RetrogeneDB ID: retro_mmus_1956

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:100058720..100059285(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082259
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mrpl28
• Ensembl ID: ENSMUSG00000024181
• Aliases: Mrpl28, 1110015G04Rik, L28mt, MAAT1, MRP-L28, p15
• Description: mitochondrial ribosomal protein L28 [Source:MGI Symbol;Acc:MGI:1915861]

Sequence

>retro_mmus_1956
TACTACCCTACAGAGTCCCAGCACGGACTGTGGGGTGAAGTCGGCTCGATTTGGGGCTACAGATACGCCAACAATGAACA
AGCTCTCCAAGAGTGCGGAGAAGGTATGGAAACCTCAGCTCTTCACTCGGGCCCTTTACAGTGAAATCCTAGACAAGAAG
TTCACTGTGCCTGTGACCATGAGGACCCTGGATTTCATTGATAAATCTTATTGGATTTGACTTCTATATTCTCAAGACCC
TTAAGGATAATCTGCTCTCCGATTTGGACATGGACGTGAACCAAGGTATGCTGCTGAGGTTTGTTCACCAGGACCCCACT
ACACCTTGATAACTCTGAGAGGAGATCAGTCATCTATCACAAGTACAGGAACTTTGTCATCCAGGTGGCAGAGGCTGAGT
AGGTTGGCCTGATGCTGGAGGACGCCCCAGAAAAACAGAGACTTCTGGAGGAAAAGGACCCTGTACCTAAAGTTCAACGT
CTGCGTAGAGGAGTTGGTCCAACTGTTTCAGGAGCATTTTCTATGCAGTCCAACAGTGGTGCAGAAGAGATCTGGTGAGT
ACGCC

Alignment

ORF - retro_mmus_1956 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.91 %
• Parental protein coverage: 73.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  HYPPESQQGLWGGEGLILGYRYANND-KLSKRVKKVWKPQLFTRELYSEILDKKFTVTVTMRTLDLIDEA
          .YP.ESQ.GLWG..G.I.GYRYANN..KLSK...KVWKPQLFTR.LYSEILDKKFTV.VTMRTLD.ID..
Retrocopy YYPTESQHGLWGEVGSIWGYRYANNE>KLSKSAEKVWKPQLFTRALYSEILDKKFTVPVTMRTLDFIDKS

Parental  Y-GFDFYILKTPKEDLGSKFGMDLKRGMLLRLARQD-PH-LHPENPERRAAIYDKYRSFVIPEAEAEWVG
          Y.GFDFYILKT.K..L.S...MD...GMLLR...QD.PH.LH..N.ERR..IY.KYR.FVI..AEAE.VG
Retrocopy Y>GFDFYILKTLKDNLLSDLDMDVNQGMLLRFVHQD<PH<LHLDNSERRSVIYHKYRNFVIQVAEAE*VG

Parental  LTLEEALEKQRLLEEKDPVP-LFKVYVEELVQRLQEQVLSRPAVVQKRAGDHA
          L.LE.A.EKQRLLEEKDPVP..F.V.VEELVQ..QE..L..P.VVQKR.G..A
Retrocopy LMLEDAPEKQRLLEEKDPVP>KFNVCVEELVQLFQEHFLCSPTVVQKRSGEYA

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	23.78 RPM
SRP007412_cerebellum	0.00 RPM	22.97 RPM
SRP007412_heart	0.00 RPM	56.41 RPM
SRP007412_kidney	0.00 RPM	38.38 RPM
SRP007412_liver	0.00 RPM	24.88 RPM
SRP007412_testis	0.00 RPM	10.25 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1956 was not detected

EST

No EST(s) were mapped for retro_mmus_1956 retrocopy.

TSS

No TSS is located nearby retro_mmus_1956 retrocopy 5' end.

Lab

retro_mmus_1956 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1956 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000000407	1 retrocopy	retro_meug_1004,
Mus musculus	ENSMUSG00000024181	1 retrocopy	retro_mmus_1956 ,
Procavia capensis	ENSPCAG00000011480	1 retrocopy	retro_pcap_155,