RetrogeneDB ID: retro_mmus_3030

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:60753362..60754010(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gkap1
• Ensembl ID: ENSMUSG00000021552
• Aliases: Gkap1, 42kDa, 4933400B15Rik, D13Ertd340e, Gkap42
• Description: G kinase anchoring protein 1 [Source:MGI Symbol;Acc:MGI:1891694]

Sequence

>retro_mmus_3030
GCACAATGGAGAAATACTCAGACAAAAGGTATAAATAAAAAAGATAAAAGGAAGAACCACCAGGGCAAGGACAAACCTGT
CACGGTGTCACTCAAAGACTTCCAGTGTGAAGATCATATTAGTAAAAAGGCAGAGGAATCGAATTCTGCTCAGACTTTAT
CACACGATGGGGGATTCTTCAATAGACTGGAAGATGATGTTCATAAGATTCTGATTAGAGAAAAAAGGAGAGAACAACTC
ACAGAGCACAACGGAACAGATAACTCTCCCGCTCCAGAGCACAACCAGGAAGTAGGTCTAAAAGATGGAAGAATTGAAAG
ACTAAAGTTAGAACTTGAAAGGAAAGACGCAGAAATTCAGAAGCTCAAAGCTGTGATCACTCAGTGGGAGGCAAAGTATA
AAGAAGTAAAAGCAAGAAATGGACAATTACTGAAAATGCTTCAGGAGGGAGAGATGAAAGATAAGGCCGAGATACTTCTG
CAAGTGGATGAGTCTCAGAGCATCAAGAACGAGCTGACGGTCCAGGTGTCTTCACTTCATGCCGCACTGGAACAAGAAAG
ATCTAAAGTGAAAGTATTACAGGCAGAATTAGCCAAATACCAGGGAGGCAGGAAGGGGAAAAGGAACTTCGAACCTGACC
ATTGCAGG

Alignment

ORF - retro_mmus_3030 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.15 %
• Parental protein coverage: 59.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AETASTQTKGINKKDKRKNHQGKDKPVTVSLKDFQCEDHISKKAEESNSAQTLSHDGGFFNRLEDDVHKI
          A....TQTKGINKKDKRKNHQGKDKPVTVSLKDFQCEDHISKKAEESNSAQTLSHDGGFFNRLEDDVHKI
Retrocopy AQWRNTQTKGINKKDKRKNHQGKDKPVTVSLKDFQCEDHISKKAEESNSAQTLSHDGGFFNRLEDDVHKI

Parental  LIREKRREQLTEHNGTDNSPAPEHNQEVGLKDGRIERLKLELERKDAEIQKLKAVITQWEAKYKEVKARN
          LIREKRREQLTEHNGTDNSPAPEHNQEVGLKDGRIERLKLELERKDAEIQKLKAVITQWEAKYKEVKARN
Retrocopy LIREKRREQLTEHNGTDNSPAPEHNQEVGLKDGRIERLKLELERKDAEIQKLKAVITQWEAKYKEVKARN

Parental  GQLLKMLQEGEMKDKAEILLQVDESQSIKNELTVQVSSLHAALEQERSKVKVLQAELAKYQGGRKGKRNF
          GQLLKMLQEGEMKDKAEILLQVDESQSIKNELTVQVSSLHAALEQERSKVKVLQAELAKYQGGRKGKRNF
Retrocopy GQLLKMLQEGEMKDKAEILLQVDESQSIKNELTVQVSSLHAALEQERSKVKVLQAELAKYQGGRKGKRNF

Parental  EPDHCR
          EPDHCR
Retrocopy EPDHCR

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	0.14 RPM	8.32 RPM
SRP007412_cerebellum	0.13 RPM	10.64 RPM
SRP007412_heart	0.37 RPM	11.86 RPM
SRP007412_kidney	0.64 RPM	27.18 RPM
SRP007412_liver	0.19 RPM	9.67 RPM
SRP007412_testis	8.42 RPM	442.11 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3030 was not detected

EST

No EST(s) were mapped for retro_mmus_3030 retrocopy.

TSS

No TSS is located nearby retro_mmus_3030 retrocopy 5' end.

Lab

retro_mmus_3030 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3030 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	ENSMUSG00000021552	1 retrocopy	retro_mmus_3030 ,