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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttaaaacaacacttctcatatcatttgaattgaatcaacccagttagatctaaacctggtgatgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAGAGACGGTGCTGGGAAGCACCTTCAGGCTGGAGCCAAGAAGGTTCTTATC

Basic information

species Arabidopsis thaliana
transcript AT1G12900.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G12900.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G28240.1 (Glycine max), 3'ss of exon 3
gtaagttaaaacaacacttc--tcatatcatttgaattgaatcaacccagttagatcta-aacctggtgatgatgtt-tagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAGAGACGGTGCTGGGAAGCACCTTCAGGCTGGAGCCAAGAAGGTTCTTATC
|||||         || |||  |   |  | ||  | | |||      ||  ||   |  |||   ||| |  ||||  |||||  | || || ||||| || || ||||||||||| |||||||| |||||||| ||||| ||||| ||| |||| || ||||| |||||||| || |||
gtaagcctctttttcatttccatgcaactagttttactcaatttttgaagaaagtggtgtaactatgtgctattgttgcagGGACTTGGGGATAGACTTGGTGATTGAAGGAACCGGGGTGTTTGTAGACAGAGAAGGTGCAGGGAAACACATTCAAGCAGGAGCTAAGAAGGTGCTCATC

upper sequence: AT1G12900.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G07590.1 (Glycine max), 3'ss of exon 4
-------------------gtaagttaaaacaacacttctca-tatcatttgaatt---gaatcaacccagttagatctaaacctggtgatgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAGAGACGGTGCTGGGAAGCACCTTCAGGCTGGAGCCAAGAAGGTTCTTATC-
                   || | ||||   || | |  ||| | || | |  |||   ||| |||     | | ||  ||   |  |     | |  |||||  | |  || |||||  | || |||||||| ||||| ||||| |||||||||||||| || |||||| |||| || ||||| |||||| || | ||| 
aaacaaagcaacaaaacttgtcatttaactaaaaaataatcaatgtcttcttgatttctgaagcaatttgatgaaatgaaacaatattatctctttacagGGACTTGGAAATCGACTTT-TGATTGAAGGAACTGGAGTATTTGTGGACAGAGACGGTGCAGGAAAGCACATTCAAGCCGGAGCAAAGAAGATTTTGATCA

upper sequence: AT1G12900.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S86_156V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------------------------------------------------------------------------------gtaagttaaaacaacacttctcatatcatttgaattgaatcaacccagttagatctaaacctggtgatgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAGAGACGGTGCTGGGAAGCACCTTCAGGCTGGAGCCAAGAAGGTTCTTATC
                                                                                                     |||| ||| |||| ||| |  ||||  |||  |||     | ||        |     || ||||  |  | |||||  | | ||| ||  | || ||||| ||||||||||||||||| |||   | ||||||||| |||||| | ||||||||||||||||||||  | |||
gtaagtacgcgttgatgactctacccccggccattcgctgtaggatctcgtactgctcaattcctgtatgtcaatgtctcatttcaacctcacatccaccgagttgaaa-aacagttcacgaatca--tgagctgacagtgctcacacg---ttgttgttgttgatactcatcagGGACATGGACATCGATCTCGTCATCGAGGGAACCGGAGTGTTTGTGGACGAGGCCGGTGCTGGCAAGCACATCCAGGCTGGAGCCAAGAAGGTATTGATC

upper sequence: AT1G12900.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S86_156V6.2 (Physcomitrella patens), 3'ss of exon 3
---------gtaagttaaaacaacacttctcatatcatttgaattgaatcaacccagttagatctaaacctggt-gatgatgtttagGGAACTAGGCATTGACTTAGT---TATCGAAGGAACCGGAGTGTTTGTTGACAGAGACG-GTGCTGGGA-AGCACCTTCAGG-----CTGGAGC-CAAGAAGGTTCTTATC--
           | |  |    |    || |          |         | | ||   ||     | ||  |  | |  || | |  |  | |||||  |      |   || | | |     ||||||  ||   |     ||  |  ||  || | || | ||||      ||   || | |  |  | |||  |  
tctcgtcatcgagggaaccggagtgtttgtggacgaggccggtgctggcaagcacatccaggctggagccaagaaggtattgatcaccgctccaggcaagGGTCCCATCCCTACCTACGTGGTGGGAGTGAATGAGCAAGACTACAAGCACTCTGACACCATCATCAGCAACGCCTCCTGCACCACCAACTGCTTGGCAC

