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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcccctcgtagatttagttgattctatgttaattcacactagagaaacagagtttgtgtctactacttggttatgatctgtgattgttgcgttctttagGTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTCTTGTTGTCCTCAACAG

Basic information

species Arabidopsis thaliana
transcript AT5G53560.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G53560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G074169_T01 (Zea mays), 3'ss of exon 1
agcccctcgtagatttagttgat-tctatgttaattcacactagagaaacagagtttgtgtctactacttggttatgatctgtgattg--ttgcgtt----ctttagGTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTCTTGTTGTCCTCAACAG
        ||  ||||  || || |     | ||     | || |  |    | |||      | |  ||    |  || ||| ||    ||   ||     || ||||||||||||| ||||| || |||||||| |||||||| || ||||| || ||| |  |   ||| |
-------tgtttattttattaatatactcataaaaatggaataaatcattgaaattttctgtcatttgttttccaatatgtgttatctctttctattaacatttcagGTGTATGATGTCACTCCTTTTATGGATGAGCATCCTGGTGGAGATGAGGTTTTGCTAGCTGTAACTG

upper sequence: AT5G53560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G41010.2 (Glycine max), 3'ss of exon 2
agcccctcgtagatttag----ttgattctatgttaattcacactagagaaacagagtttgtgtctactacttggttatgatctgtgattgttgcgttctttagGTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTCTTGTTGTCCTCAACAG
    |  ||||  ||| |    |   |||||  |  | |   | |   |  |    |||  | |||   |||     | | | |||| ||     | | || ||||||||||||| || || |||||||| |||||||| ||||| ||||| || ||||| ||  ||||||
--aactacgtaacttttgaatttcagttctagctcgagttctagttttgttatgatgttaatttctgtcactgaacaaagttatgtgctt-caatgatatt-agGTGTATGATGTCACCCCTTTCATGGAGGATCATCCCGGAGGTGATGAGGTTTTGTTATCTGCAACAG

upper sequence: AT5G53560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G41010.3 (Glycine max), 3'ss of exon 2
agcccctcgtagatttagttgattctatgttaattcacactagagaaacagagtttgtgtctactacttggttatgatctgtgattgttgcgttctttagGTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTCTTGTTGTCCTCAACAG
                                               |    |||  | |||   |||     | | | |||| ||     | | || ||||||||||||| || || |||||||| |||||||| ||||| ||||| || ||||| ||  ||||||
----------------------------------------------tatgatgttaatttctgtcactgaacaaagttatgtgctt-caatgatatt-aggtgtatgatgtcacccctttcatggaggatcatcccggaggtgatgagGTTTTGTTATCTGCAACAG

upper sequence: AT5G53560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G13840.2 (Glycine max), 3'ss of exon 2
agcccctcgtagatttagtt--gattctatgttaattcacactagagaaacagagtttgtgtctactacttggttatgatctgtgattgttgcgttctttagGTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTCTTGTTGTCCTCAACAG
| |  |       || | ||    |||||  || | |   | |   |  |    ||| || |||   |||     | | | |||| ||    |  | || ||||||||||||| || || |||||||| |||||||| ||||| ||||| || ||||| ||  ||||||
aactacataacttttgaatttcagttctagcttgagttctagttttgttatgacgttagtttctgtcactgaacaaagttgtgtgctt-caacaatatt-agGTGTATGATGTCACCCCTTTCATGGAGGATCATCCCGGAGGTGATGAGGTTTTGTTATCTGCAACAG

upper sequence: AT5G53560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv16s0098g01230.t01 (Vitis vinifera), 3'ss of exon 2
agcccctcgtagatttagttgattctatgttaattcacactagagaaacagagtttgtgtctactacttggttatgatctgtgattgttgcgttcttt------agGTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTCTTGTTGTCCTCAACAG
     |  | |  |||   || |   ||  |  |  |   | | ||        |  | | |   | ||| | || |  | | |   |  |  ||| |      ||||||||||||| ||||| ||||||||||||||||||||||| |||||||| ||| | ||  |||| |
-----cctgcaattttgaatg-tgacatagttttggatgttggtgactttattctattctatttaatttgttgataaaattttaaaatctccatctattgtaacagGTGTATGATGTAACTCCGTTCATGGATGATCATCCTGGAGGTGATGAAGTTTTGCTATCAGCAACTG

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|116447035|gb|EG489627.1|EG489627
EST:     TTTCAAAGCACAACAAAACTAAGGATTGTTGGCTTATTATTTCCGGCAAG                         GTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTC
genomic: TTTCAAAGCACAACAAAACTAAGGATTGTTGGCTTATTATTTCCGGCAAGgttagatctt ... cgttctttagGTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTC
EST: gi|116479707|gb|EG522299.1|EG522299
EST:     TTTCAAAGCACAACAAAACTAAGGATTGTTGGCTTATTATTTCCGGCAAG                         GTGTATGATGTGACTCCGTTCATGGATGATCATCCTGGAGGCGATGAAGTC
genomic: TTTCAAAGCACAACAAAACTAAGGATTGTTGGCTTATTATTTCCGGCAAGgttagatctt ... cgttctttagGTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTC
EST: gi|116428585|gb|EG471177.1|EG471177
EST:     TTTCAAAGCACAACAAAACTAAGGATTGTTGGCTTATTATTTCCGGCAAG                         GTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTC
genomic: TTTCAAAGCACAACAAAACTAAGGATTGTTGGCTTATTATTTCCGGCAAGgttagatctt ... cgttctttagGTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTC
EST: gi|116482242|gb|EG524834.1|EG524834
EST:     TTTCAAAGCACAACAAAACTAAGGATTGTTGGCTTATTATTTCCGGCAAG                         GTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTC
genomic: TTTCAAAGCACAACAAAACTAAGGATTGTTGGCTTATTATTTCCGGCAAGgttagatctt ... cgttctttagGTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTC
EST: gi|124916256|gb|EH990130.1|EH990130
EST:     TTTCAAAGCACAACAAAACTAAGGATTGTTGGCTTATTATTTCCGGCAAG                         GTGTATGATGTGA
genomic: TTTCAAAGCACAACAAAACTAAGGATTGTTGGCTTATTATTTCCGGCAAGgttagatctt ... cgttctttagGTGTATGATGTGA
EST: gi|116479506|gb|EG522098.1|EG522098
EST:     TTTCAAAGCACAACAAAACTAAGGATTGTTGGCTTATTATTTCCGGCAAG                         GTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTC
genomic: TTTCAAAGCACAACAAAACTAAGGATTGTTGGCTTATTATTTCCGGCAAGgttagatctt ... cgttctttagGTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTC
EST: gi|116425880|gb|EG468472.1|EG468472
EST:     TTTCAAAGCACAACAAAACTAAGGATTGTTGGCTTATTATTTCCGGCAAG                         GTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTC
genomic: TTTCAAAGCACAACAAAACTAAGGATTGTTGGCTTATTATTTCCGGCAAGgttagatctt ... cgttctttagGTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTC
EST: gi|116447041|gb|EG489633.1|EG489633
EST:     TTTCAAAGCACAACAAAACTAAGGATTGTTGGCTTATTATTTCCGGCAAG                         GTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTC
genomic: TTTCAAAGCACAACAAAACTAAGGATTGTTGGCTTATTATTTCCGGCAAGgttagatctt ... cgttctttagGTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTC
EST: gi|116485441|gb|EG528033.1|EG528033
EST:     TTTCAAAGCACAACAAAACTAAGGATTGTTGGCTTATTATTTCCGGCAAG                         GTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTC
genomic: TTTCAAAGCACAACAAAACTAAGGATTGTTGGCTTATTATTTCCGGCAAGgttagatctt ... cgttctttagGTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTC
EST: gi|86079009|gb|DR374766.1|DR374766
EST:     TTTCAAAGCACAACAAAACTAAGGATTGTTGGCTTATTATTTCCGGCAAG                         GTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTC
genomic: TTTCAAAGCACAACAAAACTAAGGATTGTTGGCTTATTATTTCCGGCAAGgttagatctt ... cgttctttagGTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacagagtttgtgtctactacttggttatgatctgtgattgttgcgttctttagGTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTCTTGTTGTCCTCAACAG
                                             cgttcttt  CT-rich tract
                          ttatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcccctcgtagatttagttgattctatgttaattcacactagagaaacagagtttgtgtctactacttggttatgatctgtgattgttgcgttctttagGTGTATGATGTGACTCCATTCATGGATGATCATCCTGGAGGCGATGAAGTCTTGTTGTCCTCAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - -gatttag
- - - - - - - - - - - - - - - - attcaca
- - - - - - - - - - - - - - - - - - - - - - -aaacaga