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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaattccgatttctgctcctcgttttggattcaatctgtatttgtggaatcatcttcgtttgcaagtggtctttgtatgttatgtgtgattgttctgatcctatttctatgcttagGTGATCACGAAGTTCTGTTCGGAGCGTATTGCAAAGTATGCTTTTGAGTATGCCTACCTGAACAACAGGAAGAAAGTTACAGCGGTGCATAAGGCTAACA

Basic information

species Arabidopsis thaliana
transcript AT4G35260.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G35260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os02g38200.1 (Oryza sativa), 3'ss of exon 1
gtgagaattccgatttctgctcctcgttttggattcaatctgtatttgtggaatcatcttcgtttgcaagtggtctttgtatgttatgtgtgattgtt-ctgatcctatttctatgcttagGTGATCACGAAGTTCTGTTCGGAGCGTATTGCAAAGTATGCTTTTGAGTATGCCTACCTGAACAACAGGAAGAAAGTTACAGCGGTGCATAAGGCTAACA
       ||| ||  |         ||    | ||   ||  | ||  |   |||||||        |||   | ||| |    ||| ||  | |||| || |    ||||       ||||||||||| |||||||| || ||  | ||||| ||||||||||||||||| || ||||| |||||||| |||||||| || || |||||||| || ||||
------tttctgaaatagaacgtatgtaaatgtttttgtcacttttcatttcatcatcta-------aaggaattttttt---ctatatggtactgttactaaatggatttac-----tagGTGATCACAAAGTTCTGCTCTGAAAGGATTGCCAAGTATGCTTTTGAGTACGCGTACCTCAACAACAGAAAGAAAGTGACTGCCGTGCATAAAGCAAACA

upper sequence: AT4G35260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os04g40310.2 (Oryza sativa), 3'ss of exon 1
gtgagaattccgatttctgctcctcgttttggattcaatctgtatttgtggaatcatcttcgtttgcaagtggtctttgtatgttatgtgtgattgttctgatcctatttctatgcttagGTGATCACGAAGTTCTGTTCGGAGCGTATTGCAAAGTATGCTTTTGAGTATGCCTACCTGAACAACAGGAAGAAAGTTACAGCGGTGCATAAGGCTAACA------------
                                 | | |   | ||     | | | | ||  ||| | |||  |||  |  | || |   |  ||  ||| |     |  || |  | ||||||| || ||||| || || ||| | ||||| || ||||||||||||||||| ||||| |||||| | |||||||| ||||| |||||||| || ||||            
-------------------------------attgccaatggaatgaaatgcacccttttttttttccagttctctgagcttcttttccatc-ttagtctcactgactaacttttgtcaggtgataacaaagTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACATCATGAAGCTTG

upper sequence: AT4G35260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
gtgagaattccgatttctgctcctcgttttggattcaatctgtatttgtggaatcatcttcgtttgcaagtggtctttgtatgttatgtgtgattgttctgatcctatttctatgcttagGTGATCACGAAGTTCTGTTCGGAGCGTATTGCAAAGTATGCTTTTGAGTATGCCTACCTGAACAACAGGAAGAAAGTTACAGCGGTGCATAAGGCTAACA
              || || | |  | ||   | |  |     ||     | | | | ||  ||| | |||  |||  |  | || |   |  ||  ||| |     |  || |  | ||||||| || ||||| || || ||| | ||||| || ||||||||||||||||| ||||| |||||| | |||||||| ||||| |||||||| || ||||
--------------ttgtgttacatgattgccaatggaatgaaat-----gcacccttttttttttccagttctctgagcttcttttccatc-ttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA

