RetrogeneDB ID: retro_mmur_993

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_1523:1119..2632(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTHFD1
• Ensembl ID: ENSMICG00000013011
• Aliases: None
• Description: methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase [Source:HGNC Symbol;Acc:7432]

Sequence

>retro_mmur_993
GGGGCAATAGTCATCGACTGTGGGATCAATTATGTCCCAGATGATACAAAATCAAACGGGAGAAGGATTGTGGGTGATGT
GGCATACAACGAGGCCAAAGAGGGGGCGGGCTTCATCACTCCTGTTCCTGGCGGCGTCGGGCCCATGACGGTGGCAATGC
TGATGCAGAGCACGGTAGAGAGTGCAAGGGGTTTCCTGGAGAAATACAAGCCAGGAAAGTGGAGTGTTCAGTATAACAAC
CTTAACCTGAAGACACCTGTTCCAAGTGACATTGCTATATCATGATCTTGCAAACCAAAGCCCATTGGTACGCTGGCTCG
AGAAATTGGCCTGTTCTCTGAAGAGGTGGAATAGTATGGTGAGACAAAGGCCAAAGTCCTGCTGTCAGCACTGGAACGCC
TGAAACACCAGCCTGACGGGAAATACGTGGTGGTGACTGCAATAACTCCAACGCCCCTGGGAGAAGGGAAAAGTACAACC
ACAATCGGGCTGGTGCAAGCCCTGGGTGCCCATCTTTTCCAGAACGTCTTTGCGTGTGTGCGACAGCCTTCCCAGGGCCC
CCACCTTTGGAATAAAAGGTGGTGCTGCAGGAGGCGGCTACTCCCAGGTCATTCCTAGGGAAGAGTTTAATCTCCACCTC
ACTGGTGACATCCATGCCATCACTGCAGCTAATAACCTGCTTGCCGCGGCCATTGATGCCCGGATATTCCATGAACTGAC
CCAGACAGACAAGGCTCTCTTTAATCGTTTGGTGCCCTCAGTAAATAGAGTGAGAAAGTTCTCTGATATCCAAACCCGAA
GGTTAAGGAGACTAGGCATTGAAAAGACTGACCCTACCACACTGACAGATGAAGAGATACACAGATTTGCAAGATTGGAT
ATTGATCCAGAAACCATAACTTGGCAAAGAGTGTTGGATACCAATGATAGATTCCTGCGGAAGATCACAATTGGACAGGC
TCCAACAGAGAAAGGGCACACACGGACGACCCAGTTTGATATCTCAGTGGCCAGTGAAATCATGGCTGTCCTGGCCCTCA
CCCGTTCTCTGGAAGACATGAGAGAGAGACTGGGCAAAATGGTGGTGGCCTCCAGAAGAAAGGGGAGCCCATCAGTGCCG
AAGACCTGGGGGTGAGTGGCTCATTGACAGTGCTTATGAAGGATACGATCAAGCCTAACCTCATGCAGACGTTAGAGGGC
ACTCCGGTGTTCGTCCACGCCGGCCCCTTCGCCAACATCTCACATGGCAATTTTGTTTATCATCGCAGACCGGATCGCAC
TCAAACTTGTCAGCCCAAAAGAGTCTGTAGTGACCGAAGCAGAATTCGGAGCAGACATTGGAATGGAAAAGTTTTTAAAC
ATCAAATGCAGGTACTCTGGCCTCCGCCCTCATGTGGTGGTGCTCGTTGCTACTGTCAGGGCTCTTAAAATGCACGGGGG
CGTCCCCACGGTCCTGGCTGGATTGCCTCTTCCCAAGGCTTGCATAGAGGAGAATCTGGAGCTGGTTGAAAAG

Alignment

ORF - retro_mmur_993 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.29 %
• Parental protein coverage: 55.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GAIVIDCGINYIPDNTKSNGRRIVGDVAYNEAKERAGFITPVPGGVGPMTVAMLMQSTVESARGFLEKYK
          GAIVIDCGINY.PD.TKSNGRRIVGDVAYNEAKE.AGFITPVPGGVGPMTVAMLMQSTVESARGFLEKYK
Retrocopy GAIVIDCGINYVPDDTKSNGRRIVGDVAYNEAKEGAGFITPVPGGVGPMTVAMLMQSTVESARGFLEKYK

Parental  PGKWSIQYNNLNLKTPVPSDIAISRSCKLKPIGTLAREIGLLSEEVELYGETKAKVLLSALERLKHQPDG
          PGKWS.QYNNLNLKTPVPSDIAIS.SCK.KPIGTLAREIGL.SEEVE.YGETKAKVLLSALERLKHQPDG
Retrocopy PGKWSVQYNNLNLKTPVPSDIAIS*SCKPKPIGTLAREIGLFSEEVE*YGETKAKVLLSALERLKHQPDG

Parental  KYVVVTGITPTPLGEGKSTTTIGLVQALGAHLFQNVFACVRQPSQG-PTFGIKGGAAGGGYSQVIPMEEF
          KYVVVT.ITPTPLGEGKSTTTIGLVQALGAHLFQNVFACVRQPSQG.PTFGIKGGAAGGGYSQVIP.EEF
Retrocopy KYVVVTAITPTPLGEGKSTTTIGLVQALGAHLFQNVFACVRQPSQG>PTFGIKGGAAGGGYSQVIPREEF

Parental  NLHLTGDIHAITAANNLVAAAIDARIFHELTQTDKALFNRLVPSVNGVRKFSDIQIRRLRRLGIEKTDPT
          NLHLTGDIHAITAANNL.AAAIDARIFHELTQTDKALFNRLVPSVN.VRKFSDIQ.RRLRRLGIEKTDPT
Retrocopy NLHLTGDIHAITAANNLLAAAIDARIFHELTQTDKALFNRLVPSVNRVRKFSDIQTRRLRRLGIEKTDPT

Parental  TLTDEEINRFARLDIDPETITWQRVLDTNDRFLRKITIGQAPTEKGHTRTTQFDISVASEIMAVLALTSS
          TLTDEEI.RFARLDIDPETITWQRVLDTNDRFLRKITIGQAPTEKGHTRTTQFDISVASEIMAVLALT.S
Retrocopy TLTDEEIHRFARLDIDPETITWQRVLDTNDRFLRKITIGQAPTEKGHTRTTQFDISVASEIMAVLALTRS

Parental  LEDMRERLGKMVVAS-SKKGEPISAEDLGVSGALTVLMKDAIKPNLMQTLEGTPVFVHAGPFANIAHGN-
          LEDMRERLGKMVVAS..KKGEPISAEDLGVSG.LTVLMKD.IKPNLMQTLEGTPVFVHAGPFANI.HGN.
Retrocopy LEDMRERLGKMVVAS<QKKGEPISAEDLGVSGSLTVLMKDTIKPNLMQTLEGTPVFVHAGPFANISHGN>

Parental  SSIIADRVALKLVGPEGFVVTEAGFGADIGMEKFFNIKCRYSGLRPHVVVLVATVRALKMHGGGPTVTAG
          ..IIADR.ALKLV.P...VVTEA.FGADIGMEKF.NIKCRYSGLRPHVVVLVATVRALKMHGG.PTV.AG
Retrocopy LFIIADRIALKLVSPKESVVTEAEFGADIGMEKFLNIKCRYSGLRPHVVVLVATVRALKMHGGVPTVLAG

Parental  LPLPKAYIEENLELVEK
          LPLPKA.IEENLELVEK
Retrocopy LPLPKACIEENLELVEK

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_993 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_993 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 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015967	1 retrocopy	retro_cfam_300,
Homo sapiens	ENSG00000100714	1 retrocopy	retro_hsap_4839,
Gorilla gorilla	ENSGGOG00000005251	1 retrocopy	retro_ggor_3018,
Microcebus murinus	ENSMICG00000013011	6 retrocopies	retro_mmur_1069, retro_mmur_1250, retro_mmur_1462, retro_mmur_451, retro_mmur_777, retro_mmur_993 ,
Macaca mulatta	ENSMMUG00000001319	1 retrocopy	retro_mmul_2583,
Pan troglodytes	ENSPTRG00000006435	1 retrocopy	retro_ptro_3223,