RetrogeneDB ID: retro_mluc_1182

Retrocopy location

• Organism: Microbat (Myotis lucifugus)
• Coordinates: GL429804:3219051..3219725(-)
• Located in intron of: ENSMLUG00000011781

Retrocopy information

• Ensembl ID: ENSMLUG00000026838
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LAPTM4B
• Ensembl ID: ENSMLUG00000003618
• Aliases: None
• Description: None

Sequence

>retro_mluc_1182
CCCTGCCCGCGGTCGATGAAGATGGTCGCGCCCTGGAGGCGGTTCTACTCCAACAGCTGCTGCCTGTGCTGCCATGTGCG
CAAAGGCACCATCCTGCTTGGCGTCTTGTACCTGGTCATCAATGCCGTGGTGCTGTTGATTCTGCTGAGCTCCCTGGCGG
ACCCGACCAGTGTCACTTTTCGAGTTCGGAACTGGGAGGAGACTTAGAGTTCATGGATGATGCCAACATGTGCATTGCTA
TCGCAATTTCTCTTCTCATGATCCTGATATGTGCAATGGCTACTTACGAAGCGTACAAGCGACGTGCTGCCTGGATCGTC
CCTTTCTTCTGTTACCAGATCTTTGATTTTGCTCTGAGTGCCTTGGTTGCCATCACTGTGCTGGTTTATCCAAACTCCAT
TCAGGAGTACATACGACAGCTGCCTCCTAATTTTCCCTACAAAGAGGATGCCATGTCAGTGAATTCTACCTGTTTGGTCC
CTGTTGTTCTTCTGTTTATCAGCATTCTCTTGGCTTTCAAGAGTTACTTGATTAGCTGCGTTTGCTACCAGTACATCAAC
GGCAGGAACAACTCCGACGTCCTGGTGTGTGTTACCAGCAATGACAGCTCGGTGCTGTTACCTCCGTACGATGATGCCAC
TGTGACCGGTGCAGCCAAGGAGCCGCCGCCTCCT

Alignment

ORF - retro_mluc_1182 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.11 %
• Parental protein coverage: 96.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PAVGAMKMVAPWTRFYSNSCCLCCHVRTGTILLGVSYLVINAVVLLILLSSLADP-GQRHFSSSELGGDL
          P....MKMVAPW.RFYSNSCCLCCHVR.GTILLGV.YLVINAVVLLILLSSLADP..Q.HFSSSELGGDL
Retrocopy PCPRSMKMVAPWRRFYSNSCCLCCHVRKGTILLGVLYLVINAVVLLILLSSLADP<DQCHFSSSELGGDL

Parental  EFMDDANMCIAIAISLLMILICAMATYGAYKRRAAWIVPFFCYQIFDFALSALVAITVLVYPNSIQEYIR
          EFMDDANMCIAIAISLLMILICAMATY.AYKRRAAWIVPFFCYQIFDFALSALVAITVLVYPNSIQEYIR
Retrocopy EFMDDANMCIAIAISLLMILICAMATYEAYKRRAAWIVPFFCYQIFDFALSALVAITVLVYPNSIQEYIR

Parental  QLPPNFPYKEDAMSVNSTCLVLVVLLFISILLAFKGYLISCVWNCYRYINGRNNSDVLVYVTSNDSTVLL
          QLPPNFPYKEDAMSVNSTCLV.VVLLFISILLAFK.YLISCV..CY.YINGRNNSDVLV.VTSNDS.VLL
Retrocopy QLPPNFPYKEDAMSVNSTCLVPVVLLFISILLAFKSYLISCV--CYQYINGRNNSDVLVCVTSNDSSVLL

Parental  PPYDDATVTGAAKEPPPP
          PPYDDATVTGAAKEPPPP
Retrocopy PPYDDATVTGAAKEPPPP

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_1182 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016959	3 retrocopies	retro_btau_1493, retro_btau_1759, retro_btau_786,
Callithrix jacchus	ENSCJAG00000031235	3 retrocopies	retro_cjac_1368, retro_cjac_1664, retro_cjac_3027,
Myotis lucifugus	ENSMLUG00000003618	1 retrocopy	retro_mluc_1182 ,
Mus musculus	ENSMUSG00000022257	1 retrocopy	retro_mmus_1549,
Oryctolagus cuniculus	ENSOCUG00000013689	1 retrocopy	retro_ocun_627,
Otolemur garnettii	ENSOGAG00000000512	3 retrocopies	retro_ogar_1977, retro_ogar_2856, retro_ogar_2902,