RetrogeneDB ID: retro_mmus_1117

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:71624609..71624984(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Kxd1
• Ensembl ID: ENSMUSG00000055553
• Aliases: Kxd1, 0610030B01Rik, 2810422J05Rik, C78305
• Description: KxDL motif containing 1 [Source:MGI Symbol;Acc:MGI:1922870]

Sequence

>retro_mmus_1117
ACCGTGTGACTGCAACAGATGGGTGAGTGCTTCATGCACCATACCTGTACCTTGGTGGATGTGAAGCGGGATCTGGACAG
TATTTTCTGAAAGATCAGGACACTGAAGGGGAAGCTGGCCCAGCAGCACCCAGAGACCTTCAGCCACATCCCAGAGGGTT
CATTCCTAGAGGGTGAAGATGAAGATCCTATCTCCCCCAGTACCACCACAACCATTGCCACCTAAGAGCAGAGCATGGGC
GCCTGTGACACCAGCCCTGACACTGTCTCGCCATCCCTAAGTCCTGGCTTGGAGAACCTATCACACATTCAACCTGGCTC
TCCTTCCATCAACGGCCCCAGCCAGTCAGGTGATAAGGAAGAGACACATGAAGAA

Alignment

ORF - retro_mmus_1117 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.8 %
• Parental protein coverage: 57.08 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SVRLQQMSERFMHHTRTLVDMKRDLDSIFRRIRTLKGKLARQHPEAFSHIPEGSFLEDEDEDPIPPSITT
          .V.LQQM.E.FMHHT.TLVD.KRDLDSIF..IRTLKGKLA.QHPE.FSHIPEGSFLE.EDEDPI.PS.TT
Retrocopy TV*LQQMGECFMHHTCTLVDVKRDLDSIF*KIRTLKGKLAQQHPETFSHIPEGSFLEGEDEDPISPSTTT

Parental  TIATSEQSTGSCDTSPDTVSPSLSPGFEDLSHIQPGSPAINGHRQTDDEEETHEE
          TIAT.EQS.G.CDTSPDTVSPSLSPG.E.LSHIQPGSP.ING..Q..D.EETHEE
Retrocopy TIAT*EQSMGACDTSPDTVSPSLSPGLENLSHIQPGSPSINGPSQSGDKEETHEE

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	18.08 RPM
SRP007412_cerebellum	0.00 RPM	16.80 RPM
SRP007412_heart	0.00 RPM	47.38 RPM
SRP007412_kidney	0.00 RPM	40.44 RPM
SRP007412_liver	0.00 RPM	28.18 RPM
SRP007412_testis	0.00 RPM	25.11 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1117 was not detected

EST

No EST(s) were mapped for retro_mmus_1117 retrocopy.

TSS

No TSS is located nearby retro_mmus_1117 retrocopy 5' end.

Lab

retro_mmus_1117 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1117 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010545	1 retrocopy	retro_btau_689,
Echinops telfairi	ENSETEG00000003390	2 retrocopies	retro_etel_1213, retro_etel_2129,
Macropus eugenii	ENSMEUG00000013150	1 retrocopy	retro_meug_2148,
Monodelphis domestica	ENSMODG00000003489	1 retrocopy	retro_mdom_1623,
Mus musculus	ENSMUSG00000055553	6 retrocopies	retro_mmus_1117 , retro_mmus_3557, retro_mmus_799, retro_mmus_800, retro_mmus_802, retro_mmus_804,
Rattus norvegicus	ENSRNOG00000019971	2 retrocopies	retro_rnor_2808, retro_rnor_812,