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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttggtacttggttggttatagatacagtttttggtattgagaaaatcgtatataatactcttcttgaagtaacaatcattggtaatttttcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG

Basic information

species Arabidopsis thaliana
transcript AT5G55160.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G55160.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G082390_T02 (Zea mays), 3'ss of exon 1
gttggtacttggttggttatagataca-gtttttggtattgagaaaatcgtatataatactcttcttgaag--taacaatcattggtaatttttcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG
 ||     |    | |  |  | ||||   ||||| ||| |  ||  ||   | | ||      |||||    |  | ||| ||  ||||  |  |||| |||||||| ||||| || |||||| | || |||||   ||| ||||| || || |||||||| ||||| |||||||| |||||||||||  | ||  | ||||
-ttacatgtcatattgaaaaggttacacacttttgatatcgc-aatctcaagtgttatctgtcacttgactcttttccatcttta-taataataattgtatagGATGGCAATGAGGTGTTCTTTCGCATAAAGAGGTCCACCCAGCTGAAGAAGCTGATGAACGCTTATTGTGACCGCCAGTCTGTGGACATGAATGCCATTG

upper sequence: AT5G55160.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G46500.2 (Glycine max), 3'ss of exon 1
gttggtacttggttggttatagatacagtttttggtat-tgagaaaatcgtatataatactcttcttgaag---taacaatcattggtaattt-ttcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG
     ||||   ||      |  |     | |    || | |    ||  |||     | | |  ||  |    |  ||    || ||  ||   | ||||||||||||||||||| || ||||||||||| || ||||||||||||||||| ||||| |||||||| |||||||| ||||| ||||| ||||| ||||||||||
-----tactatctttaacccaactgattatctcacaatataaatttattttatgggggaatttctttacaaatttttcatctttttgtggttgacttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTTATGAATGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG

upper sequence: AT5G55160.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G35450.1 (Glycine max), 3'ss of exon 1
---gttggtacttggttggttata------gatacagtttttggtattgagaaaatcgtatataatactcttcttgaagtaacaatcattggtaatttttcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG
    |    ||     ||  | ||       ||| |  |||   | ||| |  |||  | | ||  | | |||       | |  |   ||||    ||| ||||  ||||||| ||||| || ||||||||||| || ||||||||||||||||| ||||||||||| || |||||||| ||||| ||||| ||||| ||||||||||
actatcttaacccaactgactttatctcacaatataaatttattttttgggggaatt-tctttacaaattttcc------atctttttgtggttgacttttttgt--agGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTGATGAACGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG

upper sequence: AT5G55160.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv00s0186g00020.t01 (Vitis vinifera), 3'ss of exon 1
---gttggtacttggttggttatagatacagtttttggtattgagaaaatcgtatataatactcttcttgaagtaacaatcattggtaatttttcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG
   | ||   ||      ||| |   | ||  |  | | |||   |    |  |    | |      ||   |||| |||  ||  |  || |  |||  ||||||||||| || || |||||||||||||| |||||||| ||| |    || || |||  |||||| ||||| || ||||| ||||| || ||||| ||||
atggatgactctcctcctgttttcttttcaactcctagcattcccattcccccaccccacaagtgaatttttgtaa-aatttttatt--ttgtggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTATTGTGATCGACAGTCAGTGGAGTTAAACTCCATTG

upper sequence: AT5G55160.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv12s0059g01310.t01 (Vitis vinifera), 3'ss of exon 1
----gttggtacttggttggttatagatacagtttttggtattgagaaaatcgtatataatactcttcttgaagtaacaatcattggtaatttttcttgt-gtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG
    |   || ||  |    ||     || |  | |   | ||   |   |  ||     |   ||     |  | || |  ||  ||  | ||| || | | ||||||| |||||||| ||||| |||||||| |||||||| ||||| || || || ||||||||||| |||||||| || ||||| ||  ||||||| ||||
gggagcaagttctaag--aatttggactaaaaatatctctgtttgcagtttgcta---ggtttcctggacaagatgacgaggatgtgttgtgttttttattgcagGATGGGAATGAAGTTTTCTTCAGGATCAAAAGAAGCACACAGCTGAAGAAGCTCATGAATGCTTATTGTGACCGACAATCTGTAGACCTCAACTCGATTG

