RetrogeneDB ID: retro_mmus_915

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:6281443..6282344(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Vrk3
• Ensembl ID: ENSMUSG00000002205
• Aliases: Vrk3, AI428238
• Description: vaccinia related kinase 3 [Source:MGI Symbol;Acc:MGI:2182465]

Sequence

>retro_mmus_915
ATGACCTTCTGTCCAGTCTGTGGCAAAAGTGTCAAGGTATCATTAAAGTTCTATCCTTACTGTGGCAAGGCCCTGCCAGT
AGAGGAGGAAGGAGGCAACAAGACTGGCATTACACTTCCTGTGTCATCCTCTGAAGCTCCAGAAGAGAGCTGAACTCTGG
TTCTGCAACCTCTCCCAAGAAAGTGAAATGGTCACACATTGTCACTTCTCTCCCAACCTCCCTCCACTCTGATGGTGGCA
GTACCGAGTCTGATGATACCTTGAGTTTTCCTGAGAGAGCCACAGGCACCTGGAGCAGACCCCTGACCCCCAAAGGTAGC
CCAGTTTCCACCAGGCTGAGCCCTCAGACACTGAAGTGGAGCCCGGTGACCACTTCACTCCAGGCTTTGCCCATAGCTTT
GCCAAAGCTGACAGACCAGAATGGAAAGCACTGGGCACTGGAGGCCCTGAAGACCTGGCATAACCAAGGCAGCCTCTATG
AAGCTGAGCCCAATATTGTTGTCCCCTGTGATTCAAAGTCCCAGGAGCAGAGATTCTCACACAAACTGAACTCTAAGGAC
GGGCTCCTTTTCAATGAGCAGACCTTCTTTCAGAGAGCAGCCAAGCCTGTGAACAGGAATAACTGGAAGAAGCAGTGCTT
GGTCATCCTTATGTGTATCAGCTTTGGCATTCACCAGGACAAGTACAGGTTCCCGGAGTCCCCCAGCCTGGGGAGGATCC
TTCAGTCAGCTATGGATGACAACCTGAAATGTGTGGTATCAAAGAGATGTGTGTTGCAGGTTGCCTGAAGACTGTTAGAT
GTTCTGGAGTTTCTCCATGAAAACAAGTATATTCACAGGAACCTGACAGCTCAGAATGTCTTCGTGAATCCAGAGTTCTG
AGCCAGGTAACCCTAGTGGGC

Alignment

ORF - retro_mmus_915 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.4 %
• Parental protein coverage: 67.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ISFCPVCGKSVKVSFKFCPYCGKALPVEEDGGTQSAVTPHVSSVPG-SRRDLNSSFETSPKKVKCSHTVT
          ..FCPVCGKSVKVS.KF.PYCGKALPVEE.GG.....T..VSS....SRR.LNS...TSPKKVK.SH.VT
Retrocopy MTFCPVCGKSVKVSLKFYPYCGKALPVEEEGGNKTGITLPVSSSEA<SRRELNSGSATSPKKVKWSHIVT

Parental  SLPLSRHSDCDSSGSDNTLTSPDRATGTRSRPLTPKGSPLSNRQSPQTLKRTRVTTSLQALATGT-ELTD
          SLP.S.HSD..S..SD.TL..P.RATGT.SRPLTPKGSP.S.R.SPQTLK...VTTSLQAL......LTD
Retrocopy SLPTSLHSDGGSTESDDTLSFPERATGTWSRPLTPKGSPVSTRLSPQTLKWSPVTTSLQALPIALPKLTD

Parental  QNGKHWTLGALQIRDDQGILYEAEPTSAVPSESRTQKWRFSLKLDSKDGRLFNEQNFFQRVAKPLQVNKW
          QNGKHW.L.AL.....QG.LYEAEP...VP..S..Q..RFS.KL.SKDG.LFNEQ.FFQR.AKP...N.W
Retrocopy QNGKHWALEALKTWHNQGSLYEAEPNIVVPCDSKSQEQRFSHKLNSKDGLLFNEQTFFQRAAKPVNRNNW

Parental  KKQFLLPLLAIPTCIGFGIHQDKYRFLVFPSLGRSLQSALDDNPKHVVSERCVLQVACRLLDALEYLHEN
          KKQ.L..L.....CI.FGIHQDKYRF...PSLGR.LQSA.DDN.K.VVS.RCVLQVA.RLLD.LE.LHEN
Retrocopy KKQCLVILM----CISFGIHQDKYRFPESPSLGRILQSAMDDNLKCVVSKRCVLQVA*RLLDVLEFLHEN

Parental  EYVHGNLTAENVFVNPE-DLSQVTLVG
          .Y.H.NLTA.NVFVNPE..LSQVTLVG
Retrocopy KYIHRNLTAQNVFVNPE<VLSQVTLVG

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	15.70 RPM
SRP007412_cerebellum	0.00 RPM	22.45 RPM
SRP007412_heart	0.00 RPM	16.34 RPM
SRP007412_kidney	0.00 RPM	32.65 RPM
SRP007412_liver	0.00 RPM	18.71 RPM
SRP007412_testis	0.00 RPM	63.39 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_915 was not detected

EST

No EST(s) were mapped for retro_mmus_915 retrocopy.

TSS

No TSS is located nearby retro_mmus_915 retrocopy 5' end.

Lab

retro_mmus_915 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_915 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000002205	1 retrocopy	retro_mmus_915 ,
Mus musculus	ENSMUSG00000073563	1 retrocopy	retro_mmus_3454,
Otolemur garnettii	ENSOGAG00000008746	1 retrocopy	retro_ogar_1351,