG.KRRKR....A........T.KK.KQ.KGD
Retrocopy VVDVRDGRDEEDGRTRKAGSRAHTGSRSRGEKRRKRRSEEASWSWHR>QTTKKKKQRKGD

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_1516 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1516 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000013624	2 retrocopies	retro_mmur_1516 , retro_mmur_63,
Otolemur garnettii	ENSOGAG00000006698	1 retrocopy	retro_ogar_2053,
Rattus norvegicus	ENSRNOG00000018969	1 retrocopy	retro_rnor_2299,