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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcttttggatctagggttttattatagcatttctgggttctttgttgaccaagaagaagatttgtattgatggaatgttgttgatgttgttgtgaacagTGAGAAATCAATAAGATGTTGGAGAAAGAGTTTTTCACGGAGTATGGTGAAGCAAGTCAATATCAGATCCAAGAAGTTGTTGGCAAAGGAAGCTACGGAG

Basic information

species Arabidopsis thaliana
transcript AT2G01450.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G01450.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os06g49430.1 (Oryza sativa), 3'ss of exon 1
gtcttttggatctagggttttattatagcatttctgggttctttgttgaccaagaagaagatttgtattgatggaatgttgttgatgttgttgtgaacagTGAGAAATCA-ATAAGATGTTGGAGAAAGAGTTTTTCACGGAGTATGGTGAAGCAAGTCAATATCAGATCCAAGAAGTTGTTGGCAAAGGAAGCTACGGAG------------
    ||||  | ||||| |  ||| ||  | |   |   | ||   | ||||   |     | ||||||  | |   | |    || || |||  || | || ||  |   | || |   |||| |  ||||| ||||| |||||||| |||||||| || || |||||||| |||||  ||||||||||||| || ||||            
----tttgtttatagggct--attctactactgaagaagtttta--taaccagccac----tctgtatttttagttagcttaatattttcttgcaaa-attgtgatcttgtagAACACAGTGGAAATGGAGTTCTTCACTGAGTATGGAGAAGCAAGCCAGTACCAGATCCAGGAAGTCATTGGCAAAGGAAGTTATGGAGTAGTTGCTGCTG

upper sequence: AT2G01450.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os02g04230.2 (Oryza sativa), 3'ss of exon 1
gtcttttggatc-tagggttttattatagcatttctgggttctttgttgaccaagaagaagatttgtattgatggaatgttgttgatgttgttgtgaa-cagTGAGAAATCAATAAGATGTTGGAGAAAGAGTTTTTCACGGAGTATGGTGAAGCAAGTCAATATCAGATCCAAGAAGTTGTTGGCAAAGGAAGCTACGGAG------------
       ||||  | | |   |  || |   || |    |    || |  | |   | |   ||| ||||  ||  ||| | |  ||| | ||| |||   ||||    | |  |  |  | ||| |  ||||| || ||||| || || || ||||| ||||||||||| ||||| || |||||||| |||||||| ||||            
-------ggattgttgaggactcctaaaatgttccc---tcacatgct--ctatacacattttttctattc-tgtgatggtctatatgattttgggaaattgtgatgttttag-

upper sequence: AT2G01450.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G135904_T01 (Zea mays), 3'ss of exon 1
gtcttttggatctagggttttattatagcatttctgggttctttgttgaccaagaagaagatttgtattgatggaatgttgttgatgttgttgtgaacagTGAGAAATCAATAAGATGTTGGAGAAAGAGTTTTTCACGGAGTATGGTGAAGCAAGTCAATATCAGATCCAAGAAGTTGTTGGCAAAGGAAGCTACGGAG----------------------------------------
                             ||| || || |  |  |    |   |      |   ||        ||||  ||||  |||  ||   |    |||| ||| ||        || |  ||||| ||||| ||||| || || ||||| || || ||||||||||||||  |||| ||||| ||||||||||                                        
-----------------------------attccttggatactcatcattctgtatatctctggttaacttcaatatgtacttgaaattgcggt---cttacagaactcagta--------gaaatggagttcttcacagAGTACGGAGAGGCAAGCCAGTACCAGATCCAAGAAGTCATTGGTAAAGGGAGCTACGGAