RetrogeneDB ID: retro_mmus_584

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:87966846..87967433(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tyms
• Ensembl ID: ENSMUSG00000025747
• Aliases: Tyms, Ts
• Description: thymidylate synthase [Source:MGI Symbol;Acc:MGI:98878]

Sequence

>retro_mmus_584
ATGCTGGTGGTTGGCTCCAAGCTGCATCGGACGCTGGGCGCGGAAGCCCCGGGGCATGGAGAACTCCAGTACCTGAGGCA
GGTGGAGCACATTTTGTGCTGCGGCTTCAAGAAGGAGGACCGCATGGGCACTGGCACCCTGTAGGTGTTCGGCATGCAGG
CACGATCCAGCCTGAGAGATGAATTTCCTCTGCTCACAACCAAAGAGTGTTCTGGAAGGGTGTTTTGGAGGAGTTGTTGT
GGTTTATCAAGGGATCCACAAATGCTAAAGAATTGTCCTCCAAGGGAGTGAGAATCTGGGATGCTAATAGATCCCGAGAC
TTTCTGGACAGCTTGGGATTTTCTGCCCGACAGGAAGGGGACCTGGGCCCAGTTTATGGTTTCCAATGGAGGCATTTTGG
AGCAGAGTACAAAGACATGGATTCAGATTACTCAGGACAAGGAGTAGACCAGCTGCAAAAAGTGATTGACACCATCAAAA
CCAACCCTGATGACAGAAGAATCATGTGTGCCTGGAACCCAAAAGATCTTCCCCTGATGGCACTGCCTGCCTCCTTGCCA
TGCCCTCTGTCAGTTCTATATGGTGAA

Alignment

ORF - retro_mmus_584 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.13 %
• Parental protein coverage: 65.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLVVGSELQSDAQQLSAEAPRHGELQYLRQVEHILRCGFKKEDRTGTGTLSVFGMQARYSLRDEFPLLTT
          MLVVGS.L......L.AEAP.HGELQYLRQVEHIL.CGFKKEDR.GTGTL.VFGMQAR.SLRDEFPLLTT
Retrocopy MLVVGSKLH---RTLGAEAPGHGELQYLRQVEHILCCGFKKEDRMGTGTL*VFGMQARSSLRDEFPLLTT

Parental  K-RVFWKGVLEELLWFIKGSTNAKELSSKGVRIWDANGSRDFLDSLGFSARQEGDLGPVYGFQWRHFGAE
          K.RVFWKGVLEELLWFIKGSTNAKELSSKGVRIWDAN.SRDFLDSLGFSARQEGDLGPVYGFQWRHFGAE
Retrocopy K<RVFWKGVLEELLWFIKGSTNAKELSSKGVRIWDANRSRDFLDSLGFSARQEGDLGPVYGFQWRHFGAE

Parental  YKDMDSDYSGQGVDQLQKVIDTIKTNPDDRRIIMCAWNPKDLPLMALPPCHALCQFYVVNGE
          YKDMDSDYSGQGVDQLQKVIDTIKTNPDDRRI.MCAWNPKDLPLMAL.P....C...V..GE
Retrocopy YKDMDSDYSGQGVDQLQKVIDTIKTNPDDRRI-MCAWNPKDLPLMAL-PASLPCPLSVLYGE

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	1.75 RPM
SRP007412_cerebellum	0.00 RPM	2.34 RPM
SRP007412_heart	0.00 RPM	1.59 RPM
SRP007412_kidney	0.08 RPM	7.57 RPM
SRP007412_liver	0.03 RPM	4.70 RPM
SRP007412_testis	0.00 RPM	1.69 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_584 was not detected

EST

No EST(s) were mapped for retro_mmus_584 retrocopy.

TSS

No TSS is located nearby retro_mmus_584 retrocopy 5' end.

Lab

retro_mmus_584 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_584 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000009230	2 retrocopies	retro_fcat_1107, retro_fcat_339,
Loxodonta africana	ENSLAFG00000014910	2 retrocopies	retro_lafr_1030, retro_lafr_635,
Macropus eugenii	ENSMEUG00000009507	1 retrocopy	retro_meug_175,
Monodelphis domestica	ENSMODG00000021479	2 retrocopies	retro_mdom_1084, retro_mdom_1186,
Mustela putorius furo	ENSMPUG00000005419	2 retrocopies	retro_mputfur_1155, retro_mputfur_860,
Mus musculus	ENSMUSG00000025747	1 retrocopy	retro_mmus_584 ,
Otolemur garnettii	ENSOGAG00000024349	2 retrocopies	retro_ogar_2956, retro_ogar_3211,
Sarcophilus harrisii	ENSSHAG00000003102	1 retrocopy	retro_shar_424,
Sus scrofa	ENSSSCG00000023869	2 retrocopies	retro_sscr_810, retro_sscr_841,