RetrogeneDB ID: retro_rnor_2330

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:134354729..134357708(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Kif4a
• Ensembl ID: ENSRNOG00000038035
• Aliases: Kif4a, Kif4
• Description: Protein Kif4 [Source:UniProtKB/TrEMBL;Acc:E9PSJ3]

Sequence

>retro_rnor_2330
ATGAAGGAAGAGGTGAAAGAAATTCCTGTCAGAGTGGCATTGCGTTGCCGCCCTCTGGTTCCGAAAGAGATTGGCGAGGG
CTGTCAGGTGTGTCTTTCCTTTGTGCCTGGGAAGCCTCAGGTGGTGATTGGTACTGATAAATCATTTACCTACGATTTTG
TGTTTGACCCCTCCACTGAACAGGAAGAGGTCTTCAACACAGCAGTAGCACCACTCATTAAAGGGATATTTAAAGGTTAC
AATGCCACTGTCCTGGCTTATGGACAAACTGGCTCTGGAAAGACCTACTCCATGGGAGGTGCATATCGTGCAAATCAAGA
GGATGAACCAACCATCGGGGTCATTCCTAGGGTAATACAACTACTTTTCAAAGAAATGGAAGAAAAGAGAGACTCTGAGT
TTACACTGAGAGTGTCTTACTTGGAGATTTACAACGAAGAAATTTTGGATCTTCTGTGCTCATCTTGTGAAAAAGCTTCT
CAAATACATATCCGGGAAGATCCCAAGGCAGGAATAAAGACCGTGGGGCTCACTGAGAAGACAGTTTCAGTTGCTTCTGA
CATGGTTTCCTGTTTGGAGCAGGGAAACAACGCCAGGACTGTAGCTGCCACAGCTATGAATTCCCAGTCTTCCCGATCTC
ACGCCATCTTCACAGTTTTCATAAGGCAAAGGAAGAAAACGGACAAGAGCAGCAGCTTTCACTCTAAGTTGTGTCTGGTA
GACCTTGCCGGATCAGAAAGGCAGAAGAAAACCAAGGCTGAAGGGGACCGACTGAGAGAAGGTATTAATATCAACCGAGG
ACTTCTGTGCTTGGGAAATGTGATCAGTGCTCTTGGAGATGGCAAAAAAGGCAGCTTCGTGCCCTACAGAGATTCCAAGC
TAACTCGCTTGCTTCAAGATTCTCTGGGAGGCAACAGCCACACTCTTATGATTGCCTGTGTGAGTCCTGCTGACTCCAGT
CTAGAGGAAACATTGAATACCCTACGCTACGCTGACAGAGCTAGAAAAATCAAGAACGAACCTGTTATTAATACGGATCC
CCAGACAGCCGAACTCACTCATCTTAAGCATCAGGTACAGCAGCTACGAGTCTTACTGCTACAGGCCCATGGAGGTAGCC
TGCCTGGGTCTATAATAGCAGAACCGTCAGAGAGTCTCCAGTCTCTGATGGAGAAGAATCAGTCCCTGGGGGAGGAGAAT
GAAAAGTTAAGTCATGCTCTGAGTGAGGCAGCTGGTCAGACAGCTCAGATGTTGGAAAGGATCATTTTGACAGAGCAAGC
AAATGAACAACTGAACACCAAGCTTCAAGAGCTCAGTGATCATGTAGCCTGTAAAGTGGATCTCCAAAAGCTAACGGAGA
CTTTGGAAGACCAGGAATTAATAGAGAAAATAGAGATAATTCGCAGTCTGCAACAAGCGGTTATCCATCTATCAGATGAA
AATGTTGTGGCCACCGAGTCGGCAATGGAACTAGAAACTCAAGTGGCAATCAGTCCAAAGAGTAGGAGGTCTTCTGATGC
TCTCACCACACAGCATGCTCTACGTCAAGCTCAGATGTCTAAGGAGCTCACTGAGTTGAATAAAGCCCTTGCAGTGAAAG
AGGCCCTAGCTAGGAAGATAACTTTCAATGGTGGCCAACTACAGCCCATTCACTGCCAGTATGAGGTGAACATCAGAAGT
CTAGAATCGGAAGTCGCCAGTCTGCAGAAGGAAAAGGAACAATTGCTTTTGGATCTTCAGTTGGCCAAAAAGGATGCCAA
CCAAGCCAAGTTGGGTGAGCACCGCCGCAAATGTCTCCAAGAGCTGGAGGCTCAAATAGCTGATTTGAAGAAGAAGCTAT
CTGAGCAGTCCAAGCTTCTGAAACTGAAAGAGTCCACTGAGAATACGGTCTCCAAACTGACTCTGGAGATACAGATGATG
AAAACCCAGCGAGTCCAGTTAATGCGTCAGATGAAGGAAGATGCGGAGAAGTCTAGACAGTGGAAACAACAGAAAGACAA
GGAAGTAATCCAGTTAAGAGAACAAGACCGTAAGAGGAGGTATGAGCTGCTTAAACTTGAAAGAGACTTCCAGAAACAGT
CCAATGTGCTGAGGCGGAAAACCGAAGAGGCAGCAGCTGCAAACAAGAGACTCAAGGATGCCCTCCAAAAGCAACGGGAC
GCGGCGGATAAACGGAAAGAGACTCAGAACCGTGGGCTAGAGGGCACAGAGGCACGAGTAAAGAACTGGCTTAGCAATGA
GATTGAAGTTATGGTCAGCACTGAAGATGTCAAACACCACTTGAATGACCTTCTGGAAGAGCGAAAGATACTAGCCCTGG
ATATGGCTCAACTTAAAGAAAACAAGGAACCTGGGGAAAACCCACCTCTTAAGCTCCAGAAGTGGACATTCGCCAGTGAC
GAAGTATGTGGTCATAGTTCAGAGCCCGAGGATTCTATTACAAAGCAGATTAGGAGCCTAGAGGCTGAAATGGAACTCAG
AAATGCTCAGATTGCTGACCTACAGCAAAAGCTCCTGGATGCAGAGAGCGAAGACAGGCCAAAGCGACACTGGGAAAGCA
TTGCCACAGTTCTCGAAGCCAAATGTGCTCTAAAATATTTAGTTGGGGAGGTGGTCTCCTCCAAACTTCAGGTCAGTGAG
CTCGAAAGCAACCTGAAACAGAGCCAGGCCAGCCATTCTAAAACGCAGAAGATGCTGCTCGAGGAGCAAAGTCATCTTGT
CCAGGTAGAGGCAGAGTGGAAAGCTGAGCTGTCCAAGGCGGAGCAAAAGCACCAAGAGAAGGAGCTCTACCTCCTCAGTC
AGCTGCAGCAAAGCCAAATGGCAGAGCAGCGGTTGGAGGTGTCAGTTAGTGGAAAGGAACAGCAGCTGTTGAGCACACTG
CAATGTCAGGAGGACCAGTTTAGGAAAATGCAAGAATTATGTGAGCAAAACCAGCAGCTTCTCCAAGAGAACGAAGCCAT
CAGGCAGAAGCTGAGCCTC

Alignment

ORF - retro_rnor_2330 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.73 %
• Parental protein coverage: 80.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKEEVKGIPVRVALRCRPLVSKEINEGCQTCLSFVPGEPQVVVGTDKSFTYDFVFDPSTEQEEVFNTAVA
          MKEEVK.IPVRVALRCRPLV.KEI.EGCQ.CLSFVPG.PQVV.GTDKSFTYDFVFDPSTEQEEVFNTAVA
Retrocopy MKEEVKEIPVRVALRCRPLVPKEIGEGCQVCLSFVPGKPQVVIGTDKSFTYDFVFDPSTEQEEVFNTAVA

Parental  PLIKGVFKGYNATVLAYGQTGSGKTYSMGGAYTAEQEHDSAIGVIPRVIQLLFKEINKKTDFEFTLKVSY
          PLIKG.FKGYNATVLAYGQTGSGKTYSMGGAY.A.QE....IGVIPRVIQLLFKE...K.D.EFTL.VSY
Retrocopy PLIKGIFKGYNATVLAYGQTGSGKTYSMGGAYRANQEDEPTIGVIPRVIQLLFKEMEEKRDSEFTLRVSY

Parental  LEIYNEEILDLLCSSREKASQINIREDPKEGIKIVGLTEKTVLVASDTVSCLEQGNNCRTVASTAMNSQS
          LEIYNEEILDLLCSS.EKASQI.IREDPK.GIK.VGLTEKTV.VASD.VSCLEQGNN.RTVA.TAMNSQS
Retrocopy LEIYNEEILDLLCSSCEKASQIHIREDPKAGIKTVGLTEKTVSVASDMVSCLEQGNNARTVAATAMNSQS

Parental  SRSHAIFTISIEQRKKNDKNSSFRSKLHLVDLAGSERQKKTKAEGDRLKEGININRGLLCLGNVISALGD
          SRSHAIFT..I.QRKK.DK.SSF.SKL.LVDLAGSERQKKTKAEGDRL.EGININRGLLCLGNVISALGD
Retrocopy SRSHAIFTVFIRQRKKTDKSSSFHSKLCLVDLAGSERQKKTKAEGDRLREGININRGLLCLGNVISALGD

Parental  DKKGNFVPYRDSKLTRLLQDSLGGNSHTLMIACVSPADSNLEETLNTLRYADRARKIKNKPIINIDPQAA
          .KKG.FVPYRDSKLTRLLQDSLGGNSHTLMIACVSPADS.LEETLNTLRYADRARKIKN.P.IN.DPQ.A
Retrocopy GKKGSFVPYRDSKLTRLLQDSLGGNSHTLMIACVSPADSSLEETLNTLRYADRARKIKNEPVINTDPQTA

Parental  ELNHLKQQVQQLQVLLLQAHGGTLPGNINVKPSENLQSLMEKNQSLVEENEKLSRGLSEAAGQTAQMLER
          EL.HLK.QVQQL.VLLLQAHGG.LPG.I...PSE.L..............EKLS..LSEAAGQTAQMLER
Retrocopy ELTHLKHQVQQLRVLLLQAHGGSLPGSIIAEPSESLXXXXXXXXXXXXXXEKLSHALSEAAGQTAQMLER

Parental  IILTEQANEKMNAKLEELRQHAACKVDLQKLAETLEDQEVKENIEIICNLQQAIARLSDEAVACMTATID
          IILTEQANE..N.KL.EL..H.ACKVDLQKL.ETLEDQE..E.IEII..LQQA...LSDE.V........
Retrocopy IILTEQANEQLNTKLQELSDHVACKVDLQKLTETLEDQELIEKIEIIRSLQQAVIHLSDENV----VATE

Parental  TAGEVDTQEQSSPDTSRSSDVFSTQHALRQAQMSKELIELNKELALKEALAKKMTQNDNQLQPIQFQYQD
          .A.E..TQ...SP...RSSD...TQHALRQAQMSKEL.ELNK.LA.KEALA.K.T.N..QLQPI..QY..
Retrocopy SAMELETQVAISPKSRRSSDALTTQHALRQAQMSKELTELNKALAVKEALARKITFNGGQLQPIHCQYEV

Parental  NIKNLELEVLSLQKEKEELVLELQTAKKDVNQAKLSERRRKRLQELEGQIAELKKKLHEQSKLLKLKETT
          NI..LE.EV.SLQKEKE.L.L.LQ.AKKD.NQAKL.E.RRK.LQELE.QIA.LKKKL.EQSKLLKLKE.T
Retrocopy NIRSLESEVASLQKEKEQLLLDLQLAKKDANQAKLGEHRRKCLQELEAQIADLKKKLSEQSKLLKLKEST

Parental  ELTVSKLNQEIRMMKNQRVQLMRQMKEDAEKFRQWKQQKDKEVIQLKERDRKRQYELLKLERNFQKQSNV
          E.TVSKL..EI.MMK.QRVQLMRQMKEDAEK.RQWKQQKDKEVIQL.E.DRKR.YELLKLER.FQKQSNV
Retrocopy ENTVSKLTLEIQMMKTQRVQLMRQMKEDAEKSRQWKQQKDKEVIQLREQDRKRRYELLKLERDFQKQSNV

Parental  LRRKTEEAAAANKRLKDALQKQKEVAEKRKETQSRGMEGTAARMKSWLGNEIEVMVSTEEAKRHLNDLLE
          LRRKTEEAAAANKRLKDALQKQ...A.KRKETQ.RG.EGT.AR.K.WL.NEIEVMVSTE..K.HLNDLLE
Retrocopy LRRKTEEAAAANKRLKDALQKQRDAADKRKETQNRGLEGTEARVKNWLSNEIEVMVSTEDVKHHLNDLLE

Parental  ERKILAQDVAQLKEKRESGENPPPKLRRRTFSRDEVHGQDSGAEDSISKQIESLESELELRSAQIADLQQ
          ERKILA.D.AQLKE..E.GENPP.KL...TF..DEV.G..S..EDSI.KQI.SLE.E.ELR.AQIADLQQ
Retrocopy ERKILALDMAQLKENKEPGENPPLKLQKWTFASDEVCGHSSEPEDSITKQIRSLEAEMELRNAQIADLQQ

Parental  KLLDAESEDQPKQRWENIATILEAKCAIKYLVGELVSSKIQVSKLESGLSQSKASCIEVQKMLFEEQNHF
          KLLDAESED.PK..WE.IAT.LEAKCA.KYLVGE.VSSK.QVS.LES.L.QS.AS....QKML.EEQ.H.
Retrocopy KLLDAESEDRPKRHWESIATVLEAKCALKYLVGEVVSSKLQVSELESNLKQSQASHSKTQKMLLEEQSHL

Parental  AKIETELKEELVRVEQQHQEKVLYLLSQLQQCQVTEKQLEESVSEKEQQLLSTLKCQEEELRKMQEVCEQ
          ...E.E.K.EL...EQ.HQEK.LYLLSQLQQ.Q..E..LE.SVS.KEQQLLSTL.CQE...RKMQE.CEQ
Retrocopy VQVEAEWKAELSKAEQKHQEKELYLLSQLQQSQMAEQRLEVSVSGKEQQLLSTLQCQEDQFRKMQELCEQ

Parental  NQQLLQENSAIKQKLNL
          NQQLLQEN.AI.QKL.L
Retrocopy NQQLLQENEAIRQKLSL

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
SRP017611_brain	0.22 RPM	1.37 RPM
SRP017611_kidney	0.07 RPM	1.05 RPM
SRP017611_liver	0.00 RPM	0.34 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2330 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2330 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2330 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015566	1 retrocopy	retro_cjac_2142,
Cavia porcellus	ENSCPOG00000000211	1 retrocopy	retro_cpor_681,
Homo sapiens	ENSG00000090889	1 retrocopy	retro_hsap_18,
Gorilla gorilla	ENSGGOG00000006631	1 retrocopy	retro_ggor_2218,
Myotis lucifugus	ENSMLUG00000011048	1 retrocopy	retro_mluc_114,
Mus musculus	ENSMUSG00000034311	1 retrocopy	retro_mmus_268,
Pongo abelii	ENSPPYG00000020438	1 retrocopy	retro_pabe_2700,
Rattus norvegicus	ENSRNOG00000038035	1 retrocopy	retro_rnor_2330 ,