RetrogeneDB ID: retro_mmus_1937

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:77291330..77292437(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081611
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Prpsap2
• Ensembl ID: ENSMUSG00000020528
• Aliases: Prpsap2, A230054F23Rik
• Description: phosphoribosyl pyrophosphate synthetase-associated protein 2 [Source:MGI Symbol;Acc:MGI:2384838]

Sequence

>retro_mmus_1937
ATGTTTTGTGTGGCGCCTCCTGAATTAGAAACCAAGATGAACATAACCAAAGGAGGCCTCCTGTTGTTTTCAGCAAATTC
CAATTCATCATGTATGGAGCTTTCAAAGAAAATTGCTGAGCGGCTGGGGGTGGAGATGGGCAAAGTGCAGGTTTACCAGG
AACCTAACAGAGAAACAAGAGTTCAAATACAGGAGTCTGTGAGAGGAAAAGATGTATTTATCATCCAAACCATCTCAAAG
GACGTGAACACCACCATCATGGAGCTGCTGATCATGGTATATGCATGTAAGACCTCATGTGCCAAGAGCATCATCGGAGT
GATCCCCTACTTTCCTTAAAGCAAGCAATGCAAAATGAGAAAAAGGGGCTCCATTGTCTCAAAATTGCTGGCTTCTATGA
TGTGCAAAGCTGGTCTGACTCATCTCATCACTATGGATTTACACCAGAAGGAAATCCAGGGCTTCTTCAATATTCCAGTA
GATAATTTAAGAGCCTCCCCATTCCTGTTACAATATATTCAAGAAGAGATCCCAGATTATAGGAATGCAGTCATCGTGGC
CAAGTCTCCAGCCTCAGCCAAGAGGGCACAATCTTTTGCAGAGCGTCTACATCTGGGAATCGCAGTGATCCATGGAGAAG
CACAGGATGCTGAGTCTGACTTGGTGGATGGCCGGCACTCCCCACCAATGGTCAGGAGTGTAGCTGCCATCCACCCCAGC
CTGGAGATCCCTATGCTGATTCCTAAAGAGAAGCCCCTAATCACAGTTGTTGGTGATGTTGGAGGAAGAATCGCCATCAT
TGTGGATGACATTATTGATGATGTGGATAGCTTTCTTGCTGCAGCAGAGACCCTGAAGGAAAGAGGTGCATACAAGATCT
TTGTGATGGCCACTCACAGCTTGTTATCCTCTGATGCTCCCCGGCTGATTGAAGAGTCTGCCATTGATGAGGTGGTGGTC
ACTAACACGATCCCACACGAGATCCAGAAGCTGCAGTGCCCCAATATCAAGACTGTGGACATCAGCATGATCCTATCAGA
AGCCATCCGCCGAATTCACAGCGGGGAGTCCATGTCCTACCTTTTCAGAAACATAGGCTTAGATGAC

Alignment

ORF - retro_mmus_1937 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.1 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFCVAPPELETKMNITKGGLVLFSANSNSSCMELSKKIAERLGVEMGKVQVYQEPNRETRVQIQESVRGK
          MFCVAPPELETKMNITKGGL.LFSANSNSSCMELSKKIAERLGVEMGKVQVYQEPNRETRVQIQESVRGK
Retrocopy MFCVAPPELETKMNITKGGLLLFSANSNSSCMELSKKIAERLGVEMGKVQVYQEPNRETRVQIQESVRGK

Parental  DVFIIQTISKDVNTTIMELLIMVYACKTSCAKSIIGVIPYFPYSKQCKMRKRGSIVSKLLASMMCKAGLT
          DVFIIQTISKDVNTTIMELLIMVYACKTSCAKSIIGVIPYFP.SKQCKMRKRGSIVSKLLASMMCKAGLT
Retrocopy DVFIIQTISKDVNTTIMELLIMVYACKTSCAKSIIGVIPYFP*SKQCKMRKRGSIVSKLLASMMCKAGLT

Parental  HLITMDLHQKEIQGFFNIPVDNLRASPFLLQYIQEEIPDYRNAVIVAKSPASAKRAQSFAERLRLGIAVI
          HLITMDLHQKEIQGFFNIPVDNLRASPFLLQYIQEEIPDYRNAVIVAKSPASAKRAQSFAERL.LGIAVI
Retrocopy HLITMDLHQKEIQGFFNIPVDNLRASPFLLQYIQEEIPDYRNAVIVAKSPASAKRAQSFAERLHLGIAVI

Parental  HGEAQDAESDLVDGRHSPPMVRSVAAIHPSLEIPMLIPKEKPPITVVGDVGGRIAIIVDDIIDDVDSFLA
          HGEAQDAESDLVDGRHSPPMVRSVAAIHPSLEIPMLIPKEKP.ITVVGDVGGRIAIIVDDIIDDVDSFLA
Retrocopy HGEAQDAESDLVDGRHSPPMVRSVAAIHPSLEIPMLIPKEKPLITVVGDVGGRIAIIVDDIIDDVDSFLA

Parental  AAETLKERGAYKIFVMATHGLLSSDAPRLIEESAIDEVVVTNTIPHEIQKLQCPKIKTVDISMILSEAIR
          AAETLKERGAYKIFVMATH.LLSSDAPRLIEESAIDEVVVTNTIPHEIQKLQCP.IKTVDISMILSEAIR
Retrocopy AAETLKERGAYKIFVMATHSLLSSDAPRLIEESAIDEVVVTNTIPHEIQKLQCPNIKTVDISMILSEAIR

Parental  RIHNGESMSYLFRNIGLDD
          RIH.GESMSYLFRNIGLDD
Retrocopy RIHSGESMSYLFRNIGLDD

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	0.12 RPM	14.88 RPM
SRP007412_cerebellum	0.09 RPM	11.51 RPM
SRP007412_heart	0.03 RPM	3.05 RPM
SRP007412_kidney	0.08 RPM	8.99 RPM
SRP007412_liver	0.05 RPM	4.26 RPM
SRP007412_testis	0.00 RPM	9.15 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1937 was not detected

EST

No EST(s) were mapped for retro_mmus_1937 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_89237	545 libraries	325 libraries	194 libraries	8 libraries	0 libraries

The graphical summary, for retro_mmus_1937 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_1937 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1937 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000020528	2 retrocopies	retro_mmus_1937 , retro_mmus_3515,
Mus musculus	ENSMUSG00000031432	2 retrocopies	retro_mmus_19, retro_mmus_33,