RetrogeneDB ID: retro_mmus_1251

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:19014831..19015937(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Kif2c
• Ensembl ID: ENSMUSG00000028678
• Aliases: Kif2c, 4930402F02Rik, ESTM5, Knsl6, MCAK, X83316
• Description: kinesin family member 2C [Source:MGI Symbol;Acc:MGI:1921054]

Sequence

>retro_mmus_1251
AGGTTCACAGCAAGGCCACTGACACAGGCGATTTTTGAAGGGGGAAAAGCAACATGATTTGCCTATGGACAGAGAGGCAG
TGGGAACAGGCATACAATGGGAGGAGATTTGTCTGGTAAAAGTCAGAACACATCCAAAGGGATCTACACAATGGTTTCTC
AGGATGTCTTCCTTCTAAAGAATCAGTCTCCATACTGGAACTTAAACCTGGAAGTTTATGTGACATTCTTCGTGATCTAC
AATGGGAAGGTGTTTGATCTGCTCAACAAAAGGCCAAGTTACATGTGCTGGAGGACAGCAGGCAGCAACTGCAGGCTGTG
GGACTGCAGGAGTATCTGGTTACCTCTGCTGCTGATGTCGTCAAGATGATCAACATGGGCAGTGCCTGCAGGACTTCTGG
ACAAACATTTGCCAACTCCATTTCCTCCTGCTCCCACGCCTGCTTCCAGATTCTTCTTTGAGCTCAAGGGAGATTACATG
GCAAATTCTCTTTGGTGGATCTGACAGGGAATGAACGAGTGGCTGACATGTCTAGTGCTGACCGGCAGACTCACATGGAG
AGTGCAGAAATTAACAAGTCTCTCCTGCCTCTGAAGGAATGTATCCGGGCTCTGGGACAGAACAAGGCTCATACACCATT
CTGTGAGAGCAAGCTGACATAGCTGCTGAGGGCGTCGTTCATTGGAGAGAACTCAAGGACCTACATGACCACCATGATCT
CACTAGGCATAAGCTCCTATGAATAAATGTTCAACATGCTGAGATACACAGACAGAGTCAAGGAGCTAAGCCCTCACAGT
GGGCCCGGTTGAGAGCAGTCAGTTCAGATGGAAACTGAAGTGATGGAAGCCAGCTCTAATGGGACTTCTCTGGCTGGCAA
TGAAGAGGAGCTGTCTTCCCAGATGTCCAGCTTTAATGAAGTCATGACTCAGATCAGGGAGCTGGAAGAGAGGGCCCTGG
AAGAGCTCAGGGAGATCACACAGCAAGGCCCAAGCTGGCTTGAGCTCTCTGAGATGACAGATCAGCCAGACAATGACTTG
GAGACCTTTGTGAACAAGCCAGAATCTGCCCTGACACAGTAGGCTAAGCAGGCTAGGCACTTCTCA

Alignment

ORF - retro_mmus_1251 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.37 %
• Parental protein coverage: 55.22 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RFTARPLVQTIFEGGKATCFAYGQTGSGKTHTMGGDLSGKSQNASKGIYAMASRDVFLLKNQPRYRNLNL
          RFTARPL.Q.IFEGGKAT.FAYGQ.GSG..HTMGGDLSGKSQN.SKGIY.M.S.DVFLLKNQ..Y.NLNL
Retrocopy RFTARPLTQAIFEGGKAT*FAYGQRGSGNRHTMGGDLSGKSQNTSKGIYTMVSQDVFLLKNQSPYWNLNL

Parental  EVYVTFFEIYNGKVFDLLNK-KAKLRVLEDSRQQVQVVGLQEYLVTCADDVIKMINMGSACRTSGQTFAN
          EVYVTFF.IYNGKVFDLLNK.KAKL.VLEDSRQQ.Q.VGLQEYLVT.A.DV.KMINMGSACRTSGQTFAN
Retrocopy EVYVTFFVIYNGKVFDLLNK<KAKLHVLEDSRQQLQAVGLQEYLVTSAADVVKMINMGSACRTSGQTFAN

Parental  SNSSRSHACFQILLRTKGRLHGKFSLVDLAGNERGADTSSADRQTRMEGAEINKSLLALKECIRALGQNK
          S.SS.SHACFQILL...GRLHGKFSLVDL.GNER.AD.SSADRQT.ME.AEINKSLL.LKECIRALGQNK
Retrocopy SISSCSHACFQILL*AQGRLHGKFSLVDLTGNERVADMSSADRQTHMESAEINKSLLPLKECIRALGQNK

Parental  AHTPFRESKLTQVLRDSFIGENSRTCMIAMISPGISSCEYTLNTLRYADRVKELSPHSGPSGEQPVQMET
          AHTPF.ESKLT..LR.SFIGENSRT.M..MIS.GISS.E...N.LRY.DRVKELSPHSGP..EQ.VQMET
Retrocopy AHTPFCESKLT*LLRASFIGENSRTYMTTMISLGISSYE*MFNMLRYTDRVKELSPHSGPG*EQSVQMET

Parental  EVMEASSNGTSLTGNEEEELSSQMSSFNEAMTQIRELEERALEELREIIQQGPNWLELSEMTDQPDYDLE
          EVMEASSNGTSL.GN.EEELSSQMSSFNE.MTQIRELEERALEELREI.QQGP.WLELSEMTDQPD.DLE
Retrocopy EVMEASSNGTSLAGN-EEELSSQMSSFNEVMTQIRELEERALEELREITQQGPSWLELSEMTDQPDNDLE

Parental  TFVNKAESALTQQAKQAKHFS
          TFVNK.ESALTQ.AKQA.HFS
Retrocopy TFVNKPESALTQ*AKQARHFS

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	0.07 RPM	0.33 RPM
SRP007412_cerebellum	0.00 RPM	0.04 RPM
SRP007412_heart	0.00 RPM	0.44 RPM
SRP007412_kidney	0.00 RPM	0.87 RPM
SRP007412_liver	0.00 RPM	0.19 RPM
SRP007412_testis	0.00 RPM	365.27 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1251 was not detected

EST

No EST(s) were mapped for retro_mmus_1251 retrocopy.

TSS

No TSS is located nearby retro_mmus_1251 retrocopy 5' end.

Lab

retro_mmus_1251 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1251 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000021693	1 retrocopy	retro_mmus_68,
Mus musculus	ENSMUSG00000028678	1 retrocopy	retro_mmus_1251 ,
Mus musculus	ENSMUSG00000030677	1 retrocopy	retro_mmus_471,
Otolemur garnettii	ENSOGAG00000006916	1 retrocopy	retro_ogar_1892,
Pongo abelii	ENSPPYG00000001427	1 retrocopy	retro_pabe_88,
Pteropus vampyrus	ENSPVAG00000009856	1 retrocopy	retro_pvam_3,
Sus scrofa	ENSSSCG00000003931	1 retrocopy	retro_sscr_25,
Tursiops truncatus	ENSTTRG00000000748	1 retrocopy	retro_ttru_1318,
Drosophila melanogaster	FBgn0030268	2 retrocopies	retro_dmel_1, retro_dmel_2,