RetrogeneDB ID: retro_mluc_1404

Retrocopy location

• Organism: Microbat (Myotis lucifugus)
• Coordinates: GL429832:4686764..4687230(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMA4
• Ensembl ID: ENSMLUG00000027860
• Aliases: None
• Description: Proteasome subunit alpha type [Source:UniProtKB/TrEMBL;Acc:G1QAV4]

Sequence

>retro_mluc_1404
TCAAAGGAATTTATATTACAGTATCAGGAGCCAGTTGCTTGTGGGCGGTTGGTTACAGCACTGTGTGATATCTAACAAGC
TTATACACAGTTTGGAGAAAAACATCCCTTTGGTGTTTCACTGCTGTACATTGGCTGGGATAAGCGTTATGGCTTTCAGC
TCTATCAAAGCAACCCTAGCAGAAATTACGGGGGATGGAAAGCCACATGCATTGGAAATAATAGCGCTGCAGCTGTGTCA
ATGTTTAAACAAGACTACAAAGGAGGAGAAATGACTCTGAAGTCGGTACTTGCTTCAGTTATCAAAGTCCTCAGTAAGGC
CATGGATGTTACCAACCCCTCTGCCGAAAAAGTGGAAATTGGCCCACTAACAAGAGAGAATGGAAAGACGTTCGTCAGCG
TTCTCAAACAGAAGGAAGTGGAACTGTTGGGCAAAAAAACATGAGGAAGAAGAAGCTAAGGCCGAG

Alignment

ORF - retro_mluc_1404 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.21 %
• Parental protein coverage: 59.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATC
          .....LQYQEP..C..LVTALCDI.QAYTQFG.K.PFGVSLLYIGWDK.YGFQLYQS.PS.NYGGWKATC
Retrocopy SKEFILQYQEPVACGRLVTALCDI*QAYTQFGEKHPFGVSLLYIGWDKRYGFQLYQSNPSRNYGGWKATC

Parental  IGNNSAAAVSMLKQDYKEGEMTLKSALALAVKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEV
          IGNNSAAAVSM.KQDYK.GEMTLKS.LA...KVL.K.MDV...SAEKVEI..LTRENGKT...VLKQKEV
Retrocopy IGNNSAAAVSMFKQDYKGGEMTLKSVLASVIKVLSKAMDVTNPSAEKVEIGPLTRENGKTFVSVLKQKEV

Parental  EQL-IKKHEEEEAKAE
          E.L..KKHEEEEAKAE
Retrocopy ELL>AKKHEEEEAKAE

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_1404 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 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010369	1 retrocopy	retro_cjac_58,
Myotis lucifugus	ENSMLUG00000027860	1 retrocopy	retro_mluc_1404 ,
Mus musculus	ENSMUSG00000032301	2 retrocopies	retro_mmus_1035, retro_mmus_1707,
Tupaia belangeri	ENSTBEG00000011678	5 retrocopies	retro_tbel_1746, retro_tbel_2953, retro_tbel_3324, retro_tbel_4164, retro_tbel_614,
Tarsius syrichta	ENSTSYG00000011745	1 retrocopy	retro_tsyr_21,