RetrogeneDB ID: retro_mmus_235

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:31222938..31223595(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000026063
• Aliases: Pih1d3, 4930521A18Rik
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: E230019M04Rik
• Ensembl ID: ENSMUSG00000042433
• Aliases: None
• Description: RIKEN cDNA E230019M04 gene [Source:MGI Symbol;Acc:MGI:3607720]

Sequence

>retro_mmus_235
ATGGAATCAGAAAATGCTGAAGCTGAGAATGTGGTAACAGGGAATTTGGAAGCAAAGAGCAAGGAAGGTAAAAATATGCA
ATTTGTGACATTGTCTTCTGCCTGGTCCCTTCAAGCACTATCCAGTCTCCTCAATCCCGAAGAAGAGGATGGTTTTGATT
TTGAACAGGGGCAATGCTCATTTACTATTGGAGCCATGGGCCCTGGGAATATTGGACCACCTAAAGCAAAAGAGTCCAAA
GCTATTCCTGAACCCAGGAGTGATGAAAGTGAGAACATCTGGAATCCAGAAGAGGTTCCAGAAGGAGCAGAGCATGATGA
TATATGGGATGTTCGTGAAATTCCAGATTATGAGATTGTATTCCAACAAACTGTGGGAACTGAGGACGTATACCTAGGAT
TAACAAGAAAGGATCCTTCAACGGCATGCTGCCAGGAGCTGGTGGTGAAAATTAAACTGCCCAATACAAACCCTTCTGAA
ATTCAAATTGATATCCAAGAAATGCTCCTTGATCTTCGCACTCCTAGAAAGAAGCTGTTAGTAAACTTTCCCCAGCCCGT
GGAACGGAACAGTGCTAGAGCATCCTATATCTGGGAAGCTGAAACACTTGAAGTCAGGATGACCGTCCAAAGGGATTTGG
ATTTTAATATTTCCTGA

Alignment

ORF - retro_mmus_235 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESEIAEAEKVKTGNLEAKSMEAKNMQFEMLSSASTLQALASLLNPEEEDDFDFEQGQCTSTIRAMGPGN
          MESE.AEAE.V.TGNLEAKS.E.KNMQF..LSSA..LQAL.SLLNPEEED.FDFEQGQC..TI.AMGPGN
Retrocopy MESENAEAENVVTGNLEAKSKEGKNMQFVTLSSAWSLQALSSLLNPEEEDGFDFEQGQCSFTIGAMGPGN

Parental  IGPPKAKESKAIPEPRSDESENIWNPEEVPEGGEHDDIWDVREIPDYEIVFQQTVGTEDIYLGLTGKDPS
          IGPPKAKESKAIPEPRSDESENIWNPEEVPEG.EHDDIWDVREIPDYEIVFQQTVGTED.YLGLT.KDPS
Retrocopy IGPPKAKESKAIPEPRSDESENIWNPEEVPEGAEHDDIWDVREIPDYEIVFQQTVGTEDVYLGLTRKDPS

Parental  TACCQELVVKIKLPNTNPSEIQIDIQEMLLDLRTPKKKLLVNFPQPVERNSARASYIWEAETLEVRMTLQ
          TACCQELVVKIKLPNTNPSEIQIDIQEMLLDLRTP.KKLLVNFPQPVERNSARASYIWEAETLEVRMT.Q
Retrocopy TACCQELVVKIKLPNTNPSEIQIDIQEMLLDLRTPRKKLLVNFPQPVERNSARASYIWEAETLEVRMTVQ

Parental  RDLDFNIS
          RDLDFNIS
Retrocopy RDLDFNIS

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	0.02 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	5.08 RPM	0.82 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_235 was not detected

EST

No EST(s) were mapped for retro_mmus_235 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_73794	1063 libraries	5 libraries	1 library	0 libraries	3 libraries
TSS #2	TSS_73795	1061 libraries	7 libraries	1 library	0 libraries	3 libraries

The graphical summary, for retro_mmus_235 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_235 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_235 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000042433	1 retrocopy	retro_mmus_235 ,