RetrogeneDB ID: retro_mmus_3026

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:44299914..44300626(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Rpf1
• Ensembl ID: ENSMUSG00000028187
• Aliases: Rpf1, 2210420E24Rik, 2310066N05Rik, Bxdc5
• Description: ribosome production factor 1 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1917535]

Sequence

>retro_mmus_3026
CAATGAGTCTACGATGAAGCCACAGTAGACCCCAATGGCAAAGAGGTGGCTTATGATGAATTTGCTCCTTACTTCAACAG
TCAGACATCTCCTAGGATGTCTCATCGCAAGGTCAGATAGACCTCATGGGAGAATAGTACGACTCTGTAGCCGCTCTCAA
CACTTCTACCAGATTCACATGTTTATTACAGAAGAGGACTGACTCTGAAAAAAATCACCCCACAGTCCGTTGCAAGAGGT
TCACAAACCTGATCGTTGTTAATGAAGATCATAAAACACCCAATGGACTTATATCGAGTCACTTGCCAAATGGTCCAACT
AACTCATTTAAAAATAAGTAATGTTCGTCTTTGTAAAGAAATTAAGAAATGAGGCAAAGACCCAAAAAGAACATGTGCCC
AAGATAATTCTGAATAACTTTACAACACGGCTAGGTCATTCTATTAGATGTGTGTTTGCTTTTCTCTTTCCTCATAACCC
TCAGGTTATTAGAGGACAGGTTGCCACATCCCACAGTCAGCGGGATTACATCTTCAGGGTTCACAGATACATATTCAAGA
GTGAAAAGGAAGTAGGAATTCAGGCGCTGGCACCACATTTTACCTTAAAATTATTATCTCTTCAGAAGGGAACCTTTGAT
TCTAAAAATGGAGAATATGAATGTGTCCACGAAGCACGGGAAATGAATCCAAGTCAAAGAAAATTCCGTTTA

Alignment

ORF - retro_mmus_3026 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.28 %
• Parental protein coverage: 69.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  QRVYDETTVDPNDEEVAYDEATDEFASYFNRQTSPKI-LITTSDRPHGRTVRLCEQ-LSTVIPDSHVYYR
          Q.VYDE.TVDPN..EVAY....DEFA.YFN.QTSP...LI..SDRPHGR.VRLC...LST..PDSHVYYR
Retrocopy Q*VYDEATVDPNGKEVAY----DEFAPYFNSQTSPRM>LIARSDRPHGRIVRLCSR<LSTLLPDSHVYYR

Parental  RGLALKKIIPQCIARD-FTDLIVINEDRKTPNGLILSHLPNGPT-AHFKMSSVRLRKEIKRRGKDPT-EH
          RGL.LKKI.PQ..AR..FT.LIV.NED.KTPNGLI.SHLPNGPT..H.K.S.VRL.KEIK..GKDP..EH
Retrocopy RGLTLKKITPQSVARG<FTNLIVVNEDHKTPNGLISSHLPNGPT>THLKISNVRLCKEIKK*GKDPK>EH

Parental  VPEIILNNFTTRLGHSIGRMFASLFPHNPQFIGRQVATFHNQRDYIFFRFHRYIFKSEKKVGIQELGPRF
          VP.IILNNFTTRLGHSI...FA.LFPHNPQ.I..QVAT.H.QRDYIF.R.HRYIFKSEK.VGIQ.L.P.F
Retrocopy VPKIILNNFTTRLGHSIRCVFAFLFPHNPQVIRGQVATSHSQRDYIF-RVHRYIFKSEKEVGIQALAPHF

Parental  TLKLRSLQKGTFDSKYGEYEWVHKPREMDTSRRKFHL
          TLKL.SLQKGTFDSK.GEYE.VH..REM..S.RKF.L
Retrocopy TLKLLSLQKGTFDSKNGEYECVHEAREMNPSQRKFRL

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	0.05 RPM	7.27 RPM
SRP007412_cerebellum	0.00 RPM	8.25 RPM
SRP007412_heart	0.00 RPM	10.27 RPM
SRP007412_kidney	0.00 RPM	16.38 RPM
SRP007412_liver	0.00 RPM	13.38 RPM
SRP007412_testis	0.00 RPM	12.03 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3026 was not detected

EST

No EST(s) were mapped for retro_mmus_3026 retrocopy.

TSS

No TSS is located nearby retro_mmus_3026 retrocopy 5' end.

Lab

retro_mmus_3026 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3026 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000001097	1 retrocopy	retro_eeur_17,
Myotis lucifugus	ENSMLUG00000016028	2 retrocopies	retro_mluc_681, retro_mluc_942,
Mus musculus	ENSMUSG00000028187	1 retrocopy	retro_mmus_3026 ,
Oryctolagus cuniculus	ENSOCUG00000014803	1 retrocopy	retro_ocun_1133,
Pteropus vampyrus	ENSPVAG00000003729	1 retrocopy	retro_pvam_1489,
Rattus norvegicus	ENSRNOG00000015969	1 retrocopy	retro_rnor_1372,
Tupaia belangeri	ENSTBEG00000013600	4 retrocopies	retro_tbel_1027, retro_tbel_2204, retro_tbel_2279, retro_tbel_63,