RetrogeneDB ID: retro_mmus_645

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:53299141..53300136(-)
• Located in intron of: ENSMUSG00000038594

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_645
GGGTCCCCGGTAAAGCGCCAGAGGATGGAGTCCGCCTTGGACCAGCTCAAGCAGTTCACCACCGATGTGGCCGACAAGGG
TGATTTTAATGCCATCGATGAATACAAGCCCCAAGATGCCACCACCAACCCATCCCTGATCCTGCTGCAGCCCAGATGCC
TGCCTACCTAGAGCTGGTAGAGGAGGCCGTTGCCTACGGCAAGAAGCTGGGTGGGCCTCAAGAGGAGCAGATTAAAAATG
CCATTGACAAACTTTTTGCGCTGTTTGGAGCAGAAATATTAAAGAAGATTCCAGGCCGTGTATCCACAGAAGTTGATGCA
AGGCTTTCCTTTGATAAGGATGCCATGGTTTCCCGAGCCAGGCGCCTCATTAAGCTTTACAAAGAAGCGGGGATCGGCAA
GGACAGAATTCTCATCAAGTTATCATCAACCTGGGAGGGGATTCAGGCTGGAAAGGAGCTGGAGGAGCAGCATGGCATCC
ACTGCAACATGACACTGCTTTTCTCCTTCGCCCAGGCTGTGGCCTGTGCTGAAGTGGGCATGACGCTCATCTCTCCCTTT
GTGGGGCGCATCCTTGATGTGGCAAACACAGACAAGAAATCCTATGAACCCCAGGAGGACCCTGGGGTCAAGAGTGTCAC
CAAAATTTACTACTACAAGAAGTTTGGCTATAAGACCATTGTCATGGGCGCCTCCTTCTGCAACACCGGTGAGATTAAAC
CACTGGCGGGCTGTGACTTCCTCACCATCTCCCCGAAGCTCCTGAGGGAGCTGCTCAAGGAGAACAGCAAGCTGGCGCCT
GCGCTCTCCGTCAAGGTGGCCCAGACCAGTGACTCGGAGAAGATACATTTGGACGAGAAGGCCTTCCGTTGGCTGTACAA
CGAGGACCAAATGGCTGTGGAGAAGCTCTTCGATGGCATCCGCAAATTTGCTGCTGATGCCGTAAGGTTGGAGCAGATGT
TCACGGAACGAATGTTCAGCGCTGAGAGTTGGAAG

Alignment

ORF - retro_mmus_645 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.96 %
• Parental protein coverage: 99.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GSPVKRQRMESALDQLKQFTTVVADTGDFNAIDEYKPQDATTNPSLIL-AAAQMPAYQELVEEAIAYGKK
          GSPVKRQRMESALDQLKQFTT.VAD.GDFNAIDEYKPQDATTNPSLIL.AAAQMPAY.ELVEEA.AYGKK
Retrocopy GSPVKRQRMESALDQLKQFTTDVADKGDFNAIDEYKPQDATTNPSLIL<AAAQMPAYLELVEEAVAYGKK

Parental  LGGPQEEQIKNAIDKLFVLFGAEILKKIPGRVSTEVDARLSFDKDAMVARARRLIELYKEAGVGKDRILI
          LGGPQEEQIKNAIDKLF.LFGAEILKKIPGRVSTEVDARLSFDKDAMV.RARRLI.LYKEAG.GKDRILI
Retrocopy LGGPQEEQIKNAIDKLFALFGAEILKKIPGRVSTEVDARLSFDKDAMVSRARRLIKLYKEAGIGKDRILI

Parental  KLSSTWEGIQAGKELEEQHGIHCNMTLLFSFAQAVACAEAGVTLISPFVGRILDWHVANTDKKSYEPQED
          KLSSTWEGIQAGKELEEQHGIHCNMTLLFSFAQAVACAE.G.TLISPFVGRILD..VANTDKKSYEPQED
Retrocopy KLSSTWEGIQAGKELEEQHGIHCNMTLLFSFAQAVACAEVGMTLISPFVGRILD--VANTDKKSYEPQED

Parental  PGVKSVTKIYNYYKKFGYKTIVMGASFRNTGEIKALAGCDFLTISPKLLGELLKDNSKLAPALSVKAAQT
          PGVKSVTKIY.YYKKFGYKTIVMGASF.NTGEIK.LAGCDFLTISPKLL.ELLK.NSKLAPALSVK.AQT
Retrocopy PGVKSVTKIY-YYKKFGYKTIVMGASFCNTGEIKPLAGCDFLTISPKLLRELLKENSKLAPALSVKVAQT

Parental  SDSEKIHLDEKAFRWLHNEDQMAVEKLSDGIRKFAADAIKLERMLTERMFSAENGK
          SDSEKIHLDEKAFRWL.NEDQMAVEKL.DGIRKFAADA..LE.M.TERMFSAE..K
Retrocopy SDSEKIHLDEKAFRWLYNEDQMAVEKLFDGIRKFAADAVRLEQMFTERMFSAESWK

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	0.19 RPM	48.59 RPM
SRP007412_cerebellum	0.17 RPM	53.93 RPM
SRP007412_heart	0.44 RPM	62.60 RPM
SRP007412_kidney	0.42 RPM	99.19 RPM
SRP007412_liver	0.71 RPM	85.53 RPM
SRP007412_testis	0.14 RPM	12.58 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_645 was not detected

EST

No EST(s) were mapped for retro_mmus_645 retrocopy.

TSS

No TSS is located nearby retro_mmus_645 retrocopy 5' end.

Lab

retro_mmus_645 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_645 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,