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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtagttttcttacacgaaagaaattttttgtttctagacacaaaaaagtttctcacgtcacttttttctggttgcagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACTGGATTGGACCTAGGATGGATTTCATCCCTGGCATTGATGGTCCTAGCGA

Basic information

species Arabidopsis thaliana
transcript AT1G08200.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 4
gtatgtagttttcttacacgaaagaaattttttgtttctagacacaa----aaaagtttctcacgtcacttttttctggttg----cagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACTGGATTGGACCTAGGATGGATTTCATCCCTGGCATTGATGGTCCTAGCGA
              |    | |  || |||| |  |||  | ||  |    || | ||| | ||       ||||   | |     ||||||| || || || ||||| || |||||||| ||||| ||||| ||||| ||||||||||| || ||||| || || |||||  ||||||||||||| ||
-------------gtgagtgcagtaacttttgttattcatgtcattacctgaacactttgtaaccgtgtgctttttgagctttaaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGA

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 4
---------gtatgtagtt-ttcttacacgaaagaaattttttgtttctagacacaaaaaagtttctcacgtcacttttttctgg------ttgcagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACTGGATTGGACCTAGGATGGATTTCATCCCTGGCATTGATGGTCCTAGCGA
          ||  | ||| || || |      | |  |  | || |     | |     | ||  |   |||| |||||| | |         ||||||| ||||| || ||||| || || ||||| || || ||||| ||||| ||||||||||| |||||||| ||||| |||||  ||||||||||||| ||
gttagtaaattagcttgttatttttgccactgtgtagctgatggtcttccttctcgttttaattattattgtcatttttttattgaacatccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGA

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G167872_T02 (Zea mays), 3'ss of exon 2
-------gtatgtagttttct--tacacgaaagaaattttttgtttctagacacaaaaaagtttctcacgtcacttttttctggttg-----cagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACTGGATTGGACCTAGGATGGATTTCATCCCTGGCATTGATGGTCCTAGCGA
       |  |  | ||||    |   |    ||     ||  | |    ||||        |  |   |||| |||  | ||  |      ||||||||||||| || ||||| || || ||||| || || ||||| || || |||||||| || |||||||||||||| |||||  | ||||||||||| ||
gtcagtagagtaaaattttgcactgtgccgctgatggccttcttgttctaacacttcttttatgtttttgtcattttgatttgagtatctgccagCTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTAATTGGATTGGGCCAAGGATGGATTTCATTCCTGGTGTCGATGGTCCTAGTGA

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 4
--------gtatgtagttttcttacacgaaagaaattttttgtttctagacacaaaaaagtttctcacgtcacttttttctggttgcagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACTGGATTGGACCTAGGATGGATTTCATCCCTGGCATTGATGGTCCTAGCGA
         | |||| ||||  |    |    |  ||||||  ||  |      | ||   |||| || |    | |        ||||||||||||||||| |||||  | |||||||| |||||||| ||||| ||||||||||||||| | ||||||||||| ||||| ||||||||||| || ||
gtgagttgatttgtattttttgttt-tggtgtatgtttttttctttcaattttgataa---ttcttac-tagtgtgtgatcatcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACTGGATTGGACCTCGAATGGATTTCATTCCTGGGATTGATGGTCCAAGTGA

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G08930.1 (Glycine max), 3'ss of exon 4
----gtatgtagtt-ttcttacacgaaagaaattttttgtttctagacacaaaaaagt---ttctcacgtcacttttttctggttgcagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACTGGATTGGACCTAGGATGGATTTCATCCCTGGCATTGATGGTCCTAGCGA
    || |  | || || ||        |   |||||| |||       |||    ||   ||||||| | |  | |   |  | ||||||||||||||||| |||||  | |||||||| ||||| || || || ||||||||||||||| | ||||||||||| ||||||||||||||||| || ||
gtgagttttgatttgtttttgtttaggtgttgtttttttttttctttttcaattttgttaattctcac-tgatgtgtgattattggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTGAGGCCTTTTAACTGGATTGGACCTCGAATGGATTTCATTCCTGGCATTGATGGTCCAAGTGA

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G05440.1 (Glycine max), 3'ss of exon 2
-----------gtatgtagttttcttacacgaaagaaattttttgtttctagacacaaaaaagtttctcacgtcacttttttctggttgcagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACTGGATTGGACCTAGGATGGATTTCATCCCTGGCATTGATGGTCCTAGCGA
            | | | ||||  ||      |    || |  |||||| |       |    | |||||| | |  |     || | ||||||||||||||||| |||||  | || ||||| ||||| ||||| || || |||||||||||  | ||||||||||| || |||||||||||||| || ||
gtgagctgcttttgtttggtttaatttttt--attgcatatactgtttccatgtcttgacctttgtctcac-tgagatgacattgttggcagCTGAGGGTGCTGAAAATGGCTTGGAATTCACAATTGTGAGACCTTTTAATTGGATTGGACCACGAATGGATTTCATTCCCGGCATTGATGGTCCAAGTGA

