RetrogeneDB ID: retro_mmur_542

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_3743:612951..613841(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FUCA1
• Ensembl ID: ENSMICG00000007213
• Aliases: None
• Description: fucosidase, alpha-L- 1, tissue [Source:HGNC Symbol;Acc:4006]

Sequence

>retro_mmur_542
GTCGGAGCAGCTGTCCGGAAGACGAACACACGCTATGGACTCTGCCACCCCCTCTTCCTATGGTTCCACCCACTCTACCT
ACTGGACAAGAAAAATGGCTTTAAAATGCAGCATTTTATTAATATCGGTGTGAAAACAATGCCAGGGCTATACTACCTTG
TTAACAGGCACAAACCTGATGTGATTTGGTCTGATGGAGCGTGGGAACGTCCTGATATTTATTGGAACTCTATAGGTTTT
CTTTCTGGGCTCTACAATGATAGCCCTGTCAAGGAAGAGGTGGCAATAAATGACCAGTGGGGTCAGAAATGCTCCCATCA
CCGTGAAGGATACCACGACTGTCAAGATAAACTTAAGCCTGGGAGGTTGCCAGACCACAAGTGGGAGATGTCACTACTGA
TGAGAAACCCTGGGGTTATCATCGGACAGGGCGATGTCTGGCTTTGCAAGCGCATCTGAAAGCATTCTGGCACTGGGTCA
GACATTAAGTTTGGCAGACAGCTCCCTTCTTAACACTGGACTCGCTAAACTGATTGTTCCCATCTTCCAAGAAAGGCTTC
TTACTGTTGGGAAGTGGCTGAGCATCCAGGGATAGGCTGTCCAGGCCTTTAAGCGATGGAGGGTGTTGTGATCAGAAAAG
AACATGGTATCTGTGCGGTGTACCTCCAATGGATCGGCTGTTTATGCCATTTTACTGCAATGGCCAGAAAATGGAACCTT
CAACCTCGAATCCCCCATAACTACCGCAACTACAAAGGTAACAGTGTGGGAATCCAAGAGGATCTGAAGTGATCCACAGG
TCTGGATAGAGGCCTTCCCGTTTCTCTGCCCCAATGCCACCCTCTGCTCTCCCAGTAGAGTTTGCTTGGCCTGTAAAGCT
GACAGGAGTG

Alignment

ORF - retro_mmur_542 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.88 %
• Parental protein coverage: 63.11 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LGTALRNRSIRYGLYHSLFE-FHPLYLLDKKNGFKTQYFVR--AKTLPELYDLVLSYKPDLIWSDGEWEC
          .G.A.R....RYGL.H.LF..FHPLYLLDKKNGFK.Q.F.....KT.P.LY.LV...KPD.IWSDG.WE.
Retrocopy VGAAVRKTNTRYGLCHPLFLWFHPLYLLDKKNGFKMQHFINIGVKTMPGLYYLVNRHKPDVIWSDGAWER

Parental  PDTYWNSTEFLAWLYNDSPVKDEVVVNDRWGQNCSCHHGGYYNCQDKYKPQGLPDHKWEMCTSM-DKLSW
          PD.YWNS..FL..LYNDSPVK.EV..ND.WGQ.CS.H..GY..CQDK.KP..LPDHKWEM...M...L..
Retrocopy PDIYWNSIGFLSGLYNDSPVKEEVAINDQWGQKCSHHREGYHDCQDKLKPGRLPDHKWEMSLLM>ETLGL

Parental  GYRRDMAMSDIAEESEIIAELVQTVSLGGNYLLNIGPTKDGLIVPIFQERLLAVGKWLSINGEAIYASTP
          ...R.M.....A.ES..I..L.QT.SL....LLN.G..K..LIVPIFQERLL.VGKWLSI.G.A..A...
Retrocopy SSDRAMSGFASASES--ILALGQTLSLADSSLLNTGLAK--LIVPIFQERLLTVGKWLSIQG*AVQAFKR

Parental  WRVQ-FEKN-TSVWYTSKGGDVYAIFLQWPGNGVLNLKSPVPTPTTTIMM-LGIQEDLKWSPDPDKGVII
          WRV...EKN..SV..TS.G..VYAI.LQWP.NG..NL.SP..T.TT......GIQEDLK.S...D.G...
Retrocopy WRVL*SEKNMVSVRCTSNGSAVYAILLQWPENGTFNLESPITTATTKVTV<VGIQEDLK*STGLDRGLPV

Parental  ILPQ-LPPSAMPVEYAWTIKLTGV
          .LPQ..PPSA.PVE.AW..KLTGV
Retrocopy SLPQ<MPPSALPVEFAWPVKLTGV

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_542 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_542 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012304	2 retrocopies	retro_chof_1090, retro_chof_542,
Equus caballus	ENSECAG00000024652	1 retrocopy	retro_ecab_450,
Loxodonta africana	ENSLAFG00000015305	1 retrocopy	retro_lafr_252,
Microcebus murinus	ENSMICG00000007213	1 retrocopy	retro_mmur_542 ,
Tupaia belangeri	ENSTBEG00000013160	1 retrocopy	retro_tbel_3390,