RetrogeneDB ID: retro_mmus_695

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:19383749..19384583(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082737
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: 4930453N24Rik
• Ensembl ID: ENSMUSG00000059920
• Aliases: 4930453N24Rik, AI649104
• Description: RIKEN cDNA 4930453N24 gene [Source:MGI Symbol;Acc:MGI:1914859]

Sequence

>retro_mmus_695
GACACTGTCACCAACCGCCTGGTGCAATCTGTGGACCGCCAAGACGCTATTCATGCAATATTAGTGTATAGCCAAAATGT
AGAAGAACTTCTGAGGCGCAAAAAAGTCCACCGAGAAGTCATATTTAAGTATTTGGCAAAGCAAGGGGTGGTTGTACCTC
CAACTGCTGAAAAACACAATCTTATTCAGTATGCAAAAGATTACTAGGGAAAACAGTCACCAAAACTGAAGGACACAGCA
GAGCCAGTTACAGAGATGGAGGCCATCCAGCTCTTGGAGCAGCAGGCAAAGGAAGATAAAGCAGCTGAAAAGGTTGATTT
TCATCGCTTAGGAGAAGAATTCTGTCACTGGTTCTTTGAACTTCTTAATTCTCAGAATTCTTTTCTGGGCCCACCTCAAG
ATGACTGGGGCCCACAGCACTTTTGGCATGACGCCAAGCTTAGGTTTTATTATAACACCTCAGAACAAAACACGACAGAC
TACCAAGGAGCAGAAATCGTGAGCCTTCGCTCACTGTCATTAGTTAAAGAGGAATTTCTCTTTCTCAGTCCCAGCCTTGA
TTCTCAAGGACTAAAATGTGCATCTTCTCCTCATGGATTAGTTATGGTTGGAGTTGCAGGGACTGTCCACCGAGGAAATT
CTTGTTTGGGCATATTTGAGCAAATTTTTGGACTTATCCGTAGCCCTTTTGTGGAAAATACTTGGAAAATCAAATTTATA
AACCTGAGAATCATTGGAGGAAGTTCCCTTGCTCCTGAATCATTACTGAAGCCATCTGTAACATTTGAACCAAGTGATCT
GGAGGCCTTTTATAACGTAATCACTTTGTGCAAT

Alignment

ORF - retro_mmus_695 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.96 %
• Parental protein coverage: 79.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DTVTNRLVQPVDRQDAIHAILVYSQNVEELLRRKKVHREVIFKYLAKQGVVVPPTAEKHNLIQYAKDYWA
          DTVTNRLVQ.VDRQDAIHAILVYSQNVEELLRRKKVHREVIFKYLAKQGVVVPPTAEKHNLIQYAKDY..
Retrocopy DTVTNRLVQSVDRQDAIHAILVYSQNVEELLRRKKVHREVIFKYLAKQGVVVPPTAEKHNLIQYAKDY*G

Parental  KQSPKLKDTAEPVTKTEDIQLFKQQAKEDKEAEKVDFRRLGEEFCHWFFELLNSQNPFLGPPQDDWGPQH
          KQSPKLKDTAEPVT..E.IQL..QQAKEDK.AEKVDF.RLGEEFCHWFFELLNSQN.FLGPPQDDWGPQH
Retrocopy KQSPKLKDTAEPVTEMEAIQLLEQQAKEDKAAEKVDFHRLGEEFCHWFFELLNSQNSFLGPPQDDWGPQH

Parental  FWHDAKLRFYYNTSEQNTTDYQGAEIVSLRLLSLVKEEFLFLSPNLDSQGLKCASSPHGLVMVGVAGTVH
          FWHDAKLRFYYNTSEQNTTDYQGAEIVSLR.LSLVKEEFLFLSP.LDSQGLKCASSPHGLVMVGVAGTVH
Retrocopy FWHDAKLRFYYNTSEQNTTDYQGAEIVSLRSLSLVKEEFLFLSPSLDSQGLKCASSPHGLVMVGVAGTVH

Parental  RGNSCLGIFEQIFGLIRSPFVENTWKIKFINLRIIGGSSLAPESVLKPSVTFEPSDLEAFYNVITLCN
          RGNSCLGIFEQIFGLIRSPFVENTWKIKFINLRIIGGSSLAPES.LKPSVTFEPSDLEAFYNVITLCN
Retrocopy RGNSCLGIFEQIFGLIRSPFVENTWKIKFINLRIIGGSSLAPESLLKPSVTFEPSDLEAFYNVITLCN

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	16.38 RPM
SRP007412_cerebellum	0.00 RPM	18.11 RPM
SRP007412_heart	0.00 RPM	14.54 RPM
SRP007412_kidney	0.02 RPM	18.17 RPM
SRP007412_liver	0.00 RPM	15.70 RPM
SRP007412_testis	0.00 RPM	354.71 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_695 was not detected

EST

No EST(s) were mapped for retro_mmus_695 retrocopy.

TSS

No TSS is located nearby retro_mmus_695 retrocopy 5' end.

Lab

retro_mmus_695 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_695 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000059920	3 retrocopies	retro_mmus_2986, retro_mmus_376, retro_mmus_695 ,
Tursiops truncatus	ENSTTRG00000002941	1 retrocopy	retro_ttru_1424,