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G30490.2 (Glycine max), 3'ss of exon 4
----------------gtatgtagttttcttacacgaaagaaattttt-tgtttctagacacaaaaaagtttctcacgtcacttttttctggttgcagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACTGGATTGGACCTAGGATGGATTTCATCCCTGGCATTGATGGTCCTAGCGA
                   | || |||| |    || |     |||   | |||  |       |    | |||||| | |  |     || | ||||||||||||||||| |||||  | || ||||| ||||| || || || || |||||||||||  | ||||||||||| || ||||||||||| || || ||
gtgagctgattttgtttggtttaattttttattgcgtacactgtttccattttttcatgtcttgacctttgtctcac-tgagatgacattgttggcagCTGAGGGTGCTGAAAATGGCTTGGAATTCACAATTGTGAGGCCTTTTAATTGGATTGGACCACGAATGGATTTCATTCCCGGCATTGATGGCCCAAGTGA

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 3'ss of exon 4
--gtatgtagttttcttacacgaaagaaattttttg---tttctagaca-caaaaaagtttctcacgtcacttttttctggttg----cagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACTGGATTGGACCTAGGATGGATTTCATCCCTGGCATTGATGGTCCTAGCGA
  |  || | |||||   |       |  ||| ||    |   |    | || | |   ||||||  |   |||||| |  |||    |||||||||||||||||||||  || |||||||||||||| || || || ||||||||||| || || |||||||| || |||||||||||||||||||||||
gtgagtgaacttttccatcgatctgtacgtttcttagcatgcgtgtgtatcatacatccttctcatttttattttttttcattgtttacagCTGAGGGTGCTGAGAATGACCTAGAGTTCACCATTGTGAGGCCCTTTAACTGGATTGGGCCCAGAATGGATTTTATTCCTGGCATTGATGGTCCTAGCGA

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 4
--gtatgtagttttcttacacgaaagaaatttttt-----gtttctagacacaaaaaagtttctcacgtcacttttttc-----tggttgcagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACTGGATTGGACCTAGGATGGATTTCATCCCTGGCATTGATGGTCCTAGCGA
  |  |  | |||||   ||     ||  ||| ||     |  ||| | | || | |  ||||| |  |   |||| |      |  || ||||||| ||||| |||||||| || |||||||||||||| || || || ||||||||||| ||||| ||||||||||| |||||||||||||||||||| ||
gtgagtcaacttttccatcaatctggatgtttcttaacatgcatct-gtctcatagatctttctaattttttttttattattattatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACTGGATTGGGCCTAGAATGGATTTCATTCCTGGCATTGATGGTCCTAGTGA

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S379_19V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------------------------gtatgtagttttcttacacgaaaga-----aattttttgtttctag-acacaaaaaagtttctc----------acgtcacttttttctggttgcagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACTGGATTGGACCTAGGATGGATTTCATCCCTGGCATTGATGGTCCTAGCGA
                                                                        || ||||  ||   |  | |   |      | |||| ||    |   ||||||    |||  |             |   | ||| | |   || || ||| || |||||||||||| |  |||||||||| ||  ||||||||||||||||||| ||  | ||||||||||| || |||||||| || || || ||
gtacgaaattaatcccgacattgttcctcctagctcaagtttctaaattcgggagtggaactgaaatatggggtctgtaaattgactctaggtttgttgtctagttttctgccattgtcacacaattgtgttggttcgttgtagtggtgaagcatttattttcgtgtagGTGAAGGAGCTGAGAATGGAATGAAGTTCACCATAGTTCGACCATTCAACTGGATTGGCCCACGCATGGATTTCATACCAGGCATTGACGGACCAAGTGA

