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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatttaattttgacaaagttcttaaattttggaagatttctacactcttgagttactcacttaggtttgatgttgttgttgttgttaattctttgggcagGCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATCACTACAGTAGAAATCGATGACGAGACATATGAAGAGATTGTTCGG

Basic information

species Arabidopsis thaliana
transcript AT1G76860.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G76860.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G28300.1 (Glycine max), 3'ss of exon 1
aatttaattttgacaaagttcttaaattttggaagatttctacactcttgagttactcacttaggtttgatgttgttgttgttgttaattctt--tgggcagGCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATCACTACAGTAGAAATCGATGACGAGACATATGAAGAGATTGTTCGG
 | ||   || |  |   || | |  ||||  || ||   |    |  | ||| | |  | |   | | || |||   | | | || | | |   |  |||||| | |||||||||| | ||||||||||| |||||||||||||||| | | |||||||| ||||||||||| |||||||| ||||| |||||  ||
-agttcccttggtgattattttgatcttttaaaatatcgttggcttgataagt-attttcctttttcttattttgcactgggttttcaatttgaatttgcagGCTTATGATCAGCATCTTAATATGATTCTTGGTGATGTTGAAGAAATTGTTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG

upper sequence: AT1G76860.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G09090.1 (Glycine max), 3'ss of exon 1
aatttaattttgacaaagttcttaaattttggaagatttctacactcttgagttactcacttaggtttgatgttgttgttg--ttgttaattctttgggcagGCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATCACTACAGTAGAAATCGATGACGAGACATATGAAGAGATTGTTCGG
 |  |    |||   |   | || |  |||  || |||||     | |    ||  |        | | || ||||  | |  ||  || ||   |  | |||| | |||||||||| | ||||||||||| || |||||||||||||  || |||||||| ||||||||||| |||||||| ||||| |||||  ||
-aagtgcccttggtgattattttgatcttttaaa-atttcgttggtttgatattgattttccttttcttattttgtactgggttttctatttgggtttgtagGCTTATGATCAGCATCTTAATATGATTCTTGGCGATGTTGAAGAAATCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG

upper sequence: AT1G76860.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv18s0072g00710.t01 (Vitis vinifera), 3'ss of exon 1
---aatttaattttgacaaagttcttaaattttggaagatttctacactcttgagttactcacttaggtttgatgttgttgttgttgttaattct--ttgggcagGCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATCACTACAGTAGAAATCGATGACGAGACATATGAAGAGATTGTTCGG
    |   | ||| |||  | || ||| ||     ||||  | | || || |     | | || || ||||  | ||  ||| |||    | |||  ||   ||||| | ||||||||||||||| |||||||| |||||||||||||||| | | ||||||||||||||||| || || || |||||||| |||||||| 
aaccaaaaagtttggacttatttattacataaca-aagaagtttgcaatcct----cattaacatatgtttcttctttgtgtggtttggcaatctggtttttcagGCCTATGATCAGCATTTGAACATGATTCTTGGTGATGTTGAAGAAATTGTTACTACAGTAGAAATCGACGATGAAACTTATGAAGAAATTGTTCGA

upper sequence: AT1G76860.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S16_329V6.1 (Physcomitrella patens), 3'ss of exon 1
-----aatttaattttgacaaagttcttaaattttggaagatttctacactcttgagttactcacttaggtttgatgttgttgttgttgttaattctttgggcagGCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATCACTACAGTAGAAATCGATGACGAGACATATGAAGAGATTGTTCGG
           | |||| ||   |  ||||| | | ||   ||     |   ||||   | |  |   | |     ||  || ||    || | |  ||| |||||| |  |||||||| ||||| |||||||| ||||| || || |||  || |||| | ||||| |||||||||||||| ||||| ||||||||  ||
tatgccggccgactttg-cattttcattaaagtattgattgttgtagtat--ttgaagcagtttccctgctggcgggtccttatta--attgaatgattgtgcagGCCTACGATCAGCACTTGAACATGATTCTTGGTGAGGTGGAGGAAGTTACCACTTCGGTAGAGATCGATGACGAGACTTATGAGGAGATTGTGAGG

