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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgaaagcagagcagtagtgtgatatttagagggttgtgagtttttgatctctcatcttgggtttggattctctctcacacacacagGAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTTTAAGACCATTCCAATGGCTGATATGGAAATTGTGCTT

Basic information

species Arabidopsis thaliana
transcript AT5G13940.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G13940.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv14s0068g00980.t01 (Vitis vinifera), 3'ss of exon 8
-------gtacgaaagcagagcagtagtgtgatatttagagg----gttgtga-gtttttgatctctcatcttgggtttggattctctctcacacacacagGAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTTTAAGACCATTCCAATGGCTGATATGGAAATTGTGCTT
        |    ||      |  |      || |||   ||     ||||||   |    ||  |||||    |  |  |||      | ||     |||| |  |      |||  |  |||   || |    ||||||||||  || || || | ||||||||||||||||||||||||||| |||
cttgaaactctataaattcttctattaatcaatgttttttggtcctattgtgatagtagaaataactcattaatgtctccgatgagaaatgac-tttgcagGCGGATTAGTAAGAAAGAAAAATTGAAACGAGGAATATATGTGAGGCATTTCAAAAACATTCCAATGGCTGATATGGAAATTGTTCTT
















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|116480284|gb|EG522876.1|EG522876
EST:     AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAG                         GAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
genomic: AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAGgtacgaaagc ... acacacacagGAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
EST: gi|116481915|gb|EG524507.1|EG524507
EST:     AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAG                         GAGAGTCTCAGGGAAGAAGGAATCGGAAAGGAACATATATGTGAAACACTT
genomic: AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAGgtacgaaagc ... acacacacagGAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
EST: gi|116481924|gb|EG524516.1|EG524516
EST:     AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAG                         GAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
genomic: AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAGgtacgaaagc ... acacacacagGAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
EST: gi|116480243|gb|EG522835.1|EG522835
EST:     AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAG                         GAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
genomic: AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAGgtacgaaagc ... acacacacagGAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
EST: gi|116481923|gb|EG524515.1|EG524515
EST:     AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAG                         GAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
genomic: AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAGgtacgaaagc ... acacacacagGAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
EST: gi|116480191|gb|EG522783.1|EG522783
EST:     AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAG                         GAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
genomic: AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAGgtacgaaagc ... acacacacagGAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
EST: gi|116481912|gb|EG524504.1|EG524504
EST:     AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAG                         GAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
genomic: AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAGgtacgaaagc ... acacacacagGAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
EST: gi|116481910|gb|EG524502.1|EG524502
EST:     AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAG                         GAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
genomic: AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAGgtacgaaagc ... acacacacagGAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
EST: gi|116481921|gb|EG524513.1|EG524513
EST:     AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAG                         GAGAGTCTCAGGGAA
genomic: AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAGgtacgaaagc ... acacacacagGAGAGTCTCAGGGAA
EST: gi|116480267|gb|EG522859.1|EG522859
EST:     AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAG                         GAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
genomic: AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAGgtacgaaagc ... acacacacagGAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
EST: gi|116481918|gb|EG524510.1|EG524510
EST:     AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAG                         GAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
genomic: AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAGgtacgaaagc ... acacacacagGAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
EST: gi|116481916|gb|EG524508.1|EG524508
EST:     AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAG                         GAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
genomic: AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAGgtacgaaagc ... acacacacagGAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
EST: gi|116480218|gb|EG522810.1|EG522810
EST:     AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAG                         GAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
genomic: AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAGgtacgaaagc ... acacacacagGAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
EST: gi|116481922|gb|EG524514.1|EG524514
EST:     AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAG                         GAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
genomic: AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAGgtacgaaagc ... acacacacagGAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
EST: gi|116480168|gb|EG522760.1|EG522760
EST:     AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAG                         GAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT
genomic: AAGATAACCATCCAAGAGCCAACCTTTGAGAGAATCATTGTAGTATACAGgtacgaaagc ... acacacacagGAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttgtgagtttttgatctctcatcttgggtttggattctctctcacacacacagGAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTTTAAGACCATTCCAATGGCTGATATGGAAATTGTGCTT
                                        ctctcac  putative branch site (score: 3)
                                    ttctctctcac  CT-rich tract
         tttttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgaaagcagagcagtagtgtgatatttagagggttgtgagtttttgatctctcatcttgggtttggattctctctcacacacacagGAGAGTCTCAGGGAAGAAGGAATCAGAAAGGAACATATATGTGAAACACTTTAAGACCATTCCAATGGCTGATATGGAAATTGTGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT