RetrogeneDB ID: retro_mmus_3672

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:98513902..98514306(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081397
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Dctd
• Ensembl ID: ENSMUSG00000031562
• Aliases: Dctd, 6030466N05Rik
• Description: dCMP deaminase [Source:MGI Symbol;Acc:MGI:2444529]

Sequence

>retro_mmus_3672
AATACAGAAAACAACATTCTTGGGATTCGATACGATGGAATGTGAAAGGGGTTCAGTGACAACTTATTGTCTTGGAGAAC
AGCAGAAAATAGCTGACTACTAAATATCTTTATGTGTGCCATGCCAAGCTGAACACCATTGGGAACAAGAATTCAGCTGA
TATGAAGGGCTGCAATATGATCACTGCTTTGATCTCACGTAATGAACATGCTGAGTTCATCATCCAGGAAGGTATACAAG
AAGTTATTTTCATGTCAGATAAATACCATGACAGTGAACAGACAATGGGCATTAGGCTCGTGATTAAATTGCCTGGGGTT
ACATTCAGAAAATTCACACTGAAATGGAGCAAGATCGTCATTGACTTTGATTTAATTAATAGCCGACTGAGTCAGAAGCC
CCAG

Alignment

ORF - retro_mmus_3672 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.8 %
• Parental protein coverage: 73.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NTENKIVGIGYNGMPNGCSDDLLPWRRTAENK-LDTKYPYVCHAELNAIMNKNSADVKGCSMYVALFPCN
          NTEN.I.GI.Y.GM..G.SD.LL.WR.TAEN..L.TKY.YVCHA.LN.I.NKNSAD.KGC.M..AL...N
Retrocopy NTENNILGIRYDGM*KGFSDNLLSWR-TAENS<LTTKYLYVCHAKLNTIGNKNSADMKGCNMITALISRN

Parental  ECAKLIIQAGIKEVIFMSDKYHDSEETTAARLLFKLAGVTFRKFTPKYSKIVIDFDSINSRPSQKPQ
          E.A..IIQ.GI.EVIFMSDKYHDSE.T...RL..KL.GVTFRKFT.K.SKIVIDFD.INSR.SQKPQ
Retrocopy EHAEFIIQEGIQEVIFMSDKYHDSEQTMGIRLVIKLPGVTFRKFTLKWSKIVIDFDLINSRLSQKPQ

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	7.15 RPM
SRP007412_cerebellum	0.00 RPM	4.08 RPM
SRP007412_heart	0.00 RPM	1.46 RPM
SRP007412_kidney	0.00 RPM	1.23 RPM
SRP007412_liver	0.00 RPM	0.08 RPM
SRP007412_testis	0.00 RPM	1.51 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3672 was not detected

EST

No EST(s) were mapped for retro_mmus_3672 retrocopy.

TSS

No TSS is located nearby retro_mmus_3672 retrocopy 5' end.

Lab

retro_mmus_3672 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3672 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000017516	3 retrocopies	retro_ecab_829, retro_ecab_830, retro_ecab_915,
Mus musculus	ENSMUSG00000031562	1 retrocopy	retro_mmus_3672 ,
Rattus norvegicus	ENSRNOG00000013215	1 retrocopy	retro_rnor_2937,
Sarcophilus harrisii	ENSSHAG00000015218	1 retrocopy	retro_shar_124,
Tursiops truncatus	ENSTTRG00000001460	1 retrocopy	retro_ttru_613,