RetrogeneDB ID: retro_mmus_2223

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:12892449..12893414(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dedd
• Ensembl ID: ENSMUSG00000013973
• Aliases: Dedd, CASP8IP1, DEFT, Dedpro1, FLDED1, KE05
• Description: death effector domain-containing [Source:MGI Symbol;Acc:MGI:1333874]

Sequence

>retro_mmus_2223
ATGGCAGGTCTAAAGAGGCAGTAAAGCCAGGTGTGGCCGGAAGAGTATAGAGAGCAGGAACATGGGCTCTACAGCTTCTA
CCTCATATTTGACATTGTGGGCACCCACCTTACACACAGAGATGTTCGCATACTTTCCTTTCTCCTCGCTGATATTATTG
ATGACCATGAACGTGGACTCATCCGAAATGGACATGATTTCTTATTGGCACTGGAGTGTCAGGGCCACTGCGACAAAAGT
GACTTTTCACCAGGCACTGAAGCTGCTGTGCATCATCGCTTGCCATGACTTGCAGCCCTACATGACTCTCAAGAAGAGAC
GGGCTGAGTGTCCTGATCTTGTTGTAGACAAGTATCTGGAGGAAACATCAACTTGCTATGTGACCCCCCAGAGCCCTCAG
TGATCCAGAACCCAGGCCTTCTCAGCCCTCTAAAATAGAGCCTCCCAACTATCCTGTGGTGTGCTTCTCCACTACATGTT
CTCAAATGTATAGTAAGTAGCCAGCCCAAGGGAAAACAACACTTGAGAGCCAGTGAAGATGCCGGGAGTCAGTGATACCA
GACCCAAAGGAAAAGCAGAGCTGTGACATCACGCTGCAACTTGGAAGGGAACACTGCTAGCATGAGACTGCTCTGCAAGG
CAATATCTTCTCCAATAAGCAGGACACACTTGAGCACCATTTCGAGTGCTTTAACCAGGCCAACACTATCCTCAAGTCCT
GGTACCTGGGCTCCATCATCTGTGACATCAAGTTCTATGAGCTCACCTACTTCTACCTCGACACATTCTGGCGATGCTAC
ATTAATGGCTCATTATTAGGGGCACTGAAAGGTATCTTCATCACAGAGTCTTTCAAGTAAGCTGTGGGCCATGAAGCTAT
CAAGCTTCTGATGAACATGGATGCAGAGGAGTATGAGCTCGGCAGACAGAAACTCCTGAGGAACTTGATGTTGCAAACAT
TACCC

Alignment

ORF - retro_mmus_2223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.54 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGLKRRASQVWPEERGEQEHGLYSLHRMFDIVGTHLTHRDVRVLSFLFVDVIDDHERGLIRNGRDFLLA
          MAGLKR..SQVWPEE..EQEHGLYS....FDIVGTHLTHRDVR.LSFL..D.IDDHERGLIRNG.DFLLA
Retrocopy MAGLKRQ*SQVWPEEYREQEHGLYSFYLIFDIVGTHLTHRDVRILSFLLADIIDDHERGLIRNGHDFLLA

Parental  LERQGRCDESNF-RQVLQLLRIITRHDLLPYVTLKKRRAVCPDLV-DKYLEETSIRYVT-PRALSDPEPR
          LE.QG.CD.S.F..Q.L.LL.II..HDL.PY.TLKKRRA.CPDLV.DKYLEETS..YVT.PRALSDPEPR
Retrocopy LECQGHCDKSDF>HQALKLLCIIACHDLQPYMTLKKRRAECPDLVVDKYLEETSTCYVT>PRALSDPEPR

Parental  PPQPSKTVPPHYPVVCCPTSGSQMCSKRPARGRTTLGSQRKRRKSVTPDPKEKQTCDIRLRVRAEYCQHE
          P.QPSK..PP.YPVVC..T..SQM.SK.PA.G.TTL.SQ...R.SV.PDPKEKQ.CDI.L....E.C.HE
Retrocopy PSQPSKIEPPNYPVVCFSTTCSQMYSK*PAQGKTTLESQ*RCRESVIPDPKEKQSCDITLQLGREHC*HE

Parental  TALQGNVFSNKQDPLERQFERFNQANTILKSRDLGSIICDIKFSELT--YLDAFWRDYINGSLLEALKGV
          TALQGN.FSNKQD.LE..FE.FNQANTILKS..LGSIICDIKF.ELT..YLD.FWR.YINGSLL.ALKG.
Retrocopy TALQGNIFSNKQDTLEHHFECFNQANTILKSWYLGSIICDIKFYELTYFYLDTFWRCYINGSLLGALKGI

Parental  FITDSLKQAVGHEAIKLLVNVDEEDYELGRQKLLRNLMLQALP
          FIT.S.K.AVGHEAIKLL.N.D.E.YELGRQKLLRNLMLQ.LP
Retrocopy FITESFK*AVGHEAIKLLMNMDAEEYELGRQKLLRNLMLQTLP

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	5.56 RPM
SRP007412_cerebellum	0.00 RPM	7.99 RPM
SRP007412_heart	0.00 RPM	5.23 RPM
SRP007412_kidney	0.00 RPM	6.74 RPM
SRP007412_liver	0.00 RPM	4.97 RPM
SRP007412_testis	0.00 RPM	13.81 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2223 was not detected

EST

No EST(s) were mapped for retro_mmus_2223 retrocopy.

TSS

No TSS is located nearby retro_mmus_2223 retrocopy 5' end.

Lab

retro_mmus_2223 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2223 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000013973	1 retrocopy	retro_mmus_2223 ,
Oryctolagus cuniculus	ENSOCUG00000002387	1 retrocopy	retro_ocun_1512,
Rattus norvegicus	ENSRNOG00000003779	1 retrocopy	retro_rnor_546,