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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtggagttcccttttagaaagtagtattctttgtcttatccgtttacatgcattcgcgttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAG

Basic information

species Selaginella moellendorffii
transcript EFJ32604
intron # 2
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|169023493|gb|FE431404.1|FE431404
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169041587|gb|FE449548.1|FE449548
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169036059|gb|FE446765.1|FE446765
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169094385|gb|FE495585.1|FE495585
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169087333|gb|FE491746.1|FE491746
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169053831|gb|FE460922.1|FE460922
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169051134|gb|FE458681.1|FE458681
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169019270|gb|FE428183.1|FE428183
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169096116|gb|FE500276.1|FE500276
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169082303|gb|FE488046.1|FE488046
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169087154|gb|FE493101.1|FE493101
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169025097|gb|FE434697.1|FE434697
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169077299|gb|FE485601.1|FE485601
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169036890|gb|FE443850.1|FE443850
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169080654|gb|FE487175.1|FE487175
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169075645|gb|FE482031.1|FE482031
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169062067|gb|FE469152.1|FE469152
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|70670986|gb|DN839563.1|DN839563
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGACACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169074936|gb|FE483818.1|FE483818
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169088141|gb|FE493380.1|FE493380
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169041091|gb|FE450378.1|FE450378
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169053051|gb|FE462014.1|FE462014
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169061498|gb|FE469597.1|FE469597
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169032798|gb|FE438306.1|FE438306
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169019625|gb|FE427974.1|FE427974
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169097028|gb|FE498419.1|FE498419
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169047243|gb|FE456492.1|FE456492
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169088635|gb|FE491521.1|FE491521
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169087281|gb|FE491694.1|FE491694
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169030300|gb|FE440025.1|FE440025
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169102882|gb|FE505247.1|FE505247
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169035576|gb|FE445346.1|FE445346
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169094800|gb|FE492951.1|FE492951
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169088706|gb|FE491540.1|FE491540
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169087447|gb|FE492224.1|FE492224
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169105943|gb|FE504303.1|FE504303
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
EST: gi|169075799|gb|FE482796.1|FE482796
EST:     ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACA                         TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT
genomic: ACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 291

ACCGCCGTGGCCAATGACGAAGTGTACTCGCGATTCGAGAGTTCCAAGGATAAATCCCATGTCACAgtaagtggag ... gttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagaaagtagtattctttgtcttatccgtttacatgcattcgcgttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAG
                                            cgttctc  CT-rich tract
            tattcttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtggagttcccttttagaaagtagtattctttgtcttatccgtttacatgcattcgcgttctcgcagTGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG