RetrogeneDB ID: retro_mmus_1309

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:106211776..106212023(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sec61g
• Ensembl ID: ENSMUSG00000078974
• Aliases: None
• Description: SEC61, gamma subunit [Source:MGI Symbol;Acc:MGI:1202066]

Sequence

>retro_mmus_1309
CCTATGCTATGTGTCTCTATCTTCTCAAAATGCCATCCCATAGATATGGATCAGGTAATACAGTTTGTTGAGCTAAGTCG
GCAGTTTTCAAAGAACTCAATTCATCTAGTTAAAAGGTGCACCAAAATTCATAGAAAAGAATTCCAGAAGATTGCCAAGG
CCACAGCAATAGGACCTGCTCCTAATGGGATTCATTGGCTTCTTTGTGAAACTGATCCATATCCCCATACATAACACTGT
TGCTGGG

Alignment

ORF - retro_mmus_1309 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.29 %
• Parental protein coverage: 82. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PELRVSTLSIRHPTNMDQVMQFVEPSRQFVKDSIRLVKRCTKPDRKEFQKIAMATAIGFA-IMGFIGFFV
          P.L.VS..S..HP..MDQV.QFVE.SRQF.K.SI.LVKRCTK..RKEFQKIA.ATAIG.A..MGFIGFFV
Retrocopy PMLCVSIFSKCHPIDMDQVIQFVELSRQFSKNSIHLVKRCTKIHRKEFQKIAKATAIGPA>LMGFIGFFV

Parental  KLIHIPINNIIVG
          KLIHIPI.N...G
Retrocopy KLIHIPIHNTVAG

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	4.09 RPM
SRP007412_cerebellum	0.00 RPM	3.43 RPM
SRP007412_heart	0.00 RPM	1.28 RPM
SRP007412_kidney	0.00 RPM	1.23 RPM
SRP007412_liver	0.00 RPM	1.47 RPM
SRP007412_testis	0.09 RPM	1.78 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1309 was not detected

EST

No EST(s) were mapped for retro_mmus_1309 retrocopy.

TSS

No TSS is located nearby retro_mmus_1309 retrocopy 5' end.

Lab

retro_mmus_1309 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1309 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000078974	13 retrocopies	retro_mmus_1214, retro_mmus_1309 , retro_mmus_1382, retro_mmus_1970, retro_mmus_2055, retro_mmus_2109, retro_mmus_3042, retro_mmus_3263, retro_mmus_3349, retro_mmus_3484, retro_mmus_447, retro_mmus_538, retro_mmus_586,
Tarsius syrichta	ENSTSYG00000014302	1 retrocopy	retro_tsyr_1084,
Tursiops truncatus	ENSTTRG00000000593	1 retrocopy	retro_ttru_1836,