RetrogeneDB ID: retro_mmus_1494

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:16198317..16198675(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cdca7
• Ensembl ID: ENSMUSG00000055612
• Aliases: Cdca7, 2310021G01Rik, AU044109, JPO1
• Description: cell division cycle associated 7 [Source:MGI Symbol;Acc:MGI:1914203]

Sequence

>retro_mmus_1494
ATGGAGGCTCGCCGCGCGCGGCAAAAGGCTCTCAAAGTAAAGACCTTAAAGAAATGTCAGATATATGAAGTTGATTTCCA
TGGAGACATCGTCCTCCTCCAATGACAGTTGTGACAGCTTTGCTTCTAATAATTTTGCAAACACAAAACCAAGGCCAGAT
GCCACTAAGGAATTGGCCAGCATTTTTCATGCCGACTCTGATGGGGAATCATTTTGCGGTTTTTCAGAGAGTGAGATACA
AGATGGAATGAGACTGCAGTTCAACAGGGAAGGCTGCAGGACCCGAAGTCAGTGCTGGCACTCCGGGCCTCTCAGGGTAG
CAATGAAGTTTCCGGCACGAAATACCCGGAGGGCGGCC

Alignment

ORF - retro_mmus_1494 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.5 %
• Parental protein coverage: 61.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEARRARQKALKVKNLK-DVRYMKLISMETSSSSDDSCDSFASDNFANTKPRPDATKELASIFHADSDEE
          MEARRARQKALKVK.LK..VRYMKLISMETSSSS.DSCDSFAS.NFANTKPRPDATKELASIFHADSD.E
Retrocopy MEARRARQKALKVKTLK>NVRYMKLISMETSSSSNDSCDSFASNNFANTKPRPDATKELASIFHADSDGE

Parental  LFCGFSESEIQDGMRLQLNREGCRTRSQCRHSGPLRVAMKFPARNTRRAA
          .FCGFSESEIQDGMRLQ.NREGCRTRSQC.HSGPLRVAMKFPARNTRRAA
Retrocopy SFCGFSESEIQDGMRLQFNREGCRTRSQCWHSGPLRVAMKFPARNTRRAA

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	3.29 RPM
SRP007412_cerebellum	0.00 RPM	0.48 RPM
SRP007412_heart	0.00 RPM	1.12 RPM
SRP007412_kidney	0.00 RPM	0.73 RPM
SRP007412_liver	0.00 RPM	1.53 RPM
SRP007412_testis	0.00 RPM	3.34 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1494 was not detected

EST

No EST(s) were mapped for retro_mmus_1494 retrocopy.

TSS

No TSS is located nearby retro_mmus_1494 retrocopy 5' end.

Lab

retro_mmus_1494 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1494 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007809	1 retrocopy	retro_cjac_4087,
Cavia porcellus	ENSCPOG00000011784	2 retrocopies	retro_cpor_661, retro_cpor_691,
Homo sapiens	ENSG00000144354	1 retrocopy	retro_hsap_3438,
Mus musculus	ENSMUSG00000055612	2 retrocopies	retro_mmus_1493, retro_mmus_1494 ,
Nomascus leucogenys	ENSNLEG00000005787	1 retrocopy	retro_nleu_2295,
Pan troglodytes	ENSPTRG00000012645	1 retrocopy	retro_ptro_2331,
Ictidomys tridecemlineatus	ENSSTOG00000009026	1 retrocopy	retro_itri_369,