RetrogeneDB ID: retro_mmus_1312

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:112578958..112579981(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Galnt1
• Ensembl ID: ENSMUSG00000000420
• Aliases: None
• Description: UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1 [Source:MGI Symbol;Acc:MGI:894693]

Sequence

>retro_mmus_1312
GTTCATGTAATTCGAATGGAACAACACTCTGGGTTATTCAGAGCTAGATTAAAAGAGGCTTCTGTGTCCAAAGCCAAGTG
CTTGCCGTCTTAGATGCTCACTGTGAATGAACAGCAAGGTGGCTGGAGCCTCTATTAGCCCAGATCAAACATGATAGAAG
AACAGTGGTGTGTCCTATCATCAATGTGATCAGCAATGACACTTTCCAGTACATGGTGGGCTCTGACATGACCTATGGTG
CATTCAACTGGAAGCTCTATTTTCATTGGTATCCTCTTCCCTAACGAGAAATGGACAAAAGGAAAGGTGACTGGACTCTT
TCTGTCATAACACTTACAAGGGCAGGAGATCTTTTATCAATAGACAGAGATTACTTTCAGGAAACTGTAACATATGATGC
TGAAATAGATATTTGGGGAGGAGAAAAACCTAGAAATTTCCTTTAGAATTTGGTAGTGTGGAGGAACTTTGGCTATACTG
ACATGCTCCCATATTGGTCATGTGTTTTAGAAAGCTACACCTTACACATTTCCAGGAGGGACAGGGCAGATTGTTAATAA
TAATAACAGATGGCTTGCAGAAGTATGGATGGATGAATTCAAGAATTTATTCTGTATAATTTCTTCAGGTGTTACAAAGG
TAGATTATGGAGATATATCAAGACTCAGCCTGAGGCATAAACTATAATGCAAACCTTTCTCTTGGTACCTAGAAAATATT
TACCCTGATTCTCAAATTCGTATTCACCATTTCTCATGGGAAGAAACACAAAATGTGGAAATAAATCAATGTCTAGATAA
CATGGCTAGAAAAAAAGAATGAAAAGTTTGAAATTTATGATTGTCATGGTTGTGAGGTCAGCAGGTTTTCTCTTACACTG
CCTACAAAGATATAAGTACAGACATTCGTTTGCACATTTCCAAACTGAATGGTCCACTTACCACTCTCAAATTCCACCAC
CTAAAAGGCTACCAGGTCTGGGAGTATGATCCAGTGAAATTAACCCTGCAGCTTGTGAACAGT

Alignment

ORF - retro_mmus_1312 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.37 %
• Parental protein coverage: 61.36 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VHVIRMEQRSGLIRARLKGAAVSRG-QVITFLDAHCECTAGWLEPLLARIKHDRRTVVCPIIDVISDDTF
          VHVIRMEQ.SGL.RARLK.A.VS...QV...LDAHCE.TA.WLEPLLA.IKHDRRTVVCPII.VIS.DTF
Retrocopy VHVIRMEQHSGLFRARLKEASVSKA<QVLAVLDAHCE*TARWLEPLLAQIKHDRRTVVCPIINVISNDTF

Parental  EYMAGSDMTYGGFNWKLNFRWYPVPQREMDRRKGDRTLPVRTPTMAGGLFSIDRDYFQEIGTYDAGMDIW
          .YM.GSDMTYG.FNWKL.F.WYP.P.REMD.RKGD.TL.V.T.T.AG.L.SIDRDYFQE..TYDA..DIW
Retrocopy QYMVGSDMTYGAFNWKLYFHWYPLP*REMDKRKGDWTLSVITLTRAGDLLSIDRDYFQETVTYDAEIDIW

Parental  GGE-NLEISFRIWQCGGTLEIVTCSHVGHVFRKATPYTFPGGTGQIINKNNRRLAEVWMDEFKNFFYIIS
          GGE.NLEISFRIW.CGGTL.I.TCSH.GHVF.KATPYTFPGGTGQI.N.NNR.LAEVWMDEFKN.F.IIS
Retrocopy GGE>NLEISFRIW*CGGTLAILTCSHIGHVF*KATPYTFPGGTGQIVNNNNRWLAEVWMDEFKNLFCIIS

Parental  PGVTKVDYGDISSRLGLRRKLQCKPFSWYLENIYPDSQIPRHYFSLGEIRNVETNQCLDNMAR-KENEKV
          .GVTKVDYGDI.SRL.LR.KL.CKPFSWYLENIYPDSQI..H.FS..E..NVE.NQCLDNMAR.K.NEK.
Retrocopy SGVTKVDYGDI-SRLSLRHKL*CKPFSWYLENIYPDSQIRIHHFSWEETQNVEINQCLDNMAR>KKNEKF

Parental  GIFNCHG-MGGNQVFSYTANKEIRTDDLCLDVSKLNGPVTMLKCHHLKGNQLWEYDPVKLTLQHVNS
          .I..CHG...G.QVFSYTA.K.I.T.D..L..SKLNGP.T.LK.HHLKG.Q.WEYDPVKLTLQ.VNS
Retrocopy EIYDCHG<L*GQQVFSYTAYKDIST-DIRLHISKLNGPLTTLKFHHLKGYQVWEYDPVKLTLQLVNS

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	42.54 RPM
SRP007412_cerebellum	0.00 RPM	45.72 RPM
SRP007412_heart	0.00 RPM	74.43 RPM
SRP007412_kidney	0.00 RPM	111.55 RPM
SRP007412_liver	0.00 RPM	41.40 RPM
SRP007412_testis	0.00 RPM	24.52 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1312 was not detected

EST

No EST(s) were mapped for retro_mmus_1312 retrocopy.

TSS

No TSS is located nearby retro_mmus_1312 retrocopy 5' end.

Lab

retro_mmus_1312 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1312 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011206	1 retrocopy	retro_btau_581,
Callithrix jacchus	ENSCJAG00000021030	2 retrocopies	retro_cjac_1554, retro_cjac_865,
Myotis lucifugus	ENSMLUG00000001978	1 retrocopy	retro_mluc_163,
Mus musculus	ENSMUSG00000000420	1 retrocopy	retro_mmus_1312 ,
Mus musculus	ENSMUSG00000039774	1 retrocopy	retro_mmus_183,
Ictidomys tridecemlineatus	ENSSTOG00000003311	1 retrocopy	retro_itri_954,
Tarsius syrichta	ENSTSYG00000014610	1 retrocopy	retro_tsyr_1444,