upper sequence: AT4G35260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G006672_T02 (Zea mays), 3'ss of exon 1
gtgagaattccgatttctgctcctcgttttggattcaatctgtatttgtggaatcatcttcgtttgcaagtggtctttgtatgttatgtgtgattgttctgatcctatttctatgcttagGTGATCACGAAGTTCTGTTCGGAGCGTATTGCAAAGTATGCTTTTGAGTATGCCTACCTGAACAACAGGAAGAAAGTTACAGCGGTGCATAAGGCTAACA
     ||||   |  |     |    ||   | | |  ||| | ||||            | | |  |||   | | |   | |||    |  ||  | | |   | ||  | |||| ||||||| || || ||||| || ||  | |||||||||||||||||||||||||| ||||| |||||  | |||||||| ||||| |||||||| || || |
----taatttgaaagtgcatgcaatattgctgctcctttctat-tttgc-----------catctaaaaggcatttctccttattac---tatttactataactttgttgatttgct-agGTGATAACAAAATTCTGCTCTGAAAGAATTGCAAAGTATGCTTTTGAGTATGCATACCTTAACAATCGAAAGAAAGTGACAGCAGTGCATAAAGCCAATA

upper sequence: AT4G35260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G025366_T01 (Zea mays), 3'ss of exon 1
gtgagaattccgatttctgctcctcgttttggattcaatctgtatttgtggaatcatcttcgtttgcaagtggtctttgta--tgttatgtgtgattgttctgatcctatttctatgcttagGTGATCACGAAGTTCTGTTCGGAGCGTATTGCAAAGTATGCTTTTGAGTATGCCTACCTGAACAACAGGAAGAAAGTTACAGCGGTGCATAAGGCTAACA
                 || |  |    | | || || ||  |   |||    |  |  || ||| ||  |  | | || |  | |  |   | |||  ||| |    ||   | | | ||||||||||| ||||| || || ||| | ||||| || ||||| || |||||||| ||||| |||||| | |||||||| || || |||||||| || ||||
-----------------tgttgttgaaatagaatccactcatttaatgt----ttgtgatcctttacagttcttatctgaacctttcttccattattactcttactgaatggattt-cctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA

upper sequence: AT4G35260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G025366_T02 (Zea mays), 3'ss of exon 1
gtgagaattccgatttctgctcctcgttttggattcaatctgtatttgtggaatcatcttcgtttgcaagtggtctttgtatgttatgtgtgattgttctgatcctatttctatgcttagGTGATCACGAAGTTCTGTTCGGAGCGTATTGCAAAGTATGCTTTTGAGTATGCCTACCTGAACAACAGGAAGAAAGTTACAGCGGTGCATAAGGCTAACA------------
                             |  | ||| |   | ||||||  ||| | | |  ||   |   |    | | |   ||   |  |  | ||||    |||||      ||||||||||| ||||| || || ||| | ||||| || ||||| || |||||||| ||||| |||||| | |||||||| || || |||||||| || ||||            
-------------------------agaatccactcatttaatgtttgtg--atcctttacagttcttatctgaacctttcttccattattactcttactgaatggatttcc-----taggtgatcacaaagTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACATTATGAAGCTTG

upper sequence: AT4G35260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S212_85V6.2 (Physcomitrella patens), 3'ss of exon 2
gtgagaattccgatttctgctcctcgttttggattcaatctgtatttgtggaatcatcttc--gtttgcaagtggtctttgtatgttatgtgtgattgttctgatcctatttctatgcttagGTGATCACGAAGTTCTGTTCGGAGCGTATTGCAAAGTATGCTTTTGAGTATGCCTACCTGAACAACAGGAAGAAAGTTACAGCGGTGCATAAGGCTAACA
                  ||  |||  | |  |||  ||   ||  ||| |||| | || |  ||||     | ||  |   || |   ||| |||    || |   | ||    |  | ||||||| || || ||||| || ||||| ||||||||||| || ||||||||||| || || |||||| | |||| ||| ||||| || |||||||| ||||
------------------gcgactctatgtatattgcata-atacctgtcgaatgacctgctggtttctgccttgttgtcaaatatgtcgtg-gat--gcctcacagtgttaagcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTATGCTTATCTCAACAACCGTAAGACAGTAACAGCAGTACATAAGGCCAACA

