RetrogeneDB ID: retro_mmus_216

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:93927989..93928670(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000094935
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Lysmd1
• Ensembl ID: ENSMUSG00000053769
• Aliases: Lysmd1, 2610022K04Rik, AI415311
• Description: LysM, putative peptidoglycan-binding, domain containing 1 [Source:MGI Symbol;Acc:MGI:1919409]

Sequence

>retro_mmus_216
ATGGCTTCTCCCTCTAGACAGCCTCCCCTCGGGGGGTCAGGGCTGCTGCATGGGAGCCGTGCTCGTTCTTATGGAAGCCT
GGTACAATCATCCTGCTCCCCAGTGAGGGAAAGACGCCTGGAGCATCAATTGGAGCCTGGAGACACCCTGGCTGGATTAG
CACTCAAATACGGGGTAACGATGGAACAGATTAAGCGTACAAACCGCCTTTATACTAACGACTCCATCTTCCTGAAGAAA
ACGCTCTACATCCCCATCCTATCAGAGCCCAGAGACTTGTTTAATGGTTTGGATTCTGAGGAGGAAAATGATGGAGAGGA
AGAGGTGCGCCCGAGTAAGGATGAGATCGGATCATCTTCGGGGAGGAGGAAGAATCGAGGGTCAGGGTCGGGTCGGCCCA
ATGGCACAGGCCTCCCGCCTCACCAGGAAACCTCCACCCCCAGCCATGACCTTTCTGCCTCTGATTTCCTTAAGAAGCTT
GACTCACAGATCAGCCTGTCAAAGAAGGCTGCTGCCCAGAAGCTGAGGAAAGGGGAGAGTGGGGTACCTGAGGAGGACAC
GGGTCTCTACCCTAGCTCCCCTCGGATGCAGCAGCGAGCAGTCCTAGGCCCTGTGCCACTCACCCGGACGTCTCGGACCC
AGACACTGCGGGACCAGGAAGATGAAATCTTCAAACTCTGA

Alignment

ORF - retro_mmus_216 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MASPSRQPPLGGSGLLHGSRARSYGSLVQSSCSPVRERRLEHQLEPGDTLAGLALKYGVTMEQIKRTNRL
          MASPSRQPPLGGSGLLHGSRARSYGSLVQSSCSPVRERRLEHQLEPGDTLAGLALKYGVTMEQIKRTNRL
Retrocopy MASPSRQPPLGGSGLLHGSRARSYGSLVQSSCSPVRERRLEHQLEPGDTLAGLALKYGVTMEQIKRTNRL

Parental  YTNDSIFLKKTLYIPILSEPRDLFNGLDSEEENDGEEEVRPSKDEIGSSSGRRKNRGSGSGRPNGTGLPP
          YTNDSIFLKKTLYIPILSEPRDLFNGLDSEEENDGEEEVRPSKDEIGSSSGRRKNRGSGSGRPNGTGLPP
Retrocopy YTNDSIFLKKTLYIPILSEPRDLFNGLDSEEENDGEEEVRPSKDEIGSSSGRRKNRGSGSGRPNGTGLPP

Parental  HQETSTPSHDLSASDFLKKLDSQISLSKKAAAQKLRKGESGVPEEDTGLYPSSPRMQQRAVLGPVPLTRT
          HQETSTPSHDLSASDFLKKLDSQISLSKKAAAQKLRKGESGVPEEDTGLYPSSPRMQQRAVLGPVPLTRT
Retrocopy HQETSTPSHDLSASDFLKKLDSQISLSKKAAAQKLRKGESGVPEEDTGLYPSSPRMQQRAVLGPVPLTRT

Parental  SRTQTLRDQEDEIFKL
          SRTQTLRDQEDEIFKL
Retrocopy SRTQTLRDQEDEIFKL

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	1.71 RPM
SRP007412_cerebellum	0.00 RPM	1.52 RPM
SRP007412_heart	0.03 RPM	0.90 RPM
SRP007412_kidney	0.00 RPM	1.00 RPM
SRP007412_liver	0.00 RPM	0.68 RPM
SRP007412_testis	0.05 RPM	1.14 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_216 was not detected

EST

No EST(s) were mapped for retro_mmus_216 retrocopy.

TSS

No TSS is located nearby retro_mmus_216 retrocopy 5' end.

Lab

retro_mmus_216 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_216 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000001228	1 retrocopy	retro_meug_829,
Mus musculus	ENSMUSG00000053769	1 retrocopy	retro_mmus_216 ,