RetrogeneDB ID: retro_mluc_1185

Retrocopy location

• Organism: Microbat (Myotis lucifugus)
• Coordinates: GL429804:8222313..8223080(-)
• Located in intron of: ENSMLUG00000006652

Retrocopy information

• Ensembl ID: ENSMLUG00000027242
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FRG1
• Ensembl ID: ENSMLUG00000023179
• Aliases: None
• Description: FSHD region gene 1 [Source:HGNC Symbol;Acc:3954]

Sequence

>retro_mluc_1185
ATGGCAAAATACTCCTACGTCAAGTCCACCAAACTTGTGCTGAAGGGAACCAAGGCCAAGAGTAAGAAGAAAAAGAGCAA
GAAGAAGAGAAAAAGAGAAGATGATGAAGAAACCCAACTTGATATTGTTGGGATCTGGTGGACAGTAACAAACTTTGGTG
AAATTTCAGGAACCTTAGCTATTGAAATGGATAAGGGAACCTACATACATGCACTTGACAATGGACTTTTTACACTGGGA
ACTCCACATAAAGAAGCGGATGAAGGCCCTAGTCCCCGGAGCAGTTTATAGCTGTCAAACTGTCTGATTCCGGAAGTGCC
CTAAAATCTGGCTATGGAAAATACCTTGGTATAAATTCAGATGGACTTCTTGTTGGGCGTTCAGATGCTATTGGACCAAG
AGAACAATGGGAACCAGTCTTTCAAGATGGGAAAATGGCTTTATTGGCCTCAAATAGCTGCTTTATCAGATGCAATGAAG
CCGGCAATACAGAAGCAAAAAGTAAAACAGCAGGAGAAGAAATGATAAAGATTAGATCCTGTGCTGAAAGAGAAACTAAG
AAAAAAGATGACATCCCAGAGGAAGAAAAAGGAAATGTTAAACAGTGTGAAATCAATTATGTAAAGAAATTTCAGAGCTT
CCAAGACCTGAAACTTAAAATAAGCAAAGAAGGCAGTAAAATTCTTAAAAAGGCCCAGAGAGATGGATTTTTGCATGAAA
CACTTCTGGACAGGAGAGCCAAATTGAAAGCTGACAGATACTGCAAA

Alignment

ORF - retro_mluc_1185 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.6 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEYSYVKSTKLVLKGTKAKSKKKKSKEKRKREDDEETQLDIVGIWWTVTNFGEISGTIAIEMDKGTYIH
          MA.YSYVKSTKLVLKGTKA...............DEETQLDIVGIWWTVTNFGEISGT.AIEMDKGTYIH
Retrocopy MAKYSYVKSTKLVLKGTKAXXXXXXXXXXXXXXXDEETQLDIVGIWWTVTNFGEISGTLAIEMDKGTYIH

Parental  ALDNGLFTLGAPHKEVDEGPSP-PEQFTAVKLSDSRIALKSGYGKYLGINSDGLVVGRSDAIGPREQWEP
          ALDNGLFTLG.PHKE.DEGPSP.PEQF.AVKLSDS..ALKSGYGKYLGINSDGL.VGRSDAIGPREQWEP
Retrocopy ALDNGLFTLGTPHKEADEGPSP<PEQFIAVKLSDSGSALKSGYGKYLGINSDGLLVGRSDAIGPREQWEP

Parental  VFQDGKMALLASNSCFIRCNEAGDIEAKSKTAGEEEMIKIRSCAERETKKKDDIPEEDKGNVKQCEINYV
          VFQDGKMALLASNSCFIRCNEAG..EAKSKTAG.EEMIKIRSCAERETKKKDDIPEE.KGNVKQCEINYV
Retrocopy VFQDGKMALLASNSCFIRCNEAGNTEAKSKTAG-EEMIKIRSCAERETKKKDDIPEEEKGNVKQCEINYV

Parental  KKFQSFQDQKLKISKEDSKILKKARKDGFLHETLLDRRAKLKADRYCK
          KKFQSFQD.KLKISKE.SKILKKA..DGFLHETLLDRRAKLKADRYCK
Retrocopy KKFQSFQDLKLKISKEGSKILKKAQRDGFLHETLLDRRAKLKADRYCK

Legend:

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

Expression

RNA-Seq

Myotis lucifugus was not studied using RNA-Seq expression data.

ChIP-Seq

Myotis lucifugus was not studied using ChIP-Seq data.

EST

Myotis lucifugus was not studied using EST data.

TSS

Myotis lucifugus was not studied using FANTOM5 data.

Lab

retro_mluc_1185 was not experimentally validated.

Homology

Retrocopy orthology:

Myotis lucifugus 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013503	1 retrocopy	retro_amel_1609,
Canis familiaris	ENSCAFG00000007135	1 retrocopy	retro_cfam_718,
Felis catus	ENSFCAG00000025737	1 retrocopy	retro_fcat_464,
Myotis lucifugus	ENSMLUG00000023179	2 retrocopies	retro_mluc_1185 , retro_mluc_1490,
Rattus norvegicus	ENSRNOG00000009846	1 retrocopy	retro_rnor_88,
Sorex araneus	ENSSARG00000002471	1 retrocopy	retro_sara_368,
Tupaia belangeri	ENSTBEG00000014491	2 retrocopies	retro_tbel_1202, retro_tbel_3435,
Tarsius syrichta	ENSTSYG00000010985	2 retrocopies	retro_tsyr_1347, retro_tsyr_1778,