RetrogeneDB ID: retro_mmus_3531

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:145994290..145994811(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083908
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rrp15
• Ensembl ID: ENSMUSG00000001305
• Aliases: Rrp15, 2810430M08Rik, 5430437H21Rik
• Description: ribosomal RNA processing 15 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1914473]

Sequence

>retro_mmus_3531
ATGGCTGCAGCTGTTCAGGACTCAAGTGTGAGCCCAGGGGAAAAGCTGAAGCATTCCCCAAAGAAGAAAACCATGAAGAC
AGGGGCCAAGGCTGCAATGTCAAAGCTAGACGATGAGGTCAAAGACTCTTCTGATGGAGAAGGAAGCTGTGAATCAGAGA
TGGACCACTCAGATGATGGAGCTGTGGAAGCAAACAGTGAGGACAATGTTGAATCCTGTGAGGAAGAAAATGAAGACGCT
GCTGAGTCAAGTGCTGGGACTAACTCAGGGTGGGCAGATGCCATGGCAAAAATCCTTAACAAAAAGACTCCTAAAAGCAA
ATCCACCATCCTCACCAAAACAAAGAGCTCGGGAAGGAAAGGAAGAAGCTAAAGCAGGAGAGGCTGGAGAAAAGGAAGCA
CCTTGAAAAGAAGCAGGAGTAGGAAATGCTTTGCAGAGTGAAGCCAGATGTTGTCAAAGACAAAGAAGCAGAGAGGAACC
TTCAGAGAATTTAGAAAAGGGGTGTGATGCAGCTCTTCAAT

Alignment

ORF - retro_mmus_3531 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.8 %
• Parental protein coverage: 62.28 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAVQDSRVSPGEILKRSPKKKKKMKMVAKAAASKLEDEVKDSSDGEGSCDSEMDHSDDGAAEADSEDN
          MAAAVQDS.VSPGE.LK.SPKKK..MK..AKAA.SKL.DEVKDSSDGEGSC.SEMDHSDDGA.EA.SEDN
Retrocopy MAAAVQDSSVSPGEKLKHSPKKKT-MKTGAKAAMSKLDDEVKDSSDGEGSCESEMDHSDDGAVEANSEDN

Parental  VESCEEDNEDAAESSAGTNSGWADAMAKILNKKTPKSKATILTK-NKELEKEKEKLKQERLEKRKQLDKK
          VESCEE.NEDAAESSAGTNSGWADAMAKILNKKTPKSK.TILTK.NKEL.KE..KLKQERLEKRK.L.KK
Retrocopy VESCEEENEDAAESSAGTNSGWADAMAKILNKKTPKSKSTILTK<NKELGKERKKLKQERLEKRKHLEKK

Parental  REWEMLCRVKPDVVKDKEAERNLQRIATRGVVQLFN
          .E.EMLCRVKPDVVKDKEAERNLQRI..RGV.QLFN
Retrocopy QE*EMLCRVKPDVVKDKEAERNLQRI*KRGVMQLFN

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	8.34 RPM
SRP007412_cerebellum	0.04 RPM	7.12 RPM
SRP007412_heart	0.00 RPM	6.51 RPM
SRP007412_kidney	0.00 RPM	9.26 RPM
SRP007412_liver	0.00 RPM	12.32 RPM
SRP007412_testis	0.00 RPM	16.56 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3531 was not detected

EST

No EST(s) were mapped for retro_mmus_3531 retrocopy.

TSS

No TSS is located nearby retro_mmus_3531 retrocopy 5' end.

Lab

retro_mmus_3531 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3531 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000174	1 retrocopy	retro_chof_1961,
Callithrix jacchus	ENSCJAG00000012916	2 retrocopies	retro_cjac_3789, retro_cjac_455,
Mus musculus	ENSMUSG00000001305	1 retrocopy	retro_mmus_3531 ,
Oryctolagus cuniculus	ENSOCUG00000017863	4 retrocopies	retro_ocun_1738, retro_ocun_820, retro_ocun_962, retro_ocun_992,
Ictidomys tridecemlineatus	ENSSTOG00000001244	1 retrocopy	retro_itri_1554,
Tarsius syrichta	ENSTSYG00000012715	1 retrocopy	retro_tsyr_2006,