RetrogeneDB ID: retro_mmus_3093

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:139543460..139544470(-)
• Located in intron of: ENSMUSG00000025477

Retrocopy information

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

Parental gene information

• Parental gene symbol: 0610031J06Rik
• Ensembl ID: ENSMUSG00000001418
• Aliases: None
• Description: RIKEN cDNA 0610031J06 gene [Source:MGI Symbol;Acc:MGI:1913318]

Sequence

>retro_mmus_3093
AGGTAGGTATCTATGGAGGTTATTTCCGGCTGGCCAAATCTACAGAACCTGCTTCATATCCGGGCAATGGGCAGCAACTC
CACCCTGTGCTATGTGTGGAGCAGCCTGGGGCCTCCAGCTGTGGTGCTGGTGGCCACCAACACCACTCAGTGTCCTGAGT
GTCCACTGGCGTCTCCTGCTATCTCCTGATCCAGCTGGGACCCTGCTGGTGCTCCCCAAGAGCAGCATCCAGTGTTCTTC
CGCTCTCGTCTTCACCAGGCTGCCTGAGTTTGACAGCACCAACGTGTCTGAGGGGGCACAGCCTCCAGGAAAGCCATACC
CTCTGTACTCCTTGGCCAAGTTCTCCTGGAACAATATTACCAACTCATTGGATATTGCTACCCTGAGCATCATTTTTCAA
GGCCGCCCTGTAGATGATCCTACTGGAGCATTCGCCAATGGCAGCCTGACCTTCAAGGTCCAAGCCTTTTCTAGATCTGG
TAGACCTGATCTAGCCCCCTCTCCTCCTGCACACAGCAGATGTCTGCCAGTTAGAAGTGGCCCTGGTTGGAGCTGCTCCT
CGTGGAAACCATTCCCTGTTTGGTCTAGAGGTAGCCACCTTGGGACAGGGCCCTGTCTGCCCCTCAGTGAATGAACAGAA
CTCCATCGATGATGAATATGCACCTGCCGTCTTCCAGCTGAACCAGCTGTTGTGGGGCTCTACTCCATCTGGCTTCATGC
AATGGCAACCAGTGGCTTTCTCTGAGGAAGAGCAGGTCCAAGAATCAGCCCTCCCCTGCCAGGCTTCCACTCTTTGCTCC
ACCTTGGCATCTTCTCTTCCTCATTCAACAATTGTTCAAGCCTTCTTTGGGAACCAGAACAACTTCTGTGCCTTCACTCT
AACCTTTGGAGCTCCCATGGGCCCTGGCTACTGGAACCAATACTACCTTTGCTGGGCATTGCTTCTGGGCGTGGGCTTCC
CTCCAGTGGAAATCTTCTCTCCACTAGGCCTTGGAATCATGGCGGTGGCC

Alignment

ORF - retro_mmus_3093 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.84 %
• Parental protein coverage: 83.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RQVSMEVISGWPNPQNLLHIRAVGSNSTLHYVWSSLGPPAVVLVATNTTQ-SVLSVNWSLLLSPDPAGAL
          R.VSMEVISGWPN.QNLLHIRA.GSNSTL.YVWSSLGPPA.V......T..SVLSV.W.LLLSPDPAG.L
Retrocopy R*VSMEVISGWPNLQNLLHIRAMGSNSTLCYVWSSLGPPA-VVLVATNTT>SVLSVHWRLLLSPDPAGTL

Parental  MVLPKSSIQFSSALVFTRLLEFDSTNASEGAQPPGKPYPPYSLAKFSWNNITNSLDLANLSADFQGRPVD
          .VLPKSSIQ.SSALVFTRL.EFDSTN.SEGAQPPGKPYP.YSLAKFSWNNITNSLD.A.LS..FQGRPVD
Retrocopy LVLPKSSIQCSSALVFTRLPEFDSTNVSEGAQPPGKPYPLYSLAKFSWNNITNSLDIATLSIIFQGRPVD

Parental  DPTGAFANGSLTFKVQAFSRSGRPAQ-PPRLLHTADVCQLEVALVGASPRGNHSLFGLEVATLGQGPDCP
          DPTGAFANGSLTFKVQAFSRSGRP...PP.LLHTADVCQLEVALVGA.PRGNHSLFGLEVATLGQGP.CP
Retrocopy DPTGAFANGSLTFKVQAFSRSGRPDL>PPLLLHTADVCQLEVALVGAAPRGNHSLFGLEVATLGQGPVCP

Parental  SVNERNSIDDEYAPAVFQLNQLLWGSSPSGFMQWRPVAFSEEERARESALPCQASTLHSTLASSLPHSPI
          SVNE.NSIDDEYAPAVFQLNQLLWGS.PSGFMQW.PVAFSEEE...ESALPCQASTL.STLASSLPHS.I
Retrocopy SVNEQNSIDDEYAPAVFQLNQLLWGSTPSGFMQWQPVAFSEEEQVQESALPCQASTLCSTLASSLPHSTI

Parental  VQAFFGSQNNFCAFNLTFGAPTGPGYWDQYYLCWSMLLGMGFPPVDIFSPLVLGIMAVA
          VQAFFG.QNNFCAF.LTFGAP.GPGYW.QYYLCW..LLG.GFPPV.IFSPL.LGIMAVA
Retrocopy VQAFFGNQNNFCAFTLTFGAPMGPGYWNQYYLCWALLLGVGFPPVEIFSPLGLGIMAVA

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	0.09 RPM	24.25 RPM
SRP007412_cerebellum	0.48 RPM	25.23 RPM
SRP007412_heart	0.12 RPM	24.90 RPM
SRP007412_kidney	0.06 RPM	66.18 RPM
SRP007412_liver	0.03 RPM	41.32 RPM
SRP007412_testis	0.18 RPM	7.36 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3093 was not detected

EST

No EST(s) were mapped for retro_mmus_3093 retrocopy.

TSS

No TSS is located nearby retro_mmus_3093 retrocopy 5' end.

Lab

retro_mmus_3093 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3093 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
Macropus eugenii	ENSMEUG00000012878	1 retrocopy	retro_meug_950,
Mus musculus	ENSMUSG00000001418	1 retrocopy	retro_mmus_3093 ,