upper sequence: AT5G55160.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv00s0186g00080.t01 (Vitis vinifera), 3'ss of exon 1
----gttggtacttggttggttatagatacagtttttggtattgagaaaatcgtatataatactcttcttgaagtaacaatcattggtaatttttcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG
    | | || ||    | ||| |   | ||  ||     |||   |   | |||    | |      ||    ||| |    ||  |  || |  |||||||||||||||| || || |||||||||||||| |||||||| ||| |    || || |||  |||||||||||| |||||||| ||||| || ||||| ||||
tatggatagttctgctcttgttttcttttcaacttccaccattcccatccttgtaccccacaagtgaatttttttaaaa--tgttctt--ttctggttgtgtagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTACTGTGATCGTCAGTCAGTGGAGTTAAACTCCATTG

upper sequence: AT5G55160.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S61_57V6.1 (Physcomitrella patens), 3'ss of exon 1
gttggtacttggtt-----ggttatagatacagtttttggtattgagaaaatcgtata-taatactcttcttgaagtaacaatcattggtaatttttcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG
||||| ||    ||     || || |  ||  ||   || |  |  | ||     | | |||||   |   |||  | || |        |||   | || ||||||||||    || || |||||||||||||| || |   |     |    || |||||||| |||||||||||||| ||||||||||||     ||| ||||
gttggcacgctttttcaagggataaaactaaggtgcctgttggtatgcaatatacagaataatatgttctgtgagctgacga------aaaatcagtgttttgtagGATGGAGGGGAGGTGTTCTTTAGGATCAAAAGCACTGCCACTTTGCGCAAGCTGATGAACGCTTACTGTGACCGCCAGTCTGTGGATCCTTCCTCTATTG

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|152038446|gb|AV823309.2|AV823309
EST:     ACAAGAAGCCTGACCAAGGAGCTCACGTCAATCTCAAAGTCAAGGGACAG                         GATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAA
genomic: ACAAGAAGCCTGACCAAGGAGCTCACATCAATCTCAAAGTCAAGGGACAGgttttctatt ... tcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAA
EST: gi|116475081|gb|EG517673.1|EG517673
EST:     ACAAGAAGCCTGACCAAGGAGCTCACATCAATCTCAAAGTCAAGGGACAG                         GATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAA
genomic: ACAAGAAGCCTGACCAAGGAGCTCACATCAATCTCAAAGTCAAGGGACAGgttttctatt ... tcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAA
EST: gi|86076387|gb|DR372144.1|DR372144
EST:     ACWAGAAGCCTGACCAAGGAGCTCACATCAATCTCAAAGTCAAGGGACAG                         GATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAA
genomic: ACAAGAAGCCTGACCAAGGAGCTCACATCAATCTCAAAGTCAAGGGACAGgttttctatt ... tcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAA
EST: gi|116456891|gb|EG499483.1|EG499483
EST:     ACAAGAAGCCTGACCAAGGAGCTCACATCAATCTCAAAGTCAAGGGACAG                         GATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAA
genomic: ACAAGAAGCCTGACCAAGGAGCTCACATCAATCTCAAAGTCAAGGGACAGgttttctatt ... tcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAA
EST: gi|164118792|gb|ES036150.1|ES036150
EST:     TCAATCTCAAAGTCAAGGGACAG                         GATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAA
genomic: TCAATCTCAAAGTCAAGGGACAGgttttctatt ... tcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAA
EST: gi|86082102|gb|DR377861.1|DR377861
EST:     ACAAGAAGCCTGACCAAGGAGCTCACATCAATCTCAAAGTCAAGGGACAG                         GATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAA
genomic: ACAAGAAGCCTGACCAAGGAGCTCACATCAATCTCAAAGTCAAGGGACAGgttttctatt ... tcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgtatataatactcttcttgaagtaacaatcattggtaatttttcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG
                      aagtaac  putative branch site (score: 2)
                                         tttttcttgt  putative PPT
                                      taatttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtacttggttggttatagatacagtttttggtattgagaaaatcgtatataatactcttcttgaagtaacaatcattggtaatttttcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG

- - - - - - - - - - agataca
- - - - - - - - - - - - - -gtttttg
- - - - - - - - - - - - - - - - - - - - -gaaaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaatca