RetrogeneDB ID: retro_mmus_3515

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:120958193..120958881(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083275
• 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_3515
CATCTCATCACTATGGATTTACACAGGAAGGAAATCCAGGGCTTCTTCAATATTCCAGTGGATAATTTAAGAGCCTCCCC
ATTCCTGTTACAATATATTCAAGAAGAGATCCAAGATTATAGGAATGCAGTCATTGTGGCCAAGTCTCCAGCCTCAGCCA
AGAGGGCACAATCTTTTGCAACGTGTCTACGTCTGGGTATGTCAGTGATCCATGGAGAAGCACAAGATGCTGAGTCTGAC
TTGGTGGATGGCTGTCACTCCCCACCAATATTTAGGAGTGTAGCTGCCATCCACCACAGCCTGGAGATCCCAATGCTGAT
TCCTAAAGAGAAGCCCCCAATCACAGTTGTTGGTGATGTCCGAGGAAGTATTGCCGCCGCCATCATCATCATGGGTGAAA
TTATTGGATAGTTTTCTTGCTACAGCAGAGACCCTGAAGGAAAGAGGTGCATATAAAATCTTTGTGATGGCCACTCACGG
CTTGTTATCCTCTGATGCTACCAGGCTGATTGAAGAGTCTGCCATTGATGAGGTGTTGGTCACTAACACGATACCACAAG
AGATACAGAAGCTGCAGTGTCCCAAGATCAAGACTGTGGACATCAGCATGATTCTCTCAAAAGCCATCCGCCAAATTCAC
AACGGGGAGTCCATGTCCAACCTTTTCAGAAACATAGGCTTAGATGAC

Alignment

ORF - retro_mmus_3515 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.96 %
• Parental protein coverage: 62.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HLITMDLHQKEIQGFFNIPVDNLRASPFLLQYIQEEIPDYRNAVIVAKSPASAKRAQSFAERLRLGIAVI
          HLITMDLH.KEIQGFFNIPVDNLRASPFLLQYIQEEI.DYRNAVIVAKSPASAKRAQSFA..LRLG..VI
Retrocopy HLITMDLHRKEIQGFFNIPVDNLRASPFLLQYIQEEIQDYRNAVIVAKSPASAKRAQSFATCLRLGMSVI

Parental  HGEAQDAESDLVDGRHSPPMVRSVAAIHPSLEIPMLIPKEKPPITVVGDVGGRIAIIV-DDIIDDVDSFL
          HGEAQDAESDLVDG.HSPP..RSVAAIH.SLEIPMLIPKEKPPITVVGDV.G.IA...........DSFL
Retrocopy HGEAQDAESDLVDGCHSPPIFRSVAAIHHSLEIPMLIPKEKPPITVVGDVRGSIAAAI>SSWVKLLDSFL

Parental  AAAETLKERGAYKIFVMATHGLLSSDAPRLIEESAIDEVVVTNTIPHEIQKLQCPKIKTVDISMILSEAI
          A.AETLKERGAYKIFVMATHGLLSSDA.RLIEESAIDEV.VTNTIP.EIQKLQCPKIKTVDISMILS.AI
Retrocopy ATAETLKERGAYKIFVMATHGLLSSDATRLIEESAIDEVLVTNTIPQEIQKLQCPKIKTVDISMILSKAI

Parental  RRIHNGESMSYLFRNIGLDD
          R.IHNGESMS.LFRNIGLDD
Retrocopy RQIHNGESMSNLFRNIGLDD

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	0.02 RPM	14.88 RPM
SRP007412_cerebellum	0.00 RPM	11.51 RPM
SRP007412_heart	0.00 RPM	3.05 RPM
SRP007412_kidney	0.02 RPM	8.99 RPM
SRP007412_liver	0.00 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_3515 was not detected

EST

No EST(s) were mapped for retro_mmus_3515 retrocopy.

TSS

No TSS is located nearby retro_mmus_3515 retrocopy 5' end.

Lab

retro_mmus_3515 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3515 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	ENSMUSG00000020528	2 retrocopies	retro_mmus_1937, retro_mmus_3515 ,
Mus musculus	ENSMUSG00000031432	2 retrocopies	retro_mmus_19, retro_mmus_33,