RetrogeneDB ID: retro_mmus_1355

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:74924624..74925296(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: 1700123I01Rik
• Ensembl ID: ENSMUSG00000024786
• Aliases: None
• Description: RIKEN cDNA 1700123I01 gene [Source:MGI Symbol;Acc:MGI:1923913]

Sequence

>retro_mmus_1355
GTAAGAGGAGAAGAAATAGAGGATAAGGGAGTTATCATCCAGGAGCTGGAGGGTTCTATCCGTGCAGTCTTGGCAAACAT
GGACAGCCTGCAGCCCTTTGTTACAGAACACTTCATTGTATTTCCCTATAAAAGCAAGTGGGAGAGGGTTTCCCACCTGA
AGTCTAAACATGAAGAAATCATCCTGACCCCCTGACCCGTTTGTTTTTACTTTGTATATAGAGATGAAATGGTTTGCTGA
AGACCTGCCTTCAGGAAACCAGCAGATGATATTCCTCTTGAGCTGGTCCTAGCTGGGAAGGAAGCAGAAGAAGCCACAAT
GATGAAGTGGAAACGGAAACTCGTGGAGGAGCCCAGCTCCCCTAGCAGGCCAGGGTCACACGGGGCCAAGATGGAGACTT
CTAGTGAAGCTTCCAGCAATAAGAAGCCTCTGAAGGAGAGCAAGAGGAGCAGGGACGAAGAAGCCCAGCAGGAATACCAG
GATCCCCCAGCTTCTAATGCCATTGCTGTCAAGGAACAGGGTGCTATGTTGGGGCATGGCCTACAAGGCTTGGTTGTCCC
TCCACTGCAACACAGCAGTCCACCACCCCTGAAAGAGCCAGGAGCCAGAGGCTTCTTGAGGTTTCTAAATGCTCTCTTCC
CGTTCCAGTACTTCTTCAAGAAGAGCAGTCAG

Alignment

ORF - retro_mmus_1355 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.5 %
• Parental protein coverage: 87.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IRGEEIEDKEVIVQELEDSIRAVLANMDSLQPFVTEHFIVFPYKSKWERVSHLKFKHGESILT-PYPFVF
          .RGEEIEDK.VI.QELE.SIRAVLANMDSLQPFVTEHFIVFPYKSKWERVSHLK.KH.E.ILT.P.PFVF
Retrocopy VRGEEIEDKGVIIQELEGSIRAVLANMDSLQPFVTEHFIVFPYKSKWERVSHLKSKHEEIILT>PDPFVF

Parental  TLYIEMKWFAEDLPSG-KPADDIPLELVLAETEAEEATMRKWKRKLMEEPSSPSRQGPHRAKMETSSEAS
          TLYIEMKWFAEDLPSG.KPADDIPLELVLA..EAEEATM.KWKRKL.EEPSSPSR.G.H.AKMETSSEAS
Retrocopy TLYIEMKWFAEDLPSG<KPADDIPLELVLAGKEAEEATMMKWKRKLVEEPSSPSRPGSHGAKMETSSEAS

Parental  SNKKPLKESKRSTDEEAQQEYQDTPASNAIAVKEQDAALGHGLQGLVVPPLQHSSPPPPKEPGARGFLGF
          SNKKPLKESKRS.DEEAQQEYQD.PASNAIAVKEQ.A.LGHGLQGLVVPPLQHSSPPP.KEPGARGFL.F
Retrocopy SNKKPLKESKRSRDEEAQQEYQDPPASNAIAVKEQGAMLGHGLQGLVVPPLQHSSPPPLKEPGARGFLRF

Parental  LSALFPFRYFFKKSGQ
          L.ALFPF.YFFKKS.Q
Retrocopy LNALFPFQYFFKKSSQ

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	0.02 RPM
SRP007412_cerebellum	0.00 RPM	0.09 RPM
SRP007412_heart	0.00 RPM	0.06 RPM
SRP007412_kidney	0.00 RPM	0.04 RPM
SRP007412_liver	0.00 RPM	0.03 RPM
SRP007412_testis	0.09 RPM	9.29 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_1355 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	15:74917984..74925707

EST

No EST(s) were mapped for retro_mmus_1355 retrocopy.

TSS

No TSS is located nearby retro_mmus_1355 retrocopy 5' end.

Lab

retro_mmus_1355 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1355 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000024786	1 retrocopy	retro_mmus_1355 ,