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|116408015|gb|EG450607.1|EG450607
EST:     AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGG                         GGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
genomic: AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
EST: gi|125312743|gb|EL326828.1|EL326828
EST:     AGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCGTGGGG                         GGAACTAGGCATTGAC
genomic: AGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCC-TGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGAC
EST: gi|125307950|gb|EL322035.1|EL322035
EST:     AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGG                         GGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTG
genomic: AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTG
EST: gi|125134688|gb|EL175429.1|EL175429
EST:     TATCTGATCGTAACCCATCTAATCTCCCCT-GGG                         GGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
genomic: TATCTGATCGTAACCCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
EST: gi|125194416|gb|EL209370.1|EL209370
EST:     CCATCTAATCTCCCCT-GGG                         GGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
genomic: CCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
EST: gi|124866170|gb|EH950607.1|EH950607
EST:     TCGTAACCCATCTAATCTCCCCTGGGG                         GGAACTAGGCATTGACCTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
genomic: TCGTAACCCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
EST: gi|124944734|gb|EL020807.1|EL020807
EST:     ATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGG                         GGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACA
genomic: ATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACA
EST: gi|125116731|gb|EL166154.1|EL166154
EST:     CTAATCTCCCCT-GGG                         GGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
genomic: CTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
EST: gi|124759772|gb|EH849902.1|EH849902
EST:     AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGG                         GGAACTAGGCATTGA
genomic: AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGA
EST: gi|125033313|gb|EL105582.1|EL105582
EST:     TTGTATCTGATCGTAACCCATCTAATCTCCCCT-GGG                         GGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
genomic: TTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
EST: gi|124744027|gb|EH835189.1|EH835189
EST:     TCGTAACCCATCTAATCTCCCCTGGGG                         GGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
genomic: TCGTAACCCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
EST: gi|125187108|gb|EL202062.1|EL202062
EST:     ATCGTAACCCATCTAATCTCCCCT-GGG                         GGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
genomic: ATCGTAACCCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
EST: gi|125253918|gb|EL268003.1|EL268003
EST:     AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCGTGGGG                         G-AACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGT
genomic: AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGT
EST: gi|125193074|gb|EL208028.1|EL208028
EST:     ACCCATCTAATCTCCCCT-GGG                         GGAACGTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACA
genomic: ACCCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAAC-TAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACA
EST: gi|116473086|gb|EG515678.1|EG515678
EST:     AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCCCCCCTGGGG                         GGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
genomic: AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
EST: gi|125281167|gb|EL295252.1|EL295252
EST:     AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGG                         GGAACTAGGCATTGACTTAGTTATCGAAG
genomic: AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAG
EST: gi|125164324|gb|EL191021.1|EL191021
EST:     AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGG                         G-AACTAGGCATTGACTTAGTT
genomic: AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGACTTAGTT
EST: gi|125125261|gb|EL170795.1|EL170795
EST:     AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGG                         G-AACTAGGCATTGACTTAGTTATCGAAGGAA
genomic: AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAA
EST: gi|124956509|gb|EL031424.1|EL031424
EST:     AGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCGTGGGG                         GGAACTAGGCATTG
genomic: AGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCC-TGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTG
EST: gi|116408023|gb|EG450615.1|EG450615
EST:     AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGG                         GGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
genomic: AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
EST: gi|125026061|gb|EL098330.1|EL098330
EST:     ACCCATCTAATCTCCCCT-GGG                         GGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
genomic: ACCCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
EST: gi|125192654|gb|EL207608.1|EL207608
EST:     CCCATCTAATCTCCCCTGGGG                         GGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
genomic: CCCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
EST: gi|125249588|gb|EL263673.1|EL263673
EST:     AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGG                         GGAACTAGGCATTG
genomic: AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTG
EST: gi|124762370|gb|EH852500.1|EH852500
EST:     ATCGTAACCCATCTAATCT-CCCTGGGG                         GGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
genomic: ATCGTAACCCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
EST: gi|125050737|gb|EL123006.1|EL123006
EST:     ATCGTAACCCATCTAATCTCCCCT-GGG                         GGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
genomic: ATCGTAACCCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
EST: gi|125015186|gb|EL087455.1|EL087455
EST:     AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGG                         G-AACTAGGCATTGACTTAGTTATCGAAG
genomic: AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAG
EST: gi|124784828|gb|EH874519.1|EH874519
EST:     AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGG                         GGAACTAGGCATTGACTT
genomic: AAGATCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGGgtaagttaaa ... tgatgtttagGGAACTAGGCATTGACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatcatttgaattgaatcaacccagttagatctaaacctggtgatgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAGAGACGGTGCTGGGAAGCACCTTCAGGCTGGAGCCAAGAAGGTTCTTATC
                              atctaaa  putative branch site (score: 3)
     atttgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttaaaacaacacttctcatatcatttgaattgaatcaacccagttagatctaaacctggtgatgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAGAGACGGTGCTGGGAAGCACCTTCAGGCTGGAGCCAAGAAGGTTCTTATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG