minimal intron length

Laurent Duret duret at evol10.univ-lyon1.fr
Wed Dec 21 01:53:48 EST 1994


In article 01HKTPLL4Y6A00048L at muwayb.ucs.unimelb.edu.au, mc_fadden at botany.unimelb.edu.au (Geoff McFadden) writes:
> What's the smallest known spliceosomal intron?  So far the smallest I can
> track down is the 35bp intron in the cut7 gene of fission yeast (Nature
> 347:563-6).  Does anybody know of any published (or unpublished)
> spliceosomal introns less than 35bp?  My grad student and I have found a
> gene with three (apparently spliceosomal) introns of 19bp, so we may be
> claiming a new record.

I used HOVERGEN[1] search for short introns among GenBank vertebrate nuclear 
protein-encoding genes.
I found 5 sequences with a least one intron (declared to be) shorter than 35bp. 
These sequences are described at the end of this mail.
The shortest intron is 7 bp long!!!

What is declared in GenBank is however not necessarily carefully checked! You should
look at the original publication to verify this information.

================================================================
Laurent Duret			    duret at biomserv.univ-lyon1.fr
Tel: 	+33 72.44.81.42		    Fax:	+33 78.89.27.19
Laboratoire de Biometrie, Genetique et Biologie des Populations
Bat 741 - URA CNRS 243 Universite Claude Bernard - Lyon I
43, Bd du 11 Novembre 1918 
69622 Villeurbanne cedex FRANCE
================================================================


[1] L. Duret, D. Mouchiroud & M. Gouy (1994) HOVERGEN: a Database of 
Homologous Vertebrate Genes. Nucleic Acids Research 22:2360-2365

LOCUS       HSAQUPN2      995 bp    DNA             PRI       21-APR-1994
DEFINITION  H.sapiens gene for water channel aquaporin-2.
ACCESSION   Z29491
FEATURES             Location/Qualifiers
     intron          431..466
                     /number=1
     exon            467..631
                     /number=2
     intron          632..664
                     /number=2
     exon            665..745
                     /number=3
     intron          746..772
                     /number=3
     exon            773..>995
                     /number=4
//
LOCUS       HSPVALB      1350 bp    DNA             PRI       24-MAR-1992
DEFINITION  H.sapiens gene for parvalbumin.
ACCESSION   X63578
FEATURES             Location/Qualifiers

     intron          542..565
                     /number=1
     exon            566..633
                     /number=2
     intron          634..657
                     /number=2
     exon            658..790
                     /number=3
     intron          791..814
                     /number=3
     exon            815..918
                     /number=4
     intron          919..942
                     /number=4
     exon            943..1157
                     /number=5

//
LOCUS       HUMRSP1GPA   1935 bp ds-DNA             PRI       18-NOV-1991
DEFINITION  Human pregnancy-specific glycoprotein beta-1 (SP1) gene, last 3
            exons.
ACCESSION   M30628
FEATURES             Location/Qualifiers

     exon            46..411
                     /gene="SP1"
                     /number=1
     intron          412..751
                     /gene="SP1"
     exon            752..1308
                     /gene="SP1"
                     /note="next to last exon"
                     /number=2
//

LOCUS       MUSINTA7RS    783 bp ds-DNA             ROD       09-MAR-1994
DEFINITION  Mouse alpha-7 integrin gene, exons X-X3.
ACCESSION   L23422
FEATURES             Location/Qualifiers
     exon            8..231
                     /note="Repeat region III exon of alpha-7 integrin gene;
                     putative"
     intron          232..258
                     /note="intron X"
     exon            259..390
                     /note="exon X1 of alpha-7 integrin gene; putative"
     intron          391..421
                     /note="intron X1"
     exon            422..541
                     /note="exon X2 of alpha-7 integrin gene; putative"
     intron          542..558
                     /note="intron X2"
     exon            559..766
                     /note="Repeat region IV exon of alpha-7 integrin gene;
                     putative"
     intron          767..>783
                     /note="intron X3"
//
LOCUS       RATFN3M1     2350 bp ds-DNA             ROD       11-MAR-1994
DEFINITION  Rat fibronectin (cell-, heparin-, and fibrin-binding domains) gene
            encoding three fibronectin mRNAs, exons 1,2,3.
ACCESSION   L00191 K01269 K01270 K01271
FEATURES             Location/Qualifiers

     exon            <1..1129
                     /note="fibronectin 1"
                     /number=1
     intron          1130..1141
                     /note="f1,f2,f3 intron A"
     exon            1142..1231
                     /number=2
     intron          1232..2204
                     /note="f3 intron B"
     intron          1232..1919
                     /note="f2 intron B"
     intron          1232..1844
                     /note="f1 intron B"
     exon            1845..2311
                     /number=3
     exon            1920..2311
                     /number=3
     exon            2205..2311
                     /number=3
                     /product="fibronectin 3"
     intron          2312..>2350
                     /note="f1,f2,f3 intron C"
//









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