RetrogeneDB ID: retro_mmus_667

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:96768853..96769404(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Taldo1
• Ensembl ID: ENSMUSG00000025503
• Aliases: None
• Description: transaldolase 1 [Source:MGI Symbol;Acc:MGI:1274789]

Sequence

>retro_mmus_667
CAGGAGTGGATTAAAAATGTTATTGATAAACTTTTTGTGTTGTTTAAAGCAGAAATACTAAAGAAGGTTCCAGGCTGTGT
GGCCACAGAAGTAGATACAAGGCTTTCATTTGATAAGGATGTAATGGTGACCCAAGACAGATGCCTCATTGAGCTTTACC
AAAAAGCTGGATATAGTAATGGTAGAATTCTCATCAAGTTATCCTCAACCTGGTAAGGAATTCAGGCTGGAACGGAGCCA
GAGGAACAGCATGGCATCTATTGCAACATGACACTGCTTCAATCCTTTGCCCAGGCCACTGACTTGGGATGAAGTGGGCG
TGGCTCACACCTCTCCTTTTGTGGGGTGCATCGTTGATTGCCAAGTGGCAAAGACAGACAAAAAATTCCAAGAGCCCCAG
GAGGACCTTGGCATAAAGAATATCACCAAAATGTATAACTACTACAAGAAATTTGGCTATAAGACCATTGTCATGGGCGC
CTCCCTCAGGGTCACAGGTGAGAGCATTGCATGGGCAGGGGACAAGTTCCTCCACAGTCTCACCCAAGCTG

Alignment

ORF - retro_mmus_667 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.81 %
• Parental protein coverage: 54.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EEQIKNAIDKLFVLFGAEILKKIPGRVSTEVDARLSFDKDAMVARARRLIELYKEAGVGKDRILIKLSST
          .E.IKN.IDKLFVLF.AEILKK.PG.V.TEVD.RLSFDKD.MV...R.LIELY..AG....RILIKLSST
Retrocopy QEWIKNVIDKLFVLFKAEILKKVPGCVATEVDTRLSFDKDVMVTQDRCLIELYQKAGYSNGRILIKLSST

Parental  WEGIQAGKELEEQHGIHCNMTLLFSFAQA-VACAEAGVTLISPFVGRILDWHVANTDKKSYEPQEDPGVK
          W.GIQAG.E.EEQHGI.CNMTLL.SFAQA.....E.GV...SPFVG.I.D..VA.TDKK..EPQED.G.K
Retrocopy W*GIQAGTEPEEQHGIYCNMTLLQSFAQA>LTWDEVGVAHTSPFVGCIVDCQVAKTDKKFQEPQEDLGIK

Parental  SVTKIYNYYKKFGYKTIVMGASFRNTGEIKALAGCDFL-TISPKL
          ..TK.YNYYKKFGYKTIVMGAS.R.TGE..A.AG..FL.T.SPKL
Retrocopy NITKMYNYYKKFGYKTIVMGASLRVTGESIAWAGDKFL>TVSPKL

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	48.59 RPM
SRP007412_cerebellum	0.00 RPM	53.93 RPM
SRP007412_heart	0.00 RPM	62.60 RPM
SRP007412_kidney	0.00 RPM	99.19 RPM
SRP007412_liver	0.00 RPM	85.53 RPM
SRP007412_testis	0.00 RPM	12.58 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_667 was not detected

EST

No EST(s) were mapped for retro_mmus_667 retrocopy.

TSS

No TSS is located nearby retro_mmus_667 retrocopy 5' end.

Lab

retro_mmus_667 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_667 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010336	1 retrocopy	retro_btau_455,
Macropus eugenii	ENSMEUG00000000841	1 retrocopy	retro_meug_756,
Mus musculus	ENSMUSG00000025503	2 retrocopies	retro_mmus_645, retro_mmus_667 ,
Rattus norvegicus	ENSRNOG00000018367	1 retrocopy	retro_rnor_2661,
Xenopus tropicalis	ENSXETG00000001671	1 retrocopy	retro_xtro_16,