RetrogeneDB ID: retro_mmus_376

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:153305431..153306475(+)
• Located in intron of: ENSMUSG00000026478

Retrocopy information

• Ensembl ID: ENSMUSG00000079138
• 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_376
ATGTCGGGGCTCAGCCACTTAGAGTCGGAGGGCTGCCGAAACCTACTCGGCCTGCTGGACAACGACGAGATCATTGCCCT
TTGCGACACCATCACCAACCGCCTGGTGCAGCCTGTGGACCGCCAAGATGCTATTCATGCAATATTAGTGTATAGCCAAA
ATGTAGAAGAACTTCTGAGGCTCAAAAAAGTCCACCGAGAAGTCATACTTAAGTATTTGGCAAAGCAAGGGGTGGTTGTA
CCTCCAACTGCTGAAAAACACAATCTTATTCAGTATGCAAAAGATTACTGGGGAAAACAGTCACGAAAACTGAAGGACAC
AGCAGAGCCAGTTACAGAGACGGAGGACATCCAGCTCTTGGAGCAGCAGGCAAAGGAAGATAAAGCAGCTGAAAAGGTTG
ATTTTCGTCGCTTAGGAGAAGAATTCTGTCACTGGTTCTTTGAACTTCTTAATTCTCAGAATCCTTTTCTGGGCCCACCT
CAAAACGACTGGGGCCCACAGCCCTTCTGGCACGACGCCAAGCTTAGGTTTTATTATAACACCTCAGAACAAAACATGGT
AGACTACCAAGGAGCAGAAATCGTGAGCCTTCGCTTACTGTCATTAGCTAAAGAGGAATTTCTCTTTCTCAGTCCCAACC
TTGATTCTCAAGGACCAAAATGTGTGTCTTCTCCTCATGGATTAGTTATGGTTGGAGTTGCAGGGACTGTCCACCGAGGA
AATTCTTGTTTGGGCACATTTGAGCAAATTTTTGGACTTATCCGAAGCTCTTTTGTGGAAAATATTTGGAAAATCAAATT
TATCAACCTGAGAATCATTGGAGGAAGTTCCCTTACTCCTGAATCAGTACTGAAGCCATCTGTAACATTTAAACTGAGTG
ATCTGGAGGCCTTTTATAACGTAATCACTTTGTGTAATAGCCCTGAAGTAAGACCTAATGTAAGGCAGATAATAGATAGT
GGCACTGGAGACCAGGTTTTACATAGTGGAGATGAGGCATTGTTGAACAAAAGGGAAATGAATTTGCAAAACCCTCTAAA
GCAT

Alignment

ORF - retro_mmus_376 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.82 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGLSHLESEGCRNLLGLLDNDEIMALCDTVTNRLVQPVDRQDAIHAILVYSQNVEELLRRKKVHREVIF
          MSGLSHLESEGCRNLLGLLDNDEI.ALCDT.TNRLVQPVDRQDAIHAILVYSQNVEELLR.KKVHREVI.
Retrocopy MSGLSHLESEGCRNLLGLLDNDEIIALCDTITNRLVQPVDRQDAIHAILVYSQNVEELLRLKKVHREVIL

Parental  KYLAKQGVVVPPTAEKHNLIQYAKDYWAKQSPKLKDTAEPVTKTEDIQLFKQQAKEDKEAEKVDFRRLGE
          KYLAKQGVVVPPTAEKHNLIQYAKDYW.KQS.KLKDTAEPVT.TEDIQL..QQAKEDK.AEKVDFRRLGE
Retrocopy KYLAKQGVVVPPTAEKHNLIQYAKDYWGKQSRKLKDTAEPVTETEDIQLLEQQAKEDKAAEKVDFRRLGE

Parental  EFCHWFFELLNSQNPFLGPPQDDWGPQHFWHDAKLRFYYNTSEQNTTDYQGAEIVSLRLLSLVKEEFLFL
          EFCHWFFELLNSQNPFLGPPQ.DWGPQ.FWHDAKLRFYYNTSEQN..DYQGAEIVSLRLLSL.KEEFLFL
Retrocopy EFCHWFFELLNSQNPFLGPPQNDWGPQPFWHDAKLRFYYNTSEQNMVDYQGAEIVSLRLLSLAKEEFLFL

Parental  SPNLDSQGLKCASSPHGLVMVGVAGTVHRGNSCLGIFEQIFGLIRSPFVENTWKIKFINLRIIGGSSLAP
          SPNLDSQG.KC.SSPHGLVMVGVAGTVHRGNSCLG.FEQIFGLIRS.FVEN.WKIKFINLRIIGGSSL.P
Retrocopy SPNLDSQGPKCVSSPHGLVMVGVAGTVHRGNSCLGTFEQIFGLIRSSFVENIWKIKFINLRIIGGSSLTP

Parental  ESVLKPSVTFEPSDLEAFYNVITLCNSPEVRPNVRQIIDSGTGDQVLHSGDEALLNKREMNLLTPLKH
          ESVLKPSVTF..SDLEAFYNVITLCNSPEVRPNVRQIIDSGTGDQVLHSGDEALLNKREMNL..PLKH
Retrocopy ESVLKPSVTFKLSDLEAFYNVITLCNSPEVRPNVRQIIDSGTGDQVLHSGDEALLNKREMNLQNPLKH

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	0.09 RPM	16.38 RPM
SRP007412_cerebellum	0.04 RPM	18.11 RPM
SRP007412_heart	0.03 RPM	14.54 RPM
SRP007412_kidney	0.10 RPM	18.17 RPM
SRP007412_liver	0.11 RPM	15.70 RPM
SRP007412_testis	2.70 RPM	354.71 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_376 was not detected

EST

No EST(s) were mapped for retro_mmus_376 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_70446	907 libraries	98 libraries	35 libraries	15 libraries	17 libraries

The graphical summary, for retro_mmus_376 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_376 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_376 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,