RetrogeneDB ID: retro_mmus_1687

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:8415144..8416047(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Shc1
• Ensembl ID: ENSMUSG00000042626
• Aliases: Shc1, Shc, ShcA, p66, p66shc
• Description: src homology 2 domain-containing transforming protein C1 [Source:MGI Symbol;Acc:MGI:98296]

Sequence

>retro_mmus_1687
AAAGACCCTGTGAATCAGAGAGCCTGCCATATCCTGGAGTGTCCTGAAGGGTTTGCTCAGGATGTCATCAGCACCATCGG
GCAGGCCTTTGAGTTGTGCTTCAAACAGTATCTCAGGAATCCACCGAAGCTGGTCACCCCCCATGACAGGATGGCTGGCT
TTGATGGCTCAGCTTGGGATGAGGAGGAAGAAGAGCCCCCTGACCATCAGTACTACAATGACTTTCCAGGGAAGGAACCC
CCTCTTGGTGGGGTGGTAGATATGAGGCCTCGGGAAGGGGCTGCTCGACCCACTCTGCCTAGTGCCCAGATGTCCAGCCA
CTTGGGAGCTACACTGCCTATAGGGCAGCATGCTGCAGGAGACCATGAAGTCCGTAAACAGATGTTGCCTCCGCCACGTT
GCCCAGGCAGAGAACTCTTCGATGACCCCTCCTATGTCAACATCCAGAATCTAGACAAGGCCCGGCAGGCTGGGGGTGGG
GCTGGGCCCCCAAATCCTTCTCTTAATGGCAGTGCACCCCGAGACCTTTTTGACATGAAGCCCTTTGAAGATACACTTCG
GGTGCCATCCCCACTGCAGTCCATGTTCATGGCTGAGCAGCTGCAAGGGGAGCCCTGGTTCCACGGGAAGCTGAGCCGGA
GGGAGGCCAAGGCACTGCTGCAGCTCAATGGTGACTTCTTGGTGCGAGAGAGCACGACCACACCTGGCCAGTATGTGCTC
ACTGACCTGCAGAGTGGGCAGCCCAAGCACTTGCTGCTGGTGGACCCTGAAGGTGTGGTTCGGACAAAGGATCACTGCTT
TGAGAGTGTCAGTCACCTGATCAGCTACCACATGGACAATCACTTGCCCATCATCTCTGCGGGCAGCGAACTGTGCCTAC
AGCAACCCGTGGATCGGAAAGTG

Alignment

ORF - retro_mmus_1687 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.35 %
• Parental protein coverage: 64.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KDPVNQRACHILECPEGLAQDVISTIGQAFELRFKQYLRNPPKLVTPHDRMAGFDGSAWDEEEEEPPDHQ
          KDPVNQRACHILECPEG.AQDVISTIGQAFEL.FKQYLRNPPKLVTPHDRMAGFDGSAWDEEEEEPPDHQ
Retrocopy KDPVNQRACHILECPEGFAQDVISTIGQAFELCFKQYLRNPPKLVTPHDRMAGFDGSAWDEEEEEPPDHQ

Parental  YYNDFPGKEPPLGGVVDMRLREGAARPTLPSAQMSSHLGATLPIGQHAAGDHEVRKQMLPPPPCPGRELF
          YYNDFPGKEPPLGGVVDMR.REGAARPTLPSAQMSSHLGATLPIGQHAAGDHEVRKQMLPPP.CPGRELF
Retrocopy YYNDFPGKEPPLGGVVDMRPREGAARPTLPSAQMSSHLGATLPIGQHAAGDHEVRKQMLPPPRCPGRELF

Parental  DDPSYVNIQNLDKARQAGGGAGPPNPSLNGSAPRDLFDMKPFEDALRVPPPPQSMSMAEQLQGEPWFHGK
          DDPSYVNIQNLDKARQAGGGAGPPNPSLNGSAPRDLFDMKPFED.LRVP.P.QSM.MAEQLQGEPWFHGK
Retrocopy DDPSYVNIQNLDKARQAGGGAGPPNPSLNGSAPRDLFDMKPFEDTLRVPSPLQSMFMAEQLQGEPWFHGK

Parental  LSRREAEALLQLNGDFLVRESTTTPGQYVLTGLQSGQPKHLLLVDPEGVVRTKDHRFESVSHLISYHMDN
          LSRREA.ALLQLNGDFLVRESTTTPGQYVLT.LQSGQPKHLLLVDPEGVVRTKDH.FESVSHLISYHMDN
Retrocopy LSRREAKALLQLNGDFLVRESTTTPGQYVLTDLQSGQPKHLLLVDPEGVVRTKDHCFESVSHLISYHMDN

Parental  HLPIISAGSELCLQQPVDRKV
          HLPIISAGSELCLQQPVDRKV
Retrocopy HLPIISAGSELCLQQPVDRKV

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	8.99 RPM
SRP007412_cerebellum	0.00 RPM	10.73 RPM
SRP007412_heart	0.00 RPM	26.71 RPM
SRP007412_kidney	0.02 RPM	35.57 RPM
SRP007412_liver	0.08 RPM	38.61 RPM
SRP007412_testis	0.00 RPM	13.63 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1687 was not detected

EST

1 EST(s) were mapped to retro_mmus_1687 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BE372582	8415110	8415441	95.3	308	9	289

TSS

No TSS is located nearby retro_mmus_1687 retrocopy 5' end.

Lab

retro_mmus_1687 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1687 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
Mus musculus	ENSMUSG00000042626	1 retrocopy	retro_mmus_1687 ,
Rattus norvegicus	ENSRNOG00000020657	1 retrocopy	retro_rnor_1995,