RetrogeneDB ID: retro_mmus_1275

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:50978446..50978896(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ccdc12
• Ensembl ID: ENSMUSG00000019659
• Aliases: Ccdc12, 2700094L05Rik, C76605
• Description: coiled-coil domain containing 12 [Source:MGI Symbol;Acc:MGI:1919904]

Sequence

>retro_mmus_1275
AGGCGGAAAGAACGGCTGAAGGCCCTCCGGGAGAAAACCGGGCGCAAGGACAGGGAAGATGGGGAGCCACAGACCAAGCA
GCTCAGAGAAGAGGGAGAGGAAGTTGGGAAGCACAGGGGACTCAGGCTCAGGAACTATGTCCCAGAGGATGAAGACCTGA
AGAGGAGGCGGGTCCCCCAGGCCAAACCAGTGGCAGTGGAGGAGAAGGTGAAGGAGCAGCTGGAGGCAGCCAAGCCAGAG
CCTGTCATTGAGGAAGTGGACCTGGCCAACTTGGCACCCCGGAAACCTGATTGGGATCTCAAGAGAGATGTGGCCAAGAA
GCTAGAGAAGCTAGAAAAGCGGACCCAGAGAACCATTGCAGAGCTGATCTGTGAGCGGCTAAAAGGCCAAGAGGACAGCC
TGGCCTCTGCAGTGGACGCCACCACCGGACAAGAGGCTTGTAACTCTGAC

Alignment

ORF - retro_mmus_1275 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92. %
• Parental protein coverage: 90.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRKERLKALREKTGRKDREDGEPQTKQLREEGEEVGKHRGLRLRNYVPEDEDLKRRRVPQAKPVAVEEKV
          RRKERLKALREKTGRKDREDGEPQTKQLREEGEEVGKHRGLRLRNYVPEDEDLKRRRVPQAKPVAVEEKV
Retrocopy RRKERLKALREKTGRKDREDGEPQTKQLREEGEEVGKHRGLRLRNYVPEDEDLKRRRVPQAKPVAVEEKV

Parental  KEQLEAAKPEPVIEEVDLANLAPRKPDWDLKRDVAKKLEKLEKRTQRAIAELIRERLKGQEDSLASAVDA
          KEQLEAAKPEPVIEEVDLANLAPRKPDWDLKRDVA.........TQR.IAELI.ERLKGQEDSLASAVDA
Retrocopy KEQLEAAKPEPVIEEVDLANLAPRKPDWDLKRDVAXXXXXXXXXTQRTIAELICERLKGQEDSLASAVDA

Parental  TTGQEACDSD
          TTGQEAC.SD
Retrocopy TTGQEACNSD

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	8.85 RPM
SRP007412_cerebellum	0.09 RPM	9.42 RPM
SRP007412_heart	0.19 RPM	17.81 RPM
SRP007412_kidney	0.12 RPM	13.44 RPM
SRP007412_liver	0.03 RPM	6.39 RPM
SRP007412_testis	0.09 RPM	14.77 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1275 was not detected

EST

No EST(s) were mapped for retro_mmus_1275 retrocopy.

TSS

No TSS is located nearby retro_mmus_1275 retrocopy 5' end.

Lab

retro_mmus_1275 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1275 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002280	3 retrocopies	retro_cjac_1212, retro_cjac_2317, retro_cjac_3225,
Dipodomys ordii	ENSDORG00000016567	1 retrocopy	retro_dord_303,
Echinops telfairi	ENSETEG00000000030	2 retrocopies	retro_etel_1445, retro_etel_2038,
Homo sapiens	ENSG00000160799	1 retrocopy	retro_hsap_2257,
Macaca mulatta	ENSMMUG00000019810	1 retrocopy	retro_mmul_1025,
Mus musculus	ENSMUSG00000019659	1 retrocopy	retro_mmus_1275 ,
Nomascus leucogenys	ENSNLEG00000006219	1 retrocopy	retro_nleu_1282,
Ochotona princeps	ENSOPRG00000005086	1 retrocopy	retro_opri_746,
Pongo abelii	ENSPPYG00000013924	2 retrocopies	retro_pabe_1957, retro_pabe_2033,
Pan troglodytes	ENSPTRG00000014862	1 retrocopy	retro_ptro_1597,
Sarcophilus harrisii	ENSSHAG00000003265	1 retrocopy	retro_shar_251,