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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catataagtagtagctttggtttccaatttattttcctgtgtttattctttcctatcatatggattacagaagcattaatacatcgtttcttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCTGGGAGCACATACCGTACCCGAGATGAGATATCTGGTGTGAGGCAG

Basic information

species Arabidopsis thaliana
transcript AT1G59900.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os06g13720.1 (Oryza sativa), 3'ss of exon 3
---catataagt-agtagctttggtttc-caatttattttcctgtgtttattctttcctatcatatggattacagaagcattaatacatcgtttcttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCTGGGAGCACATACCGTACCCGAGATGAGATATCTGGTGTGAGGCAG
   |||||   |   ||| ||  ||  | | | | | |           || ||   ||   | ||| ||    | | | ||  || ||| | ||     |  ||||||||||||||||||| ||||| |||||||| ||||| ||||| ||||| |||||||| ||||| ||| ||||||| ||  | ||  | || |||
gctcatattgttcgatagattcagtgccgctaatcagtagaaaacaca-atcctgctcttggagatgcat----gtaacttttctatatcctctcggtgttgtagATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCAGGGAGCACTTACCGCACCAGAGATGAAATTGCAGGCATAAGACAG

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g50620.1 (Oryza sativa), 3'ss of exon 3
catataagtagtagctt-tggtttccaatttattttcctgtgtttattctttcctatcatatggattacagaagc-attaatacatcgtttcttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCTGGGAGCACATACCGTACCCGAGATGAGATATCTGGTGTGAGGCAG
  |    ||    |||    ||||  |     |   |||   |  | | ||||   |    |   | |  |   | | |  | |  |  |  || |||  || ||||||| ||||| || ||||||||||| || || || ||||| ||||| || ||||| ||||||||| | |||||||| || ||||| || |||
--tggttgtgcctgctagcagtttgtagcaattcacccttaatgaaatgtttcagttttagtaagtgatggttactaatgtttccccactctttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCCGGAAGCACTTACCGTACCAGGGATGAGATCTCAGGTGTAAGACAG

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G140150_T01 (Zea mays), 3'ss of exon 3
catataagtagtagctttggtttccaatttattttcctgtgtttattctttcctatcatatggattacagaagcattaatacatcgtttcttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCTGGGAGCACATACCGTACCCGAGATGAGATATCTGGTGTGAGGCAG
   ||||||  || |||          ||| ||      |  |||||   |   ||    || || |  |   |   |       |||   | |||  || | ||||||||||| || ||||||||||| || ||||| ||||| ||||| || ||||| ||||| ||| | |||||||| || ||||| ||||||
gtgataagtgataacttgttcactttgtttgttggttcataattatttaatttcatgtgctgaataatggttactaaaccctcatgttctatgtatctagGTCCTTGAGATGGATACCTACAGGTACCATGGCCACTCTATGTCAGATCCAGGAAGCACTTACCGCACCAGGGATGAGATTTCAGGTGTCAGGCAG

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G027627_T01 (Zea mays), 3'ss of exon 3
-----catataagtag--tagctttggtttccaatttattttcctgtgtttattctttcctatcatatggattacagaagcattaatacatcgtttcttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCTGGGAGCACATACCGTACCCGAGATGAGATATCTGGTGTGAGGCAG
     | |  || |||   ||  |||   ||   ||| |  | |     ||  ||||    |  ||   ||| ||    |   || |    |||||  | | | ||||| |||||||||||||| ||||| |||||||| ||||| ||||| ||||| || ||||| ||||| ||  | ||||||||  ||||  | ||||||
aggacccttaaactagacgaggcttgacatcggttttgtgattccagactt--tcttcttaaagatgctgatcaccacggttctatt----cgttttatgttt-cagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCAGGTAGCACCTACCGCACAAGGGATGAGATCGCTGGCATAAGGCAG

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G361693_T01 (Zea mays), 3'ss of exon 3
catataagtagtagctttggtttccaatttattttcctgtgtttatt-ctttcctatcatatggattacagaagcattaatac-atcgtttcttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCTGGGAGCACATACCGTACCCGAGATGAGATATCTGGTGTGAGGCAG
 |   |||   |  |  ||           |   ||   |  ||||| | || |||     || |  |  |   |   ||  | |  |||   | |||  || | ||||||||||| || ||||| ||||| || ||||| ||||| ||||| || ||||| ||||| ||| | |||||||| || ||||| ||||||
-aggcaagccttctccctgcaaatgcggagaggctcgcataattatttcatttctagtgc-tgaagaatggttactaaaaccctaaggttctatatatctagGTCCTTGAGATGGATACCTACAGATACCATGGCCACTCTATGTCAGATCCAGGAAGCACTTACCGCACCAGGGATGAGATTTCAGGTGTCAGGCAG

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G40380.1 (Glycine max), 3'ss of exon 3
-------------catataagtagtagctttggtttccaa-------tttattttcctgtgtttattctttcctatcatat-ggattacaga-agcattaatacatcgtttcttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCTGGGAGCACATACCGTACCCGAGATGAGATATCTGGTGTGAGGCAG
             | | | | | |||  | |  |||  ||       ||||  ||   |   | |||||||  |    | |   |||| |       |   ||  |   || || | | ||||||||||| |||||||||||||| ||||| || |||||||||||||||||||| |||||||||||||| || |||||||| ||||||||||| |||
gtaagtaaattaacctctcatttgtacttatattttttaagaatttttttagcttttaggaatgattcttttattctctgttatattataattgatttctctatcttaattattttgtccagATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTGAGACAG

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G17240.1 (Glycine max), 3'ss of exon 3
--------------------catataagtagtagctttggtttccaatttattttcctgtgtttattctttcctatcatat-ggattacaga-agcattaatacatcgtttcttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCTGGGAGCACATACCGTACCCGAGATGAGATATCTGGTGTGAGGCAG
                      | ||  ||      ||   ||    ||||  ||   |   | |||||||  |    | |   ||||||       |   ||  |   || || | | |||||||| ||||||||||||||||| ||||| || |||||||||||||||||||| |||||||||||||| || |||||||| |||||||| || |||
gtaagtaaatttacttcttttttgtacttatatttcttaaatttgtgtttagattttaggaatgattcttttattctctgttatattacaattgatttctctatcttaattattttgtccagATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTAAGACAG

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G04470.2 (Glycine max), 3'ss of exon 1
-----catataagtagtagctttg-gtttccaatttattttcctgtgtttattctttcctatcatatggattacagaagcattaatacatcgtttcttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCTGGGAGCACATACCGTACCCGAGATGAGATATCTGGTGTGAGGCAG
      | |||  |   |  | ||   ||   ||| | ||  |   ||||||||| |   ||   || |||| |        ||    || | || |||| | ||||||||||| |||||||| ||||| ||||| || ||||| |||||||||| ||| |||||||||||||| || ||||| || ||||||||||| |||
attttaacatagctgtcatttgtgtagttttgattaaattatcaaagtttattctgttagatttgattgatttct------ctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCATGGCAGCACATACCGTACACGTGATGAAATTTCTGGTGTGAGACAG

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 3
-----catataagtagtagctttggtttccaatttattttcctgtgtttattctttcctatcatatggattacagaagcattaatacatcgtttcttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCTGGGAGCACATACCGTACCCGAGATGAGATATCTGGTGTGAGGCAG
     ||||   ||  |   | | ||||  | |  ||| || |  ||||||||| |  ||  || ||  | |      |  ||    || | || |||| | ||||||||||| |||||||| ||||| ||||| || ||||| |||||||||||||| ||||||||||| || || ||||| || ||||||||||| |||
tttatcatagctgtcatttgtgtagttttgattgaattatcata-gtttattctctgttag-atttgattgattt---ctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCTGGCAGCACATACCGGACACGTGATGAAATTTCTGGTGTGAGACAG

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 3
catataagtagtagctttggtttccaatttattttcctgtgtttattctttcctatcatatggattacagaagcattaatacatc--gtttcttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCTGGGAGCACATACCGTACCCGAGATGAGATATCTGGTGTGAGGCAG
| |  | || || |||     || |  | | ||||    |  | ||  |||  | | | || || ||         |  | | ||    | ||  | | ||||||||||| |||||||| || |||||||| ||||||||||||||||||||||||||||| |||||||| || |||||||| ||||||||||| |||
ctttaatgttgttgctagtaatttc--tctcttttggcattgtcatcattttatgtgagattgactaattgctttatttttcttctaaatgctggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGCACCTACCGTACACGTGATGAGATTTCTGGTGTGAGACAG

upper sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv09s0018g01940.t01 (Vitis vinifera), 3'ss of exon 3
catataagtagtagctttggtttccaatttattttcctgtgtttattctttcctatcatatggattacagaagcattaatacatc--gtttcttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCTGGGAGCACATACCGTACCCGAGATGAGATATCTGGTGTGAGGCAG
|      | | |  ||||  ||      ||       | |||  ||  |||   || | || || ||    |    |  | | ||    | ||| | | ||||||||||| |||||||| || |||||||| |||||||||||||||||||||||||| ||||||||||| || |||||||| ||||||||||| |||
cccgcctgcaatt-ctttcattctttgcttgagcatgtctgtc-atcattttacatgagattgactaattgatttatctttcttctaaatgcttgtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGTACATACCGTACGCGTGATGAGATTTCTGGTGTGAGACAG

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|124743059|gb|EH834221.1|EH834221
EST:     CGTTGGAGAAGGGGCCAATA                         ATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCT
genomic: CGTTGGAGAAGGGGCCAATAgtaagtttgt ... ttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCT
EST: gi|124941966|gb|EL018273.1|EL018273
EST:     CATGCGTTGGAGAAGGGGCCAATA                         ATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTACTGATCC
genomic: CATGCGTTGGAGAAGGGGCCAATAgtaagtttgt ... ttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGT-CTGATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttcctatcatatggattacagaagcattaatacatcgtttcttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCTGGGAGCACATACCGTACCCGAGATGAGATATCTGGTGTGAGGCAG
                            cattaat  putative branch site (score: 3)
                                      tcgtttcttct  putative PPT
                             attaatacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catataagtagtagctttggtttccaatttattttcctgtgtttattctttcctatcatatggattacagaagcattaatacatcgtttcttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCTGGGAGCACATACCGTACCCGAGATGAGATATCTGGTGTGAGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - -gctttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acagaag