RetrogeneDB ID: retro_mmus_380

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:159378401..159378909(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ccdc115
• Ensembl ID: ENSMUSG00000042111
• Aliases: Ccdc115, 2310061I09Rik, Ccp1
• Description: coiled-coil domain containing 115 [Source:MGI Symbol;Acc:MGI:1916918]

Sequence

>retro_mmus_380
TGCTTACAGCTGCTCGGTGACCTGGAGGAACTGGAGGTGAAACGGGCGGCACTGAACGCCTGGGTGGAGGAGGGTTGGCT
CTCACTTGCCAAGGCTCACTATGCCATGGGAGCTAAGTCAGTAGGGCCCCTGCAGTATGCTTCCCCTATGGAACCTCAGG
TCTGCGTGCATACAGGCGAGGCCCAGGATGGACCCCAGACATTCAGAGTGATCAAAGCTGACACCCAGGCCCCCAAGCAA
TTGGGGACCTAGCGAAGCATCTCTGCTCTGTGCAGGCACAAGGGCCCTACCGAGACCAGAGTCAGGATCCTCTATAGTTC
ATCAAGATCCCTTGAACTGGTTTGGAATCCTGGTTCCTCACAGTCTGCTGCAGGCCCAAGCCAGCTTCTGGGATGGCCTA
CAGCTGACTGCAGATATAGCCAGCCTCGAGACTCACATCAAATGGGGTCGAAGTCAGCTCTGAGGTGTCCAGAAAAAAAA
ACTGAAGGAGTTGGACCCTGAGCCTTCC

Alignment

ORF - retro_mmus_380 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.84 %
• Parental protein coverage: 92.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CLQLLSDLEELEAKRAALNARVEEGWLSLAKARYAMGAKSVGPLQYASRMEPQVCVRASEAQDGPQTFRV
          CLQLL.DLEELE.KRAALNA.VEEGWLSLAKA.YAMGAKSVGPLQYAS.MEPQVCV...EAQDGPQTFRV
Retrocopy CLQLLGDLEELEVKRAALNAWVEEGWLSLAKAHYAMGAKSVGPLQYASPMEPQVCVHTGEAQDGPQTFRV

Parental  IKADAQTPEEVGP--SEASLRRRK-GPTKTK-ELGSAVVPQDPLNWFGILVPHSLRQAQASFRDGLQLAA
          IKAD.Q.P...G...S...L.R.K.GP.....E.GS..V.QDPLNWFGILVPHSL.QAQASF.DGLQL.A
Retrocopy IKADTQAPKQLGT*RSISALCRHK<GPYRDQ<ESGSSIVHQDPLNWFGILVPHSLLQAQASFWDGLQLTA

Parental  DIASLQTRINWGQSQLRGLQ-KKLKELDPGPA
          DIASL.T.I.WG.SQL.G.Q...LKELDP.P.
Retrocopy DIASLETHIKWGRSQL*GVQXXXLKELDPEPS

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	0.02 RPM	9.91 RPM
SRP007412_cerebellum	0.00 RPM	9.99 RPM
SRP007412_heart	0.00 RPM	11.77 RPM
SRP007412_kidney	0.00 RPM	10.72 RPM
SRP007412_liver	0.00 RPM	7.02 RPM
SRP007412_testis	0.00 RPM	10.47 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_380 was not detected

EST

No EST(s) were mapped for retro_mmus_380 retrocopy.

TSS

No TSS is located nearby retro_mmus_380 retrocopy 5' end.

Lab

retro_mmus_380 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_380 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000010588	2 retrocopies	retro_mdom_200, retro_mdom_435,
Mus musculus	ENSMUSG00000042111	2 retrocopies	retro_mmus_2696, retro_mmus_380 ,
Oryctolagus cuniculus	ENSOCUG00000005099	1 retrocopy	retro_ocun_1651,
Otolemur garnettii	ENSOGAG00000000166	2 retrocopies	retro_ogar_2849, retro_ogar_3466,
Tursiops truncatus	ENSTTRG00000012598	1 retrocopy	retro_ttru_781,