Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgagacaagacaaagaaagaggctactttgtgcagtatcatgatcttttgtatgaatgagttagattttctatgtgtacttaattataatctatttcagGTGAGAAGATATCTCCAATTGAAGTGGATGCAGTACTCTTAACGCATCCTGACGTTTCTCAGGGTGTTGCATTCGGTGTTCCTGATGAGAAATATGGGGA

Basic information

species Arabidopsis thaliana
transcript AT3G48990.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G48990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0025g03660.t01 (Vitis vinifera), 3'ss of exon 2
atgagacaagacaaagaaagaggctactttgtgcagtatcatgatcttttgtatgaatgagttagattttctatgtgtacttaattataatctatttcagGTGAGAAGATATCTCCAATTGAAGTGGATGCAGTACTCTTAACGCATCCTGACGTTTCTCAGGGTGTTGCATTCGGTGTTCCTGATGAGAAATATGGGGA
    |    ||     | ||||  |  ||  ||   | |||   |  ||| | |   ||  |  |       |  ||   |   | | |||   ||||||| ||||||||||| ||||||||||| ||||| || ||  |  | ||||| |||||| | || ||||||||||| || || |||||||| || ||||||||
----gtattgattttaacagagcatcattattggcatctcacatttgtttatgtttgtgtttgtggaccatcaactgggttgtttcaaaat---tttcagGGGAGAAGATATCGCCAATTGAAGTAGATGCGGTGCTTCTGTCTCATCCGGACGTTGCCCAAGGTGTTGCATTTGGAGTCCCTGATGACAAGTATGGGGA

upper sequence: AT3G48990.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv16s0050g00390.t01 (Vitis vinifera), 3'ss of exon 2
--atgagacaagacaaagaaagaggctactttgtgcagtatcatgatcttttgtatgaatgagttagattttctat-gtgtacttaattataatctatttcagGTGAGAAGATATCTCCAATTGAAGTGGATGCAGTACTCTTAACGCATCCTGACGTTTCTCAGGGTGTTGCATTCGGTGTTCCTGATGAGAAATATGGGGA
   |    ||| |  |  ||| |  | |||   | |  | | || |  |   | ||   | |   |||||| | || |||    |  ||||      ||||||| ||||||||||| ||||| ||||||||||| || || ||| | ||||| ||| || |||| |  ||||| || || ||||| ||||| ||||| || ||
tcttaccgcaaaattaccaaatat-ccactc-attctatttaattaggtcacgcattgcttaaa-agatttccaatagtggtagtccttatccatattttcagGAGAGAAGATATCACCAATCGAAGTGGATGCTGTCCTTTTATCACATCCAGACATTGCTCAAGCGGTTGCTTTTGGGGTTCCAGATGACAAATACGGCGA
















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|116467688|gb|EG510280.1|EG510280
EST:     TGGGTATTTGCATCTGGTGGGTCGGATCAAAGAGCTTATTAACCGTGGAG                         GTGAGAAGATATCTCCAATTGAAGTGGATGCAGTACTCTTAACGCATCCTG
genomic: TGGGTATTTGCATCTGGTGGGTCGGATCAAAGAGCTTATTAACCGTGGAGgttagtctca ... tctatttcagGTGAGAAGATATCTCCAATTGAAGTGGATGCAGTACTCTTAACGCATCCTG
EST: gi|116467687|gb|EG510279.1|EG510279
EST:     TGGGTATTTGCATTTGGTGGGTCGGATCAAAGAGCTTATTAACCGTGGAG                         GTGAGAAGATATTTCCAATTGAAGTGGATGCAGTACTTTTAACGCATCCTG
genomic: TGGGTATTTGCATCTGGTGGGTCGGATCAAAGAGCTTATTAACCGTGGAGgttagtctca ... tctatttcagGTGAGAAGATATCTCCAATTGAAGTGGATGCAGTACTCTTAACGCATCCTG
EST: gi|125203160|gb|EL218114.1|EL218114
EST:     TCTGGTGGGTCGGATCAAAGAGCTTATTAACCGTGGAG                         GTGAGAAGATATCTCCAATTGAAGTGGATGCAGTACTCTTAACGCATCCTG
genomic: TCTGGTGGGTCGGATCAAAGAGCTTATTAACCGTGGAGgttagtctca ... tctatttcagGTGAGAAGATATCTCCAATTGAAGTGGATGCAGTACTCTTAACGCATCCTG
EST: gi|86081105|gb|DR376862.1|DR376862
EST:     TGGGTATTTGCATCTGGTGGGTCGGATCAAAGAGCTTATTAACCGTGGAG                         GTGAGAAGATATCTCCAATTGAAGTGGATGCAGTACTCTTAACGCATCCTG
genomic: TGGGTATTTGCATCTGGTGGGTCGGATCAAAGAGCTTATTAACCGTGGAGgttagtctca ... tctatttcagGTGAGAAGATATCTCCAATTGAAGTGGATGCAGTACTCTTAACGCATCCTG
EST: gi|116483995|gb|EG526587.1|EG526587
EST:     TGGGTATTTGCATCTGGTGGGTCGGATCAAAGAGCTTATTAACCGTGGAG                         GTGAGAAGATATCTCCAATTGAAGTGGATGCAGTACTCTTAACGCATCCTG
genomic: TGGGTATTTGCATCTGGTGGGTCGGATCAAAGAGCTTATTAACCGTGGAGgttagtctca ... tctatttcagGTGAGAAGATATCTCCAATTGAAGTGGATGCAGTACTCTTAACGCATCCTG
EST: gi|124918262|gb|EH992118.1|EH992118
EST:     TGGGTATTTGCATCTGGTGGGTCGGATCAAAGAGCTTATTAACCGTGGAG                         GTGAGAAGATATCTCCAATTGAAGTGGATGCAGTACTCTTAACG
genomic: TGGGTATTTGCATCTGGTGGGTCGGATCAAAGAGCTTATTAACCGTGGAGgttagtctca ... tctatttcagGTGAGAAGATATCTCCAATTGAAGTGGATGCAGTACTCTTAACG
EST: gi|116464394|gb|EG506986.1|EG506986
EST:     TGGGTATTTGCATCTGGTGGGTCGGATCAAAGAGCTTATTAACCGTGGAG                         GTGAGAAGATATCTCCAATTGAAGTGGATGCAGTACTCTTAACGCATCCTG
genomic: TGGGTATTTGCATCTGGTGGGTCGGATCAAAGAGCTTATTAACCGTGGAGgttagtctca ... tctatttcagGTGAGAAGATATCTCCAATTGAAGTGGATGCAGTACTCTTAACGCATCCTG
EST: gi|116464272|gb|EG506864.1|EG506864
EST:     TGGGTATTTGCATCTGGTGGGTCGGATCAAAGAGCTTATTAACCGTGGAG                         GTGAGAAGATATCTCCAATTGAAGTGGATGCAGTACTCTTAACGCATCCTG
genomic: TGGGTATTTGCATCTGGTGGGTCGGATCAAAGAGCTTATTAACCGTGGAGgttagtctca ... tctatttcagGTGAGAAGATATCTCCAATTGAAGTGGATGCAGTACTCTTAACGCATCCTG
EST: gi|124864757|gb|EH949194.1|EH949194
EST:     TGGGTATTTGCATCTGGTGGGTCGGATCAAAGAGCTTATTAACCGTGGAG                         GTGAGAAGATATCTCCAATTGAAGTGGATGCAGTA
genomic: TGGGTATTTGCATCTGGTGGGTCGGATCAAAGAGCTTATTAACCGTGGAGgttagtctca ... tctatttcagGTGAGAAGATATCTCCAATTGAAGTGGATGCAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttgtatgaatgagttagattttctatgtgtacttaattataatctatttcagGTGAGAAGATATCTCCAATTGAAGTGGATGCAGTACTCTTAACGCATCCTGACGTTTCTCAGGGTGTTGCATTCGGTGTTCCTGATGAGAAATATGGGGA
                                 acttaat  putative branch site (score: 4)
                                             tctatttc  putative PPT
                              tgtacttaattataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgagacaagacaaagaaagaggctactttgtgcagtatcatgatcttttgtatgaatgagttagattttctatgtgtacttaattataatctatttcagGTGAGAAGATATCTCCAATTGAAGTGGATGCAGTACTCTTAACGCATCCTGACGTTTCTCAGGGTGTTGCATTCGGTGTTCCTGATGAGAAATATGGGGA

- - - - agacaaa
- - - - - - - -gaaagag