RetrogeneDB ID: retro_mmus_441

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:51317530..51318249(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Thoc3
• Ensembl ID: ENSMUSG00000025872
• Aliases: Thoc3, 2410044K02Rik, AL033344
• Description: THO complex 3 [Source:MGI Symbol;Acc:MGI:1920916]

Sequence

>retro_mmus_441
AACCTTTTTGTCACCGCATCTGGAGATAAAACCAATTGCATCTGGGATGTGAGGACTATAAAATGCATTGCACTGTGAAC
ATGAAAGAGGAGAACATTAACATCTGCTGGAGTCCTGATGGGCAGACCATCGCAGTGGGCAACAAGGACAACATTGTGAC
CTTCATTGATGCCACGACGCACGGCTCCAAAGCGGAGGAGCAATTCAAGTTTCAGGTCAATGAGATCTCATGGGACAACG
ATAACACGTTCTTCTTGACCGATGGCAATGGCTGTATTAACATCCTCAGCTACCCAGAACTGAAGCCTGTGAAGTCCATC
AATGCTCATCCTTCTAACTGCATCTGTATCAAGTTTTAGCCCATGGGGAAATATTTTGCCACAGGAAGCACAGATGCCTT
GGTCAGTCTCTGGGACATTGATGAGTTATTGTCCGTGCGGTGCTTTTCCAGACTAGATTGGCCTGTGAGGACCCTTAGTT
TTAGCTTTAGCCACGGTGGGAAAATGCTGGCGTCGTCTTCGGAGGATCAGTTCATTGATATAACTGAAGTAGAGACAGGA
AACAAGCTATGGGAGGTGCAGTGTGAGTCCCCTACTTTCACTGTGGCTGGGCACCCCAAGAGGTCTCTGCTGGCTTTTGC
CTGTGATGACAAAGCTGGCAAATATGACAGCAGTCGGGAGGCTGGAACTGTGAAGCTGTTTGGGCTTCCCAATGACTCC

Alignment

ORF - retro_mmus_441 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.78 %
• Parental protein coverage: 68.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DLFVTASGDKTIRIWDVRTTKCIA-TVNTKGENINICWSPDGQTIAVGNKDDVVTFIDAKTHRSKAEEQF
          .LFVTASGDKT..IWDVRT.KCIA.TVN.K.ENINICWSPDGQTIAVGNKD..VTFIDA.TH.SKAEEQF
Retrocopy NLFVTASGDKTNCIWDVRTIKCIA<TVNMKEENINICWSPDGQTIAVGNKDNIVTFIDATTHGSKAEEQF

Parental  KFEVNEISWNNDNNMFFLTNGNGCINILSYPELKPVQSINAHPSNCICIKFDPMGKYFATGSADALVSLW
          KF.VNEISW.NDN..FFLT.GNGCINILSYPELKPV.SINAHPSNCICIKF.PMGKYFATGS.DALVSLW
Retrocopy KFQVNEISWDNDNT-FFLTDGNGCINILSYPELKPVKSINAHPSNCICIKF*PMGKYFATGSTDALVSLW

Parental  DVDELVCVRCFSRLDWPVRTLSFS--HDGKMLASASEDHFIDIAEVETGDKLWEVQCESPTFTVAWHPKR
          D.DEL..VRCFSRLDWPVRTLSFS..H.GKMLAS.SED.FIDI.EVETG.KLWEVQCESPTFTVA.HPKR
Retrocopy DIDELLSVRCFSRLDWPVRTLSFSFSHGGKMLASSSEDQFIDITEVETGNKLWEVQCESPTFTVAGHPKR

Parental  PLLAFACDDKDGKYDSSREAGTVKLFGLPNDS
          .LLAFACDDK.GKYDSSREAGTVKLFGLPNDS
Retrocopy SLLAFACDDKAGKYDSSREAGTVKLFGLPNDS

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	0.05 RPM	21.24 RPM
SRP007412_cerebellum	0.09 RPM	21.45 RPM
SRP007412_heart	0.03 RPM	13.70 RPM
SRP007412_kidney	0.00 RPM	18.50 RPM
SRP007412_liver	0.00 RPM	18.46 RPM
SRP007412_testis	0.00 RPM	21.27 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_441 was not detected

EST

No EST(s) were mapped for retro_mmus_441 retrocopy.

TSS

No TSS is located nearby retro_mmus_441 retrocopy 5' end.

Lab

retro_mmus_441 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_441 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006495	2 retrocopies	retro_cjac_1571, retro_cjac_3072,
Macropus eugenii	ENSMEUG00000001068	2 retrocopies	retro_meug_1061, retro_meug_19,
Monodelphis domestica	ENSMODG00000005339	1 retrocopy	retro_mdom_164,
Mus musculus	ENSMUSG00000025872	2 retrocopies	retro_mmus_1821, retro_mmus_441 ,
Otolemur garnettii	ENSOGAG00000003503	1 retrocopy	retro_ogar_3005,
Sarcophilus harrisii	ENSSHAG00000010757	1 retrocopy	retro_shar_4,