RetrogeneDB ID: retro_mmus_448

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:60592250..60592712(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082160
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Lix1
• Ensembl ID: ENSMUSG00000047786
• Aliases: Lix1, 5730466L18Rik
• Description: limb expression 1 homolog (chicken) [Source:MGI Symbol;Acc:MGI:1913893]

Sequence

>retro_mmus_448
AAGGGCACGTTAGATGATGCGGATGACCCAAGCACAAGTGTGGGAGCCTATCACTACATGCTGGAGTCAAACATGGGGAA
GACTATGCTGGAGTTTCAGGAACTAATGACCATTTTCCAACTACTGCACTGGAATGGAAGCCTGAAAGCCCTCCGTGAAA
CAAAGTGCTCTCGACAGGAAGTCATCTCCTACTATTCCCAATATTCTTTAGATGAAAAGATGCGTAGCCACATGGCCCTG
GACTGGATTATGAAGGAGCGTGAATCACCAGGAATTCTCTCTCAAGAGCTGCGTGCAGCCCTAGGGCAGCTGGAGGAAGC
CAGGAAGGCTGGACAAGAACTACGATTTTACAAAGAAAAAAAAGAAATCCTGAGCTTGGCCCTGACTCAGATCTATAGTG
ACCCTGACCCTTCCTCACCCAGTGATGACCAGCTAAGCCTCACGGCTCTGTGTGGCTATCAT

Alignment

ORF - retro_mmus_448 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.4 %
• Parental protein coverage: 54.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGTLDDADDPSTSVGAYHYMLESNMGKTMLEFQELMTIFQLLHWNGSLKALRETKCSRQEVISYYSQYSL
          .GTLDDADDPSTSVGAYHYMLESNMGKTMLEFQELMTIFQLLHWNGSLKALRETKCSRQEVISYYSQYSL
Retrocopy KGTLDDADDPSTSVGAYHYMLESNMGKTMLEFQELMTIFQLLHWNGSLKALRETKCSRQEVISYYSQYSL

Parental  DEKMRSHMALDWIMKERESPGILSQELRAALGQLEEARKAGQELRFYKEKKEILSLALTQIYSDPDPSSP
          DEKMRSHMALDWIMKERESPGILSQELRAALGQLEEARKAGQELRFYK...EILSLALTQIYSDPDPSSP
Retrocopy DEKMRSHMALDWIMKERESPGILSQELRAALGQLEEARKAGQELRFYKXXXEILSLALTQIYSDPDPSSP

Parental  SDDQLSLTALCGYH
          SDDQLSLTALCGYH
Retrocopy SDDQLSLTALCGYH

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	23.60 RPM
SRP007412_cerebellum	0.00 RPM	4.91 RPM
SRP007412_heart	0.00 RPM	1.90 RPM
SRP007412_kidney	0.00 RPM	0.96 RPM
SRP007412_liver	0.03 RPM	0.11 RPM
SRP007412_testis	0.00 RPM	0.59 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_448 was not detected

EST

No EST(s) were mapped for retro_mmus_448 retrocopy.

TSS

No TSS is located nearby retro_mmus_448 retrocopy 5' end.

Lab

retro_mmus_448 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_448 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000012335	1 retrocopy	retro_dnov_2085,
Equus caballus	ENSECAG00000021643	1 retrocopy	retro_ecab_1013,
Mus musculus	ENSMUSG00000047786	1 retrocopy	retro_mmus_448 ,