RetrogeneDB ID: retro_mmus_1821

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:27961273..27961792(+)
• Located in intron of: ENSMUSG00000040929

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_1821
ATAGCCTGGAGCTAGGGTGGGTTTCACTCAGCTTGGAATTCTTTGACATGACTGCAAGGGTCTTCTTGCTGGAGGAGGGC
ACTCTGAACAAAGAAAAAGGCTACAGGGGATGTGGAGATAGTGTGATTTGATTTTCTTGGTATCCAAGTAACCCTGATCC
CTTCGTCTCTGTGTGTGGAGATAAAGACATTTCTGTGGGGATATGAAGACCACAAACACACTGACACTAAACTTTAAGCA
GAACATTAATATCTGCGGGAGTCCCATTGGGGAGATAATAGCTATGGGCATCAAGGATAATGTTGCAACCTTTACTGATG
CCAAGACCCACCATTCCAAAGCACAGACACTGTTTGAGTTTGAGGTCAACGATATTTCCTAGAACAATGATGACATGTTC
CCCCTGACAAGCAGCTATAGTTTATCAACAGTCTCAGCTACACAGTACTTATTGTACAATATATACAGGCCCATCCTTCT
AATCTCATCGGAATCAATCTTAACCCCATTGTGAAATTT

Alignment

ORF - retro_mmus_1821 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.7 %
• Parental protein coverage: 50.71 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VAWSCDGRRLASGS-FDKTASVFLLEKDRLVKENNYRGHGDSVDQLCWHPSNPDLFVTASGDKTIRIW-D
          .AWS..G...A..S.FD.TA.VFLLE...L.KE..YRG.GDSV....W.PSNPD.FV...GDK.I....D
Retrocopy IAWS*GGFHSAWNS<FDMTARVFLLEEGTLNKEKGYRGCGDSVI*FSWYPSNPDPFVSVCGDKDISVG<D

Parental  VRTTKCIATVNTKGENINICWSPDGQTIAVGNKDDVVTFIDAKTHRSKAEEQFKFEVNEISWNNDNNMFF
          ..TT....T.N.K..NINIC.SP.G..IA.G.KD.V.TF.DAKTH.SKA...F.FEVN.IS.NND..MF.
Retrocopy MKTTNTL-TLNFK-QNINICGSPIGEIIAMGIKDNVATFTDAKTHHSKAQTLFEFEVNDIS*NND-DMFP

Parental  LTNGNGC-INILSYPELKPVQSINAHPSNCICIKFDPMGKY
          LT......IN.LSY..L..VQ.I.AHPSN.I.I...P..K.
Retrocopy LTSSYSL<INSLSYTVL-IVQYIQAHPSNLIGINLNPIVKF

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	0.00 RPM	21.45 RPM
SRP007412_heart	0.00 RPM	13.70 RPM
SRP007412_kidney	0.02 RPM	18.50 RPM
SRP007412_liver	0.00 RPM	18.46 RPM
SRP007412_testis	0.05 RPM	21.27 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1821 was not detected

EST

No EST(s) were mapped for retro_mmus_1821 retrocopy.

TSS

No TSS is located nearby retro_mmus_1821 retrocopy 5' end.

Lab

retro_mmus_1821 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1821 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,