RetrogeneDB ID: retro_mmus_2204

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:135122074..135122446(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dcun1d2
• Ensembl ID: ENSMUSG00000038506
• Aliases: Dcun1d2, AW495713, mFLJ10704
• Description: DCN1, defective in cullin neddylation 1, domain containing 2 (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:2142792]

Sequence

>retro_mmus_2204
CCACAGAACAAAAACAAAATCGGAATTGATGGGATTCAGTAGTTCTGTGATGACCTGAGTCTGGTCCCTGCCAGTATCAG
TGTTTTGGTCATAGCATAGAAGTTCAGGACTGACACTCAATGTGAATTTAGCAAAAAGGAATTCGTGGATGGCATGACAG
AGCTGGGGTGTGATAGCACAGAGAGGCTGAAAACTCTTCCACCCAAACTGGAACAGGAACTTAAGGACTCAGCGAAGTTC
AAGGACTTTTACCAGTTTACTAATTTCGCTAAGAACCCTGGGCAGAAGGGCTTAGGATCGCGGCTTGTCCTTATAAATGA
CTTTGTAGAATATGCACGACCAGTAGTCACAGGTGGGAGATGTGGACCTTTC

Alignment

ORF - retro_mmus_2204 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84. %
• Parental protein coverage: 62.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PQDENKIGIDGIQQFCDDLSLDPASISVLVIAWKFRAATQCEFSKKEFVDGMTELGCDSTERLKALLPRL
          PQ..NKIGIDGIQ.FCDDLSL.PASISVLVIA.KFR..TQCEFSKKEFVDGMTELGCDSTERLK.L.P.L
Retrocopy PQNKNKIGIDGIQ*FCDDLSLVPASISVLVIA*KFRTDTQCEFSKKEFVDGMTELGCDSTERLKTLPPKL

Parental  EQELKDPAKFKDLYQFTFTFAKNPGQKGLGAWPVLIDDFVEYARPVVTGGRRSPF
          EQELKD.AKFKD.YQFT..FAKNPGQKGLG...VLI.DFVEYARPVVTGGR..PF
Retrocopy EQELKDSAKFKDFYQFT-NFAKNPGQKGLGSRLVLINDFVEYARPVVTGGRCGPF

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	41.84 RPM
SRP007412_cerebellum	0.00 RPM	49.72 RPM
SRP007412_heart	0.00 RPM	67.80 RPM
SRP007412_kidney	0.00 RPM	35.61 RPM
SRP007412_liver	0.00 RPM	17.20 RPM
SRP007412_testis	0.00 RPM	6.86 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2204 was not detected

EST

No EST(s) were mapped for retro_mmus_2204 retrocopy.

TSS

No TSS is located nearby retro_mmus_2204 retrocopy 5' end.

Lab

retro_mmus_2204 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2204 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007821	4 retrocopies	retro_chof_1022, retro_chof_1937, retro_chof_461, retro_chof_771,
Mus musculus	ENSMUSG00000027708	1 retrocopy	retro_mmus_1009,
Mus musculus	ENSMUSG00000038506	1 retrocopy	retro_mmus_2204 ,
Pongo abelii	ENSPPYG00000005527	1 retrocopy	retro_pabe_2894,