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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatataatatggtttctcttgtaatgatatctttcgtttgtctctttcaaaaccatgactaatgttttcattcttggtctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAATGAGCTCATTAAGCAATTTAAAAGTCCTTTGCTTTTCCAGTCGCAACTC

Basic information

species Arabidopsis thaliana
transcript AT3G55440.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G55440.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv13s0019g01090.t01 (Vitis vinifera), 3'ss of exon 8
------gtacatataatatggtttctcttgtaatg-atatctttcgtttgtctctt--tcaaaaccatgactaatgttttcattcttggtctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAATGAGCTCATTAAG-CAATTTAAAAGTCCTTTGC--TTTTCCAGTCGCAACTC
       ||    |  | |  || |  |||   |    || || |   ||  | ||  |       ||||   || |  |  | | |   |  | | |||||||||||||| ||||| || ||| |||| ||||||||||||| |   |  | ||||   || | | | | |  ||     ||    |||  ||  |    | 
gtagtgatattctttttgtttttgcctttgcccttcgcattttcctcatggttgttggttgggctgatgagatatttgatgctccctctcccctctacagCCTGAGTTTATTGACATTATCAAGTCCGCCGAGGTGAAGAAAAAT---TGCTAAGCTTGGTACGACGAATGAGTAGCTGAGTGAGACTTTGAAGCTGTGGGTT
















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|86079485|gb|DR375242.1|DR375242
EST:     GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
genomic: GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
EST: gi|163987864|gb|EL987853.1|EL987853
EST:     CTTCTCTAAAG                         CCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
genomic: CTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
EST: gi|116470932|gb|EG513524.1|EG513524
EST:     GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
genomic: GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
EST: gi|164204407|gb|ES121298.1|ES121298
EST:     GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGACATCATTAAGGCCG
genomic: GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCG
EST: gi|164191674|gb|ES137039.1|ES137039
EST:     CGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTAAGCCT
genomic: CGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGT--GCCT
EST: gi|164101449|gb|ES110820.1|ES110820
EST:     ACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
genomic: ACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
EST: gi|125120736|gb|EL168301.1|EL168301
EST:     GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGACATCATTAAGGCCGCAGAGG
genomic: GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGG
EST: gi|86078618|gb|DR374375.1|DR374375
EST:     GTGGA--GGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
genomic: GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
EST: gi|124880978|gb|EH959880.1|EH959880
EST:     GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGA
genomic: GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGA
EST: gi|164222366|gb|ES089693.1|ES089693
EST:     GTCGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
genomic: GTCGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
EST: gi|116443935|gb|EG486527.1|EG486527
EST:     GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
genomic: GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
EST: gi|116443947|gb|EG486539.1|EG486539
EST:     GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGACATCGTTAAGGCCGCAGAGGTGAAGAAAAGTGCC
genomic: GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCC
EST: gi|116443934|gb|EG486526.1|EG486526
EST:     GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGACATCAT
genomic: GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCAT
EST: gi|124890633|gb|EH969535.1|EH969535
EST:     GGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
genomic: GGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
EST: gi|86081436|gb|DR377193.1|DR377193
EST:     GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
genomic: GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
EST: gi|116470943|gb|EG513535.1|EG513535
EST:     GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
genomic: GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
EST: gi|116483114|gb|EG525706.1|EG525706
EST:     GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
genomic: GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
EST: gi|116470942|gb|EG513534.1|EG513534
EST:     GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
genomic: GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
EST: gi|124912287|gb|EH986367.1|EH986367
EST:     GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGACATCATTAAGGCCGCAGAGG
genomic: GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGG
EST: gi|124933258|gb|EL010434.1|EL010434
EST:     GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGACATCATTAAGGCCG
genomic: GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCG
EST: gi|164086420|gb|ES132395.1|ES132395
EST:     CGGTGGTGCTTCTCT-AAG                         CCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
genomic: CGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
EST: gi|124880217|gb|EH959119.1|EH959119
EST:     GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
genomic: GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
EST: gi|116470931|gb|EG513523.1|EG513523
EST:     GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
genomic: GTGGACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
EST: gi|125311782|gb|EL325867.1|EL325867
EST:     TGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
genomic: TGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
EST: gi|124748142|gb|EH838272.1|EH838272
EST:     ACAGGCCGATGTTGATGG-TTCTTGGTCGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAA
genomic: ACAGGCCGATGTTGATGGTTTCTTGGTCGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAA
EST: gi|125112726|gb|EL163778.1|EL163778
EST:     TGGTTTCTTGGTCGGTGGTGCTTCTCTAAAG                         CCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA
genomic: TGGTTTCTTGGTCGGTGGTGCTTCTCTAAAGgtacatataa ... ctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtttgtctctttcaaaaccatgactaatgttttcattcttggtctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAATGAGCTCATTAAGCAATTTAAAAGTCCTTTGCTTTTCCAGTCGCAACTC
                       gactaat  putative branch site (score: 2)
                                     ttcttggtcttttt  putative PPT
                          taatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatataatatggtttctcttgtaatgatatctttcgtttgtctctttcaaaaccatgactaatgttttcattcttggtctttttgcagCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTAATGAGCTCATTAAGCAATTTAAAAGTCCTTTGCTTTTCCAGTCGCAACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA