RetrogeneDB ID: retro_mmus_2942

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:67593662..67593941(+)
• Located in intron of: ENSMUSG00000030556

Retrocopy information

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

Parental gene information

• Parental gene symbol: Lgalsl
• Ensembl ID: ENSMUSG00000042363
• Aliases: Lgalsl, 1110067D22Rik, A530071M23, Grpa, Hspc159, Lgalsla
• Description: lectin, galactoside binding-like [Source:MGI Symbol;Acc:MGI:1916114]

Sequence

>retro_mmus_2942
GTGGCAGGGTCGGTAGCTGACAGCGATGCTGTGGTGAAACTTGATGATGGGCACTTAACTCCCTGGGTTCTCCAGTTCAA
GCCGACGGACGTGTACTTCCCTTAACTGATAGTTACATTTTGAGGGCACATTAAAGGTAGCATGAGACCAGGCAAGAAGG
TATCAGTGATGGGCATGGTAGATCTCAACCCAGAAAGCTTTGCCATCAGATTGACCTGTGGTGATTCTGAAGAGCCTCCT
GCTGATGTGGCGATTGAACTCAAAGCTGTGTTCACAGAA

Alignment

ORF - retro_mmus_2942 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.49 %
• Parental protein coverage: 54.07 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGSVADSDAVVKLDDGHLNNSLGSPVQADVYFPRLIVPFCGHIKGGMRPGKKVLVMGIVDLNPESFAIS
          .AGSVADSDAVVKLDDGHL..........DVYFP.LIV.F.GHIKG.MRPGKKV.VMG.VDLNPESFAI.
Retrocopy VAGSVADSDAVVKLDDGHLTPWVLQFKPTDVYFP*LIVTF*GHIKGSMRPGKKVSVMGMVDLNPESFAIR

Parental  LTCGDSEDPPADVAIELKAVFTD
          LTCGDSE.PPADVAIELKAVFT.
Retrocopy LTCGDSEEPPADVAIELKAVFTE

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	0.05 RPM	66.86 RPM
SRP007412_cerebellum	0.00 RPM	52.50 RPM
SRP007412_heart	0.00 RPM	21.23 RPM
SRP007412_kidney	0.00 RPM	15.67 RPM
SRP007412_liver	0.22 RPM	5.79 RPM
SRP007412_testis	0.05 RPM	2.01 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2942 was not detected

EST

No EST(s) were mapped for retro_mmus_2942 retrocopy.

TSS

No TSS is located nearby retro_mmus_2942 retrocopy 5' end.

Lab

retro_mmus_2942 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2942 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001067	1 retrocopy	retro_amel_429,
Bos taurus	ENSBTAG00000000156	1 retrocopy	retro_btau_1263,
Dasypus novemcinctus	ENSDNOG00000015222	1 retrocopy	retro_dnov_493,
Felis catus	ENSFCAG00000001209	1 retrocopy	retro_fcat_1280,
Monodelphis domestica	ENSMODG00000003226	2 retrocopies	retro_mdom_1350, retro_mdom_233,
Mus musculus	ENSMUSG00000042363	3 retrocopies	retro_mmus_1637, retro_mmus_272, retro_mmus_2942 ,
Mus musculus	ENSMUSG00000057554	1 retrocopy	retro_mmus_1650,
Sarcophilus harrisii	ENSSHAG00000011885	2 retrocopies	retro_shar_315, retro_shar_732,