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|86022362|gb|DR318115.1|DR318115
EST:     GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGC-GCAAGCTTCAC                         GCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
genomic: GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCGGCAAGCTTCACgtacgttttc ... ctttgggcagGCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
EST: gi|86022363|gb|DR318116.1|DR318116
EST:     GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCG-CAAGCTTCAC                         GCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
genomic: GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCGGCAAGCTTCACgtacgttttc ... ctttgggcagGCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
EST: gi|86022365|gb|DR318118.1|DR318118
EST:     GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCG-CAAGCTTCAC                         GCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
genomic: GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCGGCAAGCTTCACgtacgttttc ... ctttgggcagGCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
EST: gi|86077880|gb|DR373637.1|DR373637
EST:     GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCGGCAAGCTTCAC                         GCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
genomic: GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCGGCAAGCTTCACgtacgttttc ... ctttgggcagGCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
EST: gi|86081372|gb|DR377129.1|DR377129
EST:     GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCGGCAAGCTTCAC                         GCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
genomic: GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCGGCAAGCTTCACgtacgttttc ... ctttgggcagGCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
EST: gi|86022357|gb|DR318110.1|DR318110
EST:     GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGC-GCAAGCTTCAC                         GCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
genomic: GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCGGCAAGCTTCACgtacgttttc ... ctttgggcagGCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
EST: gi|86022361|gb|DR318114.1|DR318114
EST:     GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCGCCAAGCTTCAC                         GCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
genomic: GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCGGCAAGCTTCACgtacgttttc ... ctttgggcagGCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
EST: gi|86022367|gb|DR318120.1|DR318120
EST:     GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGC-GCAAGCTTCAC                         GCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
genomic: GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCGGCAAGCTTCACgtacgttttc ... ctttgggcagGCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
EST: gi|152038489|gb|AV824231.2|AV824231
EST:     GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCGGCAAGCTTCAC                         GCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
genomic: GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCGGCAAGCTTCACgtacgttttc ... ctttgggcagGCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
EST: gi|86022358|gb|DR318111.1|DR318111
EST:     GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGC-GCAAGCTTCAC                         GCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
genomic: GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCGGCAAGCTTCACgtacgttttc ... ctttgggcagGCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
EST: gi|86022366|gb|DR318119.1|DR318119
EST:     GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCGM-AAGCTTCAC                         GCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
genomic: GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCGGCAAGCTTCACgtacgttttc ... ctttgggcagGCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
EST: gi|86022364|gb|DR318117.1|DR318117
EST:     GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCG-CAAGCTTCAC                         GCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
genomic: GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCGGCAAGCTTCACgtacgttttc ... ctttgggcagGCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
EST: gi|86022360|gb|DR318113.1|DR318113
EST:     GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCGGCAAGCTTCAC                         GCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
genomic: GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCGGCAAGCTTCACgtacgttttc ... ctttgggcagGCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
EST: gi|86022359|gb|DR318112.1|DR318112
EST:     GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGC-GCAAGCTTCAC                         GCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
genomic: GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCGGCAAGCTTCACgtacgttttc ... ctttgggcagGCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
EST: gi|86022368|gb|DR318121.1|DR318121
EST:     GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGC-GCAAGCTTCAC                         GCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC
genomic: GAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCGGCAAGCTTCACgtacgttttc ... ctttgggcagGCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgagttactcacttaggtttgatgttgttgttgttgttaattctttgggcagGCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATCACTACAGTAGAAATCGATGACGAGACATATGAAGAGATTGTTCGG
                                           ttcttt  CT-rich tract
                                       ttaattcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatttaattttgacaaagttcttaaattttggaagatttctacactcttgagttactcacttaggtttgatgttgttgttgttgttaattctttgggcagGCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATCACTACAGTAGAAATCGATGACGAGACATATGAAGAGATTGTTCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - -gacaaag
- - - - - - - - - - - - -attttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtttga