RetrogeneDB ID: retro_mmur_1250

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_36192:4087..6232(-)
• 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_1250
GGCGACAGACATGATTCCAATCTTTATATAAATGTGAAGCTGAAGGCTGCTGAAGAGGTTGGGATCAAAGCCACTCACAT
TAAATTACCAAGAACAGCCACAGAATCTGAGGTGTTAAAGTACATTAGATCTTTGAATGAAGACTCTACCGTACATGGAT
TCATACTGCAGCTACCTTTAGATTCAGAAAATGCTATTAACATTGAAGCAGTGATCAATGCTATCACACCCGAAAAGGAT
GTGGATGGATTGACTAGTATCAGTGCTGGGAAACTCACTAGAGGTGATCTAAATGACTGTTTTGTCCCTTGTACGCCTAA
AGGATGCTTGGAACTCATCAAAGAGACAGGGGTGGAGATCGCCGGAAAGTACGCCATGGTGGTCGGGTGCAGTAAAATAG
TAGGAGCCCCAATGTATGACTTGCTTCTGTGGAACAATGCCACAGTGACCACCTGCCACTCTAAGTCTGCCAGTCTGGGC
GAGGAGGTAAATAAGGTGACATCCTGGTGGTTGCAACTGGTCAGCCTGAAATGGTGAAAGGAGAGTGGATCAAACCTGGG
GCAATAGTCATCGACTATGGGATCAATTATGTCCCAGATGATACAAAATCAAATGGGAGAAGGATTGTGGGTGATGTGGC
ATACAATGAGGCCAAAGAGCGGGCGGGATTCATCACTCCTGTTCTCGGTGGCGTCGGGCCCATGACGGTGGCAATGCTGA
TGCAGAGCACGGTAGAGAGTGCAAGGGGTTTCCTGGAGAAATACAAGCCAGGAAATGGAGTATTCAGTATAACAACCTTA
ACCTGAAGACACCTGTTCCAAGTGACATTGCTATATCACGATCTTACAAACCAAAGCCCATTGGTACACTGGCTCGAGAA
TTTGGCCTGTTCTCTGAAGAGGTGGAATTGTATGGTGAGACAAAGGCCAAAGTCCTGCTGTCAGCACCAGAACGCCTGAA
ACACCAGCCTGACGGGAAATACGCGGCGGTGACTGGAATAACTCCAACGCCCCTGGGAGAAGGGAAAAGTACAACCACAG
TCGGGCTGGTGCAAGCCCTGGGTGCCCATCTTTTCCAGAACGTCTTTGCGTGTGTGCAACAGCCTTCCCAGGGCCCCACC
TTTGGAATAAAAGGTGGTGCTGCAGGAGGTGGCTACCCCCAGGTCATTCCTATGGAAGAGTTTAATCTCCACCTCACTGG
TGACATCCATGCCATCACTGCAGCTAATAACCTGGTTGCTGCGGCCATTGATGCCCGCATATTCCATGAACTGACCCAGA
CAGACAAGGCTCTCTGTAATCGTTTGATGCCCTCAGTAAATGGAGTGAGAAAGTTTTCTGATATCCAAATCCGAAGGTTA
AGGAGACTAGGCATTGAAAAGACTGACCCTACCACACTGACAGACGAAGAGATAAACAGATTTGCAAGATTGGATAGTGA
TCCAGAAACCATAACTTGGCAAAGAGTGTTGGATACCAATGATAGATTCCTGTGGAAGATCACAATTGGACAGGCTCCAA
TGGAGAAAGGGCACACACGGACGACCCAGTTTGATATCTCAGTGGCCAGTGAAATCATGGCTGTCCTGGGCCTCACCAGT
TCTCTGGAAGACATGAGAGAGGGACTGGGCAAAATGGTGGTGGCCTCCAGCAAAACAGGGGAGCCCATCAGTGCGGAAGA
CCTGGGGGTGAGTGGCGCGTTGACAGTGCTTATGAAGGACGCGATCAAGCCTAACCTCATGCAGACGTCAGAGGGCACTC
GGGTGTTCGTCCACGCCGGCCCGCTCGCCAACATCGCACGTGGGAATTTGTGTATCATCGCAGACCGGGTCGCACTCAAG
CTTGTCGGCCCAGAAGGGTTTGTGGTGACCGAAGCTGGATTGGGAGCAGACATTGGAATGGAAAAGTTTTTTAACATCAA
ATGCCGGTACTCTGGCCTCCGCCCTCACGTGGTGGTGCTCGTTGCTACTGTCAGGGCTCTTAAAATGCAGGGGGCAGCCC
CACGGTCACCGCCGGACTGCCTCTTCCCAAGGCTTACATAGAGGAGAACCTGGAGCTGGTTGAAAAAGGTTTCAGTAACT
TGAAGAAACAAATTGAAAATGCAAGAATGTTTGGAGTTCCGGTTGTAGTGGCTGTGAATGCGTTC