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|116456216|gb|EG498808.1|EG498808
EST:     GAGGTGGTCACATGCTTGTGCAAAGCAACTTATTGAGAGACTTGTTTACG                         CTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACT
genomic: GAGGTGGTCATATGCTTGTGCAAAGCAACTTATTGAGAGACTTGTTTACGgtatgtagtt ... ctggttgcagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACT
EST: gi|116471821|gb|EG514413.1|EG514413
EST:     GAGGTGGTCATATGCTTGTGCAAAGCAACTTATTGAGAGACTTGTTTACG                         CTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACT
genomic: GAGGTGGTCATATGCTTGTGCAAAGCAACTTATTGAGAGACTTGTTTACGgtatgtagtt ... ctggttgcagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACT
EST: gi|124958977|gb|EL033685.1|EL033685
EST:     GAGGTGGTCATATGCTTGTGCAAAGCAACTTATTGAGAGACTTGTTTACG                         CTAGAGGGTGCTGAGAATGGACTCGAGTT
genomic: GAGGTGGTCATATGCTTGTGCAAAGCAACTTATTGAGAGACTTGTTTACGgtatgtagtt ... ctggttgcagCT-GAGGGTGCTGAGAATGGACTCGAGTT
EST: gi|125293142|gb|EL307227.1|EL307227
EST:     ATTGAGAGACTTGTTTACG                         CTGAGGGTGCTGAGAATGGACTCGAGTTCA
genomic: ATTGAGAGACTTGTTTACGgtatgtagtt ... ctggttgcagCTGAGGGTGCTGAGAATGGACTCGAGTTCA
EST: gi|125324800|gb|EL338880.1|EL338880
EST:     GAGGTGGTCATATGCTTGTGCAAAGCAACTTATTGAGAGACTTGTTTACG                         CTGAGGGTGCTGAGAATGG
genomic: GAGGTGGTCATATGCTTGTGCAAAGCAACTTATTGAGAGACTTGTTTACGgtatgtagtt ... ctggttgcagCTGAGGGTGCTGAGAATGG
EST: gi|116456222|gb|EG498814.1|EG498814
EST:     GAGGTGGTCATATGCTTGTGCAAAGCAACTTATTGAGAGACTTGTTTACG                         CTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACT
genomic: GAGGTGGTCATATGCTTGTGCAAAGCAACTTATTGAGAGACTTGTTTACGgtatgtagtt ... ctggttgcagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACT
EST: gi|164236838|gb|ES032543.1|ES032543
EST:     TATGCTTGTGCAAAGCAACTTATAGAGAGACTTGTTTACG                         CTGAGGGTGCTGAGAATGGACTCGAGTTCAC
genomic: TATGCTTGTGCAAAGCAACTTATTGAGAGACTTGTTTACGgtatgtagtt ... ctggttgcagCTGAGGGTGCTGAGAATGGACTCGAGTTCAC
EST: gi|125194014|gb|EL208968.1|EL208968
EST:     GAGGTGGTCATATGCTTGTGCAAAGCAACTTATTGAGAGACTTGTTTACG                         CTGAGGGTGCTGAGAATGGACTCGAGTT
genomic: GAGGTGGTCATATGCTTGTGCAAAGCAACTTATTGAGAGACTTGTTTACGgtatgtagtt ... ctggttgcagCTGAGGGTGCTGAGAATGGACTCGAGTT
EST: gi|124739961|gb|EH831123.1|EH831123
EST:     GAGGTGGTCATATGCTTGTGCAAAGCAACTTATTGAGAGACTTGTTTACG                         CTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATT
genomic: GAGGTGGTCATATGCTTGTGCAAAGCAACTTATTGAGAGACTTGTTTACGgtatgtagtt ... ctggttgcagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATT
EST: gi|124705052|gb|EH796454.1|EH796454
EST:     AGACTTGTTTACG                         CTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACT
genomic: AGACTTGTTTACGgtatgtagtt ... ctggttgcagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACT
EST: gi|116456221|gb|EG498813.1|EG498813
EST:     GAGGTGGTCATATGCTTGTGCAAAGCAACTTATTGAGAGACTTGTTTACG                         CTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACT
genomic: GAGGTGGTCATATGCTTGTGCAAAGCAACTTATTGAGAGACTTGTTTACGgtatgtagtt ... ctggttgcagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACT
EST: gi|116456217|gb|EG498809.1|EG498809
EST:     GAGGTGGTCACATGCTTGTGCAAAGCAACTTATTGAGAGACTTGTTTACG                         CTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACT
genomic: GAGGTGGTCATATGCTTGTGCAAAGCAACTTATTGAGAGACTTGTTTACGgtatgtagtt ... ctggttgcagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttttgtttctagacacaaaaaagtttctcacgtcacttttttctggttgcagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACTGGATTGGACCTAGGATGGATTTCATCCCTGGCATTGATGGTCCTAGCGA
                           ttctcac  putative branch site (score: 2)
                          tttctcacgtcacttt  CT-rich tract
                   aaaaaagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtagttttcttacacgaaagaaattttttgtttctagacacaaaaaagtttctcacgtcacttttttctggttgcagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACTGGATTGGACCTAGGATGGATTTCATCCCTGGCATTGATGGTCCTAGCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA