RetrogeneDB ID: retro_mmus_3232

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:109751036..109751564(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Larp1b
• Ensembl ID: ENSMUSG00000037814
• Aliases: Larp1b, 1700108L22Rik, 4933421B21Rik, AA690246, Larp2
• Description: La ribonucleoprotein domain family, member 1B [Source:MGI Symbol;Acc:MGI:1914604]

Sequence

>retro_mmus_3232
GGCCGGGGCCGAGGCCGAAGAAACCCTAGATTGAACTCTGATTATTCATATGGTTTTCGAGAGCCAGGGGAAAGGACTGA
GCAGCCATATTCTACAGAGCTTAACACCAGCATGATGCATCACTATGATGACCTCACAGGTGTGCAGGTGTGTCCTGTGG
AAGAAACACTGCTTAATGAGTACATTAAGCGCCAAATTGAGTGTATTACTTCAGCATAGAGAACTTGGAATGGGACTTCT
TCGAAGAAAGATGGATGAGCAGGGAGTCCCACTCCCTGATTGCTGGTTTTCACCGCGTGCAGGCTCTCACCACAGACCCT
AATCTCATCTTGGAGGCACTTAAGGATAGCACAGAAGTAGAAATTGTGGATGAGAAAATGAGGAAAAAGATAGAACCAGA
AAAATGGCCAATTCTTGGCTCTCTTCCAGGAAATGTGCCACAAACAGACTTCTCTCAGTTGACTGATTGTCCGGAGTTCA
TACCTGGCCAGGCCTTTGGCGTCCCATACAGTCGGGGTGATGATCTAC

Alignment

ORF - retro_mmus_3232 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.11 %
• Parental protein coverage: 53.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GRGRGRGNPRLNFDYSYGYREPGERTEQPFSTELNTSMMYYYDDGTGVRVYPVEETLLKEYIKRQIE-YY
          GRGRGR.NPRLN.DYSYG.REPGERTEQP.STELNTSMM..YDD.TGV.V.PVEETLL.EYIKRQIE..Y
Retrocopy GRGRGRRNPRLNSDYSYGFREPGERTEQPYSTELNTSMMHHYDDLTGVQVCPVEETLLNEYIKRQIE<VY

Parental  F-STENLERDFFLRRKMDEQGFLPISLIAGFHRVQALTTNLNLILEALKDSTEVEIVDEKMRKKIEPEKW
          ..S.ENLE.DFF..R.M........SLIAGFHRVQALTT..NLILEALKDSTEVEIVDEKMRKKIEPEKW
Retrocopy YFSIENLEWDFFEERWMSRESH---SLIAGFHRVQALTTDPNLILEALKDSTEVEIVDEKMRKKIEPEKW

Parental  PIPGPPPRNVPQTDFSQLIDCPEFIPGQAFG-SHTVRVMIY
          PI.G..P.NVPQTDFSQL.DCPEFIPGQAFG.SHTV.VMIY
Retrocopy PILGSLPGNVPQTDFSQLTDCPEFIPGQAFG>SHTVGVMIY

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	9.77 RPM
SRP007412_cerebellum	0.00 RPM	8.47 RPM
SRP007412_heart	0.03 RPM	42.40 RPM
SRP007412_kidney	1.87 RPM	41.29 RPM
SRP007412_liver	0.00 RPM	70.43 RPM
SRP007412_testis	0.05 RPM	273.61 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_3232 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	8:109750463..109752265

EST

No EST(s) were mapped for retro_mmus_3232 retrocopy.

TSS

No TSS is located nearby retro_mmus_3232 retrocopy 5' end.

Lab

retro_mmus_3232 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3232 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000015900	1 retrocopy	retro_ggor_2037,
Mus musculus	ENSMUSG00000037814	1 retrocopy	retro_mmus_3232 ,