Alignment

ORF - retro_mmur_1250 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.91 %
• Parental protein coverage: 78.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GDRDDSNLYINVKLKAAEEVGIKATHVKLPRTATESEV-KYIRSL-EDSTIHGFILQLPLDSENAINTEA
          GDR.DSNLYINVKLKAAEEVGIKATH.KLPRTATESEV.KYIRSL.EDST.HGFILQLPLDSENAIN.EA
Retrocopy GDRHDSNLYINVKLKAAEEVGIKATHIKLPRTATESEVLKYIRSLNEDSTVHGFILQLPLDSENAINIEA

Parental  VINAIAPEKDVDGLTSISAGKLSRGDLNDCFIPCTPKGCLELIKETGVQIAGKHAVVVGRSKIVGAPMHD
          VINAI.PEKDVDGLTSISAGKL.RGDLNDCF.PCTPKGCLELIKETGV.IAGK.A.VVG.SKIVGAPM.D
Retrocopy VINAITPEKDVDGLTSISAGKLTRGDLNDCFVPCTPKGCLELIKETGVEIAGKYAMVVGCSKIVGAPMYD

Parental  LLLWNNATVTTCHSKTANLGEEVNK-GDILVVATGQPEMVKGEWIKPGAIVIDCGINYIPDNTKSNGRRI
          LLLWNNATVTTCHSK.A.LGEEVNK.GDILVVATGQPEMVKGEWIKPGAIVID.GINY.PD.TKSNGRRI
Retrocopy LLLWNNATVTTCHSKSASLGEEVNK<GDILVVATGQPEMVKGEWIKPGAIVIDYGINYVPDDTKSNGRRI

Parental  VGDVAYNEAKERAGFITPVPGGVGPMTVAMLMQSTVESARGFLEKYKPG-KWSIQYNNLNLKTPVPSDIA
          VGDVAYNEAKERAGFITPV.GGVGPMTVAMLMQSTVESARGFLEKYKPG.KWSIQYNNLNLKTPVPSDIA
Retrocopy VGDVAYNEAKERAGFITPVLGGVGPMTVAMLMQSTVESARGFLEKYKPG<KWSIQYNNLNLKTPVPSDIA

Parental  ISRSCKLKPIGTLAREIGLLSEEVELYGETKAKVLLSALERLKHQPDGKYVVVTGITPTPLGEGKSTTTI
          ISRS.K.KPIGTLARE.GL.SEEVELYGETKAKVLLSA.ERLKHQPDGKY..VTGITPTPLGEGKSTTT.
Retrocopy ISRSYKPKPIGTLAREFGLFSEEVELYGETKAKVLLSAPERLKHQPDGKYAAVTGITPTPLGEGKSTTTV

Parental  GLVQALGAHLFQNVFACVRQPSQGPTFGIKGGAAGGGYSQVIPMEEFNLHLTGDIHAITAANNLVAAAID
          GLVQALGAHLFQNVFACV.QPSQGPTFGIKGGAAGGGY.QVIPMEEFNLHLTGDIHAITAANNLVAAAID
Retrocopy GLVQALGAHLFQNVFACVQQPSQGPTFGIKGGAAGGGYPQVIPMEEFNLHLTGDIHAITAANNLVAAAID

Parental  ARIFHELTQTDKALFNRLVPSVNGVRKFSDIQIRRLRRLGIEKTDPTTLTDEEINRFARLDIDPETITWQ
          ARIFHELTQTDKAL.NRL.PSVNGVRKFSDIQIRRLRRLGIEKTDPTTLTDEEINRFARLD.DPETITWQ
Retrocopy ARIFHELTQTDKALCNRLMPSVNGVRKFSDIQIRRLRRLGIEKTDPTTLTDEEINRFARLDSDPETITWQ

Parental  RVLDTNDRFLRKITIGQAPTEKGHTRTTQFDISVASEIMAVLALTSSLEDMRERLGKMVVASSKKGEPIS
          RVLDTNDRFL.KITIGQAP.EKGHTRTTQFDISVASEIMAVL.LTSSLEDMRE.LGKMVVASSK.GEPIS
Retrocopy RVLDTNDRFLWKITIGQAPMEKGHTRTTQFDISVASEIMAVLGLTSSLEDMREGLGKMVVASSKTGEPIS

Parental  AEDLGVSGALTVLMKDAIKPNLMQTLEGTPVFVHAGPFANIAHGNSSIIADRVALKLVGPEGFVVTEAGF
          AEDLGVSGALTVLMKDAIKPNLMQT.EGT.VFVHAGP.ANIA.GN..IIADRVALKLVGPEGFVVTEAG.
Retrocopy AEDLGVSGALTVLMKDAIKPNLMQTSEGTRVFVHAGPLANIARGNLCIIADRVALKLVGPEGFVVTEAGL

Parental  GADIGMEKFFNIKCRYSGLRPHVVVLVATVRALKMH-GGGPTVTAGLPLPKAYIEENLELVEKGFSNLKK
          GADIGMEKFFNIKCRYSGLRPHVVVLVATVRALKM..GG.PTVTAGLPLPKAYIEENLELVEKGFSNLKK
Retrocopy GADIGMEKFFNIKCRYSGLRPHVVVLVATVRALKMQ<GGSPTVTAGLPLPKAYIEENLELVEKGFSNLKK

Parental  QIENARMFGVPVVVAVNVF
          QIENARMFGVPVVVAVN.F
Retrocopy QIENARMFGVPVVVAVNAF

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_1250 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1250 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,