RetrogeneDB ID: retro_mmus_471

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:99638432..99640218(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Kif22
• Ensembl ID: ENSMUSG00000030677
• Aliases: Kif22, AU021460, C81217, Kid, Kif22a
• Description: kinesin family member 22 [Source:MGI Symbol;Acc:MGI:109233]

Sequence

>retro_mmus_471
CTATGCCCATTTATGGATGAAGAAAAAAAAGGAAAGGGATGCCCTTGTGTAAGAGGCATATAAAGCTGCTCTCTTGAGGT
GGCCACCTTGAGGAAATCCTATGAGAATACTAAATATCAGTTTAATGTCTTTTATTGAGAGAAGAGCACTCAGCAGAACA
TCTAAGTAGGTTCAGTACAGCCTATCCTGTGGCACTTGCTGGATGGGCAGAATACCAGTGTGCTTACATATGGGACTATT
GAGGCAGGGAAGACACATATAATACTGGGTAGCCCCATGGGAACAACATGGAGTGATTCCTTAGCCTCTCATAGACCTCC
TGCAGATAACAAGGGAAGAAAGTGCTGAAGGCTGGCCATGGGACATTTCTGTCAGGATGTCCTATTTAGAGGTCTACCAG
GAAAAGGTATTAGACCTCTTATATCCTGCATCAGGAGACCTAGTGATATGAGAAGATTGTCGAGGGAACATCCTGATTCC
AGTTCTCACCCAGGACCCCAATACTTGCTTCTCTGACTTTGAGCAGTACTTCTGCCAGCCTGTAGAAATCAAGTTGTAGG
AGCTACTCTGCTTAAGCAGTGCTCTTACCATATCATTCAATGCTCTTTATCAAGGTGGATCAGCATGGACATTTGACTCT
GTTTCACTAGTGAAAAGGAAAACTCTACCATATTGATTTGGTTGGCTCAGAGGACAACCACAACAAGGGAACCAGTGCAT
TCAACTCAAAGAGAGTGGCGCCATCAACACCTGCTTCTTGTACTGGGCAAAGTGGAGGTTGCATCATATTAGGGCTCCCC
TCCTATATTATACTGGGACAGAAAAATCATTTGCCTATTGCCAGACTCTCTGGAAGGCTCAGCTCATAACATCATCATTA
CCAACACTGCTCCTGAAAGACATTTTTACTTGGAATCATTCTGAGCATTGAACTTCACTGCTAGGTCCAAGGAGCTGATT
AATTGGCCTTTCACCAATGGGAGTCTACAGCCTCATGCCTACACACCTGTTAAGCTTTGGCAAAAAGAACTTCTAGGCCC
ATCAAAGGCAAAGAAAGCCAAAGGTCTTGTAGAAGAATCAATGGGGAGTCCTAACTCTACAGCAGTTTTATCAACTGCCT
CCCAGAAACTAAGCCTCTTATAGAACCTAAGCAATGTGGATCCAGCTATGTTGGAGAAGTTCCTGAGTTTATATCATTTG
TTGGGATCTCAGGGGAACAAGAAGGTATACTTCTACTGAATACCCCAAAGCAAGACAAGAATGGTACTCATTAAGACAGT
GTAGGAAAGAACTTGGAGATTGAGAGACTTAAGGTGAAGTAGAAAGAACTATAGGCAAAGGTGTTGGCACAGGAGATCCT
AGATATGAAGGGAAAAAATGTCTCATGATTTCCAGCCCCCTTCCACTTGTACAAACACAGTGGCAAAACCTCAGAAAAAA
GTGGTGATGACCCTGCAACTGATTCAGAAGCAGGCATAATCCTCAAACACAATTTACTTTCTAAAAAACACAACAAAAAT
AAGCCATCACATGTGTCAGAGGCTATGGAAAAGGCTGAAGACTGCTAGAAGCTACAGATTAGCCCAGAGTTACTAGCACT
TGTCACAAACAAGTATTGGATCTTCTGAATGAAGGCTCAGCTCAGGATCTGTGCATGTTGTATCATACTGGCCAGAAGAA
GGCCTAGTTCACTGTGGGCTGGAGGGATCTCCATGGCCCCTTTAGGGAACTGAAGGACTTGGAACAGCAGGAAGGCATCT
CTGGAAAGCAGGTAAAGTCTTTCCTT

Alignment

ORF - retro_mmus_471 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.01 %
• Parental protein coverage: 90.91 %
• Number of stop codons detected: 17
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  LRPFMDGETEAKELPCVRAIDSCSLEVANWKKYQETLKYQFDAFYGEKSTQQEVYVGSVQPILRHLLEGQ
          L.PFMD.....K..PCVR.I.SCSLEVA...K..E..KYQF..FY.EKSTQQ...VGSVQPIL.HLL.GQ
Retrocopy LCPFMDEXXXGKGCPCVRGI*SCSLEVATLRKSYENTKYQFNVFY*EKSTQQNI*VGSVQPILWHLLDGQ