upper sequence: AT4G35260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S101_151V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgagaattccgatttctgctcctcgttttggattcaatctgtatttgtggaatcatcttcgtttgcaagtggtctttgtatgtta--tgtgtgattgttctgatcctatttctatgcttagGTGATCACGAAGTTCTGTTCGGAGCGTATTGCAAAGTATGCTTTTGAGTATGCCTACCTGAACAACAGGAAGAAAGTTACAGCGGTGCATAAGGCTAACA
                   ||||||||  ||  ||||   || |||   | ||| |||||   |     |||||   |||    ||  | ||| | ||  || |   |      ||| | |||| ||||| |||||||| |||||||| ||||| || || || ||||||||||| || || |||||| | |||| ||| ||||| ||||| ||||| ||||
-----------------atctcctcgtcatgc-ttca---tgcattgtggaaataatcttatctactgcgtggtacctgtcaaataattctgtaagtgc-cttacagtgccaagatgttcagGTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTATGCTTATCTCAACAACCGCAAGACAGTAACAGCAGTGCACAAGGCCAACA

upper sequence: AT4G35260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S152_81V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgagaattccgatttctgctcctcgttttggattcaatctgtatttgtggaatcatcttcgtttgcaagtggtctttgtatgttatgtgtgattgttctgatcctatttctatgcttagGTGATCACGAAGTTCTGTTCGGAGCGTATTGCAAAGTATGCTTTTGAGTATGCCTACCTGAACAACAGGAAGAAAGTTACAGCGGTGCATAAGGCTAACA
           ||   ||  ||   ||  ||  |   ||| |||| ||  |          |||| | | | | | |  ||||  ||   |||   | || ||  |      ||  | ||||||| || || ||||| || ||||| || ||||| ||||||||||| ||||| || || |||||| | ||||  |||||||| ||||| ||||| ||||
--------caagagggcttgtcagtgtcatgtgtatgatc-gtatctgcag----------gtttcctacttgccatc-tatgagattgatgagattcctaatggtgccaaaattgtcagGTGATTACAAAATTCTGCTCCGAGCGCATAGCAAAATATGCTTTTGAATATGCATATCTTAACAACCGCAAGACGGTTACAGCAGTGCACAAGGCGAACA

upper sequence: AT4G35260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ13705 (Selaginella moellendorffii), 3'ss of exon 1
gtgagaattccgatttctgctcctcgttttggattcaatctgtatttgtggaatcatcttcgt-ttgcaagtggtctttgtatgttatgtgtgattgttctgatcctatttcta--tgc---ttagGTGATCACGAAGTTCTGTTCGGAGCGTATTGCAAAGTATGCTTTTGAGTATGCCTACCTGAACAACAGGAAGAAAGTTACAGCGGTGCATAAGGCTAACA
                                                             ||  | ||| |  |  |  | || | ||   |   | ||        |||||   |||     |||||||||||||||| || || || || ||||| ||||| || |||||||| ||||||||||||||||| ||||  || || |||||||| ||||| ||||
-------------------------------------------------------------gtactccaatttcttctcctctgctttgctcggccgctccagctacgtttcttcttgcgcaccagGTGATCACGAAGTTTTGCTCCGAACGGATTGCCAAGTACGCGTTTGAGTACGCCTACCTGAACAACAGAAAGACGGTGACGGCGGTGCACAAGGCCAACA

upper sequence: AT4G35260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ29002 (Selaginella moellendorffii), 3'ss of exon 1
gtgagaattccgatttctgctcctcgttttggattcaatctgtatttgtggaatcatcttcgt-ttgcaagtggtctttgtatgttatgtgtgattgttctgatcctatttcta--tgc---ttagGTGATCACGAAGTTCTGTTCGGAGCGTATTGCAAAGTATGCTTTTGAGTATGCCTACCTGAACAACAGGAAGAAAGTTACAGCGGTGCATAAGGCTAACA
                                                             ||  | ||| |  |  |  | || | ||   |   | ||        |||||   |||     |||||||||||||||| || || ||||| ||||| ||||| || |||||||| ||||||||||||||||| ||||  || || |||||||| ||||| ||||
-------------------------------------------------------------gtactccaatttcttctcctctgctttgctcggccgctccagctacgtttcttcttgcgcaccagGTGATCACGAAGTTTTGCTCCGAGCGGATTGCCAAGTACGCGTTTGAGTACGCCTACCTGAACAACAGAAAGACGGTGACGGCGGTGCACAAGGCCAACA

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|125284719|gb|EL298804.1|EL298804
EST:     GCTTGAGCACGAGGTTGTTCCTGGTGTCGTTGAGAGTCTGAAG                         GTGATCACGAAGTTCTGTTCGGAGCGTA
genomic: GCTTGAGCACGAGGTTGTTCCTGGTGTCGTTGAGAGTCTGAAGgtgagaattc ... ctatgcttagGTGATCACGAAGTTCTGTTCGGAGCGTA
EST: gi|124993120|gb|EL065389.1|EL065389
EST:     TTGAGCACGAGGTTGTTCCTGGTGTCGTTGAGAGTCTGAAG                         GTGATCACGAAGTTCTGTTCGGAGCGTATTG
genomic: TTGAGCACGAGGTTGTTCCTGGTGTCGTTGAGAGTCTGAAGgtgagaattc ... ctatgcttagGTGATCACGAAGTTCTGTTCGGAGCGTATTG
EST: gi|124984182|gb|EL056856.1|EL056856
EST:     CGGGGCTTTGAGCACGAGGTTGTTCCTGGTGTCGTTGAGAGTCTGAAG                         GTGATCACGAAGTTCTGTTCGGAGCGTA
genomic: CGGGGC-TTGAGCACGAGGTTGTTCCTGGTGTCGTTGAGAGTCTGAAGgtgagaattc ... ctatgcttagGTGATCACGAAGTTCTGTTCGGAGCGTA
EST: gi|124832646|gb|EH917085.1|EH917085
EST:     GCTTGAGCACGAGGTTGTTCCTGGTGTCGTTGAGAGTCTGAAG                         GTGATCACGAAGTTCTGTTCGGAGCGTATTGCAAAG
genomic: GCTTGAGCACGAGGTTGTTCCTGGTGTCGTTGAGAGTCTGAAGgtgagaattc ... ctatgcttagGTGATCACGAAGTTCTGTTCGGAGCGTATTGCAAAG
EST: gi|125251470|gb|EL265555.1|EL265555
EST:     CGGGGCTTGAGCACGAGGTTGTTCCTGGTGTCGTTGAGAGTCTGAAG                         GTGATCACGAAGTTCTGTTCGGAGCGTA
genomic: CGGGGCTTGAGCACGAGGTTGTTCCTGGTGTCGTTGAGAGTCTGAAGgtgagaattc ... ctatgcttagGTGATCACGAAGTTCTGTTCGGAGCGTA
EST: gi|125273578|gb|EL287663.1|EL287663
EST:     ACGCGGGGCTTGAGCACGAGGTTGTTCCTGGTGTCGTTGAGAGTCTGAAG                         GTGATCACGAAGTTCTGTTCGGAGCGTATTGCAAAGTATGCTTTTGAG
genomic: ACGCGGGGCTTGAGCACGAGGTTGTTCCTGGTGTCGTTGAGAGTCTGAAGgtgagaattc ... ctatgcttagGTGATCACGAAGTTCTGTTCGGAGCGTATTGCAAAGTATGCTTTTGAG
EST: gi|164145543|gb|EL967368.1|EL967368
EST:     ACGCGGGGCTTGAGCACGAGGTTGTTCCTGGTGTCGTTGAGAGTCTGAAG                         GTGATCACGAAG
genomic: ACGCGGGGCTTGAGCACGAGGTTGTTCCTGGTGTCGTTGAGAGTCTGAAGgtgagaattc ... ctatgcttagGTGATCACGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaagtggtctttgtatgttatgtgtgattgttctgatcctatttctatgcttagGTGATCACGAAGTTCTGTTCGGAGCGTATTGCAAAGTATGCTTTTGAGTATGCCTACCTGAACAACAGGAAGAAAGTTACAGCGGTGCATAAGGCTAACA
                               ttctgat  putative branch site (score: 3)
                                     tcctatttct  CT-rich tract
                                        tatttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaattccgatttctgctcctcgttttggattcaatctgtatttgtggaatcatcttcgtttgcaagtggtctttgtatgttatgtgtgattgttctgatcctatttctatgcttagGTGATCACGAAGTTCTGTTCGGAGCGTATTGCAAAGTATGCTTTTGAGTATGCCTACCTGAACAACAGGAAGAAAGTTACAGCGGTGCATAAGGCTAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA