RetrogeneDB ID: retro_mmus_1731

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:60426291..60427206(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000073554
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: 2610318N02Rik
• Ensembl ID: ENSMUSG00000049916
• Aliases: 2610318N02Rik, AL033325
• Description: RIKEN cDNA 2610318N02 gene [Source:MGI Symbol;Acc:MGI:1917708]

Sequence

>retro_mmus_1731
ATGGAAGTCCTGGATGAGTTCGACAACGAATTCCCCCTGAGTGTGACCTTCTGCCAGCTCATTTCCGAGGATGACTTCGA
GAGGCAAGCAGCGACCTACACAGAGCGTGCGCTGCGACGACTCTTCAGCACCTTGGATCGCAATCCAGCACTGGCAGAGA
GAGTCGTGCGGAAGGGCAAGCAGACTGAGTTCGAGCAGCGCGGGCTCCTCTGCAGCCTCTGGGCGAAGTTTGTCTGCGCT
GTGCAGGGGGATCTAAACCAGTGCAATGACATGGGTGCCATAGAGATGCTTCGGCGCCTGGAGCAGCTGAAGAGGCGCAT
ACATCGTGTGCATCTGTATTCCCAGGATGCCAAGAAGAGGAGGAGGAGGCCGAAACCAAAGAAACCAGATCCTATCTTTC
GAGATCAGTCAACCTCCGCATGCCTGCCACCAGCTCTCTTACCACCACCGCTGCTGCCGCCACCACCACAACCTGTCACC
ACCGTGGCCTCTGTAGTGGCTGCATCACCCTCTGTCTACACTATGCCCTGGGTCTTTGGCCCTTTCCCTCCACTGTCAGG
CAAGCCGATGGAGAAACTGGATATTTCAAGTTCTGAAGTGAAACTAAACTGGAGTGGTCTTTCATCAACGTCAAAGAGCC
ACATGGTTGATCTGAACCCCTTGGTTCTCAATCCCGGAGGCTTCCATTTCTCATATTTGGCAGGAAGCAGTGCACACAAG
CTCCATTGTCCTGGCTTTCCCTGGACGCCAGCCTGTAGCAGACCCTCCAACACAGATGAGACACCATCTCCTGTTGTGAA
AACCTCCATCTTCACTCCGCCTGTACTGCTCAAGTTCCAGCCTGTGCCCAGACCCAATGATGATTCAGAGAATGACCCTG
GCAGCGCAGAGTCCACTCCTGCCAAGGAGAGCCAG

Alignment

ORF - retro_mmus_1731 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEVLDEFDNEFPLSVTFCQLISEDDFERQAATYTERALRRLFRTLDRNPALAERVVRKGKQTEFEQRGLL
          MEVLDEFDNEFPLSVTFCQLISEDDFERQAATYTERALRRLF.TLDRNPALAERVVRKGKQTEFEQRGLL
Retrocopy MEVLDEFDNEFPLSVTFCQLISEDDFERQAATYTERALRRLFSTLDRNPALAERVVRKGKQTEFEQRGLL

Parental  CSLWAKFVCAVQGDLNQCNDMGAIEMHRRLEQLKRRIHRVHLYSQDAKKRRRRPKPKKPDPIFRDQSTSA
          CSLWAKFVCAVQGDLNQCNDMGAIEM.RRLEQLKRRIHRVHLYSQDAKKRRRRPKPKKPDPIFRDQSTSA
Retrocopy CSLWAKFVCAVQGDLNQCNDMGAIEMLRRLEQLKRRIHRVHLYSQDAKKRRRRPKPKKPDPIFRDQSTSA

Parental  CLPPALLPPPLLPPPPQPVTTVASVVAASPSVYTMPRVFGPFPPLSGKPMEKLDISSSEVKLNWSGLSST
          CLPPALLPPPLLPPPPQPVTTVASVVAASPSVYTMP.VFGPFPPLSGKPMEKLDISSSEVKLNWSGLSST
Retrocopy CLPPALLPPPLLPPPPQPVTTVASVVAASPSVYTMPWVFGPFPPLSGKPMEKLDISSSEVKLNWSGLSST

Parental  SKSHMVDLTPLVLNPGGFHFSYLAGSSAHKLHCPGFPWTPACSRPSNTDETPSPVVKTSIFTPPVLLKFQ
          SKSHMVDL.PLVLNPGGFHFSYLAGSSAHKLHCPGFPWTPACSRPSNTDETPSPVVKTSIFTPPVLLKFQ
Retrocopy SKSHMVDLNPLVLNPGGFHFSYLAGSSAHKLHCPGFPWTPACSRPSNTDETPSPVVKTSIFTPPVLLKFQ

Parental  PVPRPNDDSENDSGSAESTPAKESQ
          PVPRPNDDSEND.GSAESTPAKESQ
Retrocopy PVPRPNDDSENDPGSAESTPAKESQ

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	0.02 RPM	0.63 RPM
SRP007412_cerebellum	0.00 RPM	0.17 RPM
SRP007412_heart	0.00 RPM	0.06 RPM
SRP007412_kidney	0.00 RPM	0.08 RPM
SRP007412_liver	0.00 RPM	0.08 RPM
SRP007412_testis	8.32 RPM	598.22 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1731 was not detected

EST

No EST(s) were mapped for retro_mmus_1731 retrocopy.

TSS

No TSS is located nearby retro_mmus_1731 retrocopy 5' end.

Lab

retro_mmus_1731 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1731 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008805	1 retrocopy	retro_amel_579,
Mustela putorius furo	ENSMPUG00000003165	1 retrocopy	retro_mputfur_1029,
Mus musculus	ENSMUSG00000049916	1 retrocopy	retro_mmus_1731 ,