RetrogeneDB ID: retro_rnor_987

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:980997..982136(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Kpna3
• Ensembl ID: ENSRNOG00000014945
• Aliases: Kpna3, importin
• Description: importin subunit alpha-3 [Source:RefSeq peptide;Acc:NP_001014792]

Sequence

>retro_rnor_987
ACTAATATACCATCAGGAACTTCTGCACAGACTCAAGCTGATGTACAGTCCAATGCAGTACCACATTTTTCTGTGACTCC
TCCATTTCCCACATCAGAATGTTTGTGAACAAGTGGTGTGGGCTTTGGGAAACAATGTAGGTGATGGTCTTCATGCAGAT
TGTGTCTTATCACTGGGAGTTGTCAAACTTCTTCTGTCCTTAATCAATTCTTCCATTCCTATCACCTTTCTTCAGAATGT
CACATGTGTCATTGTCAATCTTTGTAGAAATAAAGAACCCTCACCACCTATGGAGACCGTTCAGGAGATTTTGCCAGCTT
TATATGTCCTCATCTACCATACAACATTAGACATTCTTGTAGACACTGTTTGGGTACTGTCCTACTTGACAGGAAATGAG
CAGATACAGATGGTTACTGATTTAGGTGTTGAACCCTTCCTCATGCCCCTTCTGAGTCACCAGAAAGTCAAAGTTCAAAC
TGCAGCACTCAGAGAAGTTGGGAACATAGTTACTGGCACTGATGTGCAGACCCAAGTGCTTCTTAGTTGTGGTGTGCTGT
CCCACTTTCCAAACCTGTTGACACACCCAAAAGAGAAAATAATAAGGAAGCAGTATGGTTCCTTTCCAATATAACAGCAG
GCAATGAGCAGCAAGTTCAAACTGTAATAGATGCTGGGTTAATCCCTATGATTATTCATCAGCTCCCTAAGGGGGACTTC
AGAACACAAAAGGAAGCTCCTTGGGCAATTAGCAGTTTAACAATAAGTGGCAGAAAAGGTCAAGTTGAATACCTTGTACA
ACAGAATGCAATACCACCATTCTGTAATTTACTGTCATTAAAAAATCTCAAGTGGTGCAGGTAGTTCTAGATGGTCTAAA
AAAATCATGCTGACTGATGTCTGATGATGAAGCAAGTACAATAGCTTAGATCATAGAAAAGTATGGAGGCTTGGAGAAAA
TTGAAGTTTTGCAGCAACATGAAATTGAAGACATATATAAATTAGCATTTTAAATCATAAATCAATACTTTTCAGGTGAT
GATATTGATGAAGATCCTAGACTCATTCCTGAAGCAACACAAAGAGTTACTTAGAATTTTGATCCAACAGCCAACCTTCA
AACAAAAGAATTTAATTTC

Alignment

ORF - retro_rnor_987 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.12 %
• Parental protein coverage: 73.32 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TNIASGTSAQTQAVVQSNAVP-LFLRLLHSPHQNVCEQAVWALGNIIGDGPQCRDYVISLGVVKPLLSFI
          TNI.SGTSAQTQA.VQSNAVP..FL.LLH.PHQNVCEQ.VWALGN..GDG....D.V.SLGVVK.LLS.I
Retrocopy TNIPSGTSAQTQADVQSNAVP>IFL*LLHFPHQNVCEQVVWALGNNVGDGLHA-DCVLSLGVVKLLLSLI

Parental  NPSIPITFLRNVTWVIVNLCRNKDPPPPMETVQEILPALCVLIYHTDINILVDTVWALSYLTDGGNEQIQ
          N.SIPITFL.NVT.VIVNLCRNK.P.PPMETVQEILPAL.VLIYHT...ILVDTVW.LSYLT..GNEQIQ
Retrocopy NSSIPITFLQNVTCVIVNLCRNKEPSPPMETVQEILPALYVLIYHTTLDILVDTVWVLSYLT--GNEQIQ

Parental  MVIDSGVVPFLVPLLSHQEVKVQTAALRAVGNIVTGTDEQTQVVLNCDVLSHFPNLLSHPKEKI-NKEAV
          MV.D.GV.PFL.PLLSHQ.VKVQTAALR.VGNIVTGTD.QTQV.L.C.VLSHFPNLL.HPKEKI.NKEAV
Retrocopy MVTDLGVEPFLMPLLSHQKVKVQTAALREVGNIVTGTDVQTQVLLSCGVLSHFPNLLTHPKEKI<NKEAV

Parental  WFLSNITAGNQQQVQAVIDAGLIPMIIHQLAKGDFGTQKEAAWAISNLTISGRKDQVEYLVQQNVIPPFC
          WFLSNITAGN.QQVQ.VIDAGLIPMIIHQL.KGDF.TQKEA.WAIS.LTISGRK.QVEYLVQQN.IPPFC
Retrocopy WFLSNITAGNEQQVQTVIDAGLIPMIIHQLPKGDFRTQKEAPWAISSLTISGRKGQVEYLVQQNAIPPFC

Parental  NLLS-VKDSQVVQVVLDGLKNIL-IMAGDEASTIAEIIEECGGLEKIEVLQQHENEDIYKLAFEIIDQYF
          NLLS..K.SQVVQVVLDGLK.....M..DEASTIA.IIE..GGLEKIEVLQQHE.EDIYKLAF.II.QYF
Retrocopy NLLS<IKKSQVVQVVLDGLKKSC*LMSDDEASTIA*IIEKYGGLEKIEVLQQHEIEDIYKLAF*IINQYF

Parental  SGDDIDEDPSLIPEATQGGTYNFDPTANLQTKEFNF
          SGDDIDEDP.LIPEATQ..T.NFDPTANLQTKEFNF
Retrocopy SGDDIDEDPRLIPEATQRVT*NFDPTANLQTKEFNF

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	0.00 RPM	42.71 RPM
SRP017611_kidney	0.00 RPM	22.89 RPM
SRP017611_liver	0.00 RPM	17.21 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_987 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_987 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_987 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
Bos taurus	ENSBTAG00000004850	1 retrocopy	retro_btau_1842,
Rattus norvegicus	ENSRNOG00000010768	1 retrocopy	retro_rnor_592,
Rattus norvegicus	ENSRNOG00000014945	1 retrocopy	retro_rnor_987 ,
Rattus norvegicus	ENSRNOG00000015329	1 retrocopy	retro_rnor_42,
Ictidomys tridecemlineatus	ENSSTOG00000003006	1 retrocopy	retro_itri_1777,
Tarsius syrichta	ENSTSYG00000008134	1 retrocopy	retro_tsyr_1547,