Parental  NASVLAYGPTGAGKTHTMLG-SP-EQPGVIPRALMDLLQLAREESAEGRPWDVSVAMSYLEIYQEKVLDL
          N.SVL.YG...AGKTH..LG..P.EQ.GVIP..L.DLLQ..REESAEG.PWD.SV.MSYLE.YQEKVLDL
Retrocopy NTSVLTYGTIEAGKTHIILG>APWEQHGVIP*PLIDLLQITREESAEGWPWDISVRMSYLEVYQEKVLDL

Parental  LDPASGDLVIREDCRGNILIPGLTQKPITSFSDFEQHF-LPASRNRAVGATRLNQRSSRS-HAVLLVKVD
          L.PASGDLVI.EDCRGNILIP.LTQ.P.T.FSDFEQ.F.LPA.RN..VGAT.L.Q.S....H..L..KVD
Retrocopy LYPASGDLVI*EDCRGNILIPVLTQDPNTCFSDFEQYF<LPACRNQVVGATLLKQCSYHI<HSMLFIKVD

Parental  QRERLTPFRQREGKLYLIDLAGSEDNR-RTGNQGIRLKESGAINTS-LFVLGKVVDALNQGLPRIPYRDS
          Q...LT.F....GKLY.IDL.GSEDN....GNQ.I.LKESGAINT..L.VLGKV..A...G.P.I.Y.D.
Retrocopy QHGHLTLFH**KGKLYHIDLVGSEDNH<QQGNQCIQLKESGAINTC<LLVLGKVEVASY*GSPPILYWDR

Parental  KLTRLLQDSLGGSAHSILIANIAPERRFYQDTISALNFTARSKEVINRPFTNESLQPHALAPVKLSQKEL
          K...LL.DSL.GSAH.I.I.N.APER.FY.....ALNFTARSKE.IN.PFTN.SLQPHA..PVKL.QKEL
Retrocopy KIICLLPDSLEGSAHNIIITNTAPERHFYLESF*ALNFTARSKELINWPFTNGSLQPHAYTPVKLWQKEL

Parental  LGPSEAKKAKGPEEESTGSPESTAAPASASQKLSLLQKLSNMDPAMLENLLSMERLLGSQ-GSQ-GTPLL
          LGPS.AKKAKG..EES.GSP.STA....ASQKLSLL..LSN.DPAMLE..LS...LLGSQ.G.Q.G..LL
Retrocopy LGPSKAKKAKGLVEESMGSPNSTAVLSTASQKLSLL*NLSNVDPAMLEKFLSLYHLLGSQ<GEQEGILLL

Parental  NTPKRE-RMVLMKTVEEKNLEIERLKMKQKELEAKVLAQEAPDPREKENTPTILQPPASYSGTVAKPLKK
          NTPK...RMVL.KTV.E.......L....K..............REK.......QPP.....TVAKP.KK
Retrocopy NTPKQD>RMVLIKTV*ERTWRLRDLR*SRKNYRQRCWHRRS*I*REKMSHD--FQPPSTCTNTVAKPQKK

Parental  AVVMPLQRIQKQRESSNQIQLL-KKGPKRKLEPSPESEAVEKDEDYWEVQISPELLA-HGRKKLLDLLNE
          .VVM.LQ.IQKQ..SSN.I..L.KK..K.K..PS..SEA.EK.ED....QISPELLA....K..LDLLNE
Retrocopy -VVMTLQLIQKQA*SSNTIYFL<KKHNKNK--PSHVSEAMEKAEDC*KLQISPELLA<TCHKQVLDLLNE

Parental  GSARELRSLQRIGQKKAQLIVGWRELHGPFSEVEDLEQVEGISGKQVESFL
          GSA..L..L...GQKKA...VGWR.LHGPF.E..DLEQ.EGISGKQV.SFL
Retrocopy GSAQDLCMLYHTGQKKA*FTVGWRDLHGPFRELKDLEQQEGISGKQVKSFL

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	4.04 RPM
SRP007412_cerebellum	0.00 RPM	8.60 RPM
SRP007412_heart	0.00 RPM	0.97 RPM
SRP007412_kidney	0.00 RPM	1.44 RPM
SRP007412_liver	0.00 RPM	0.41 RPM
SRP007412_testis	0.00 RPM	19.26 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_471 was not detected

EST

No EST(s) were mapped for retro_mmus_471 retrocopy.

TSS

No TSS is located nearby retro_mmus_471 retrocopy 5' end.

Lab

retro_mmus_471 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_471 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007193	1 retrocopy	retro_cjac_144,
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	ENSOGAG00000000266	1 retrocopy	retro_ogar_2234,
Pteropus vampyrus	ENSPVAG00000017206	1 retrocopy	retro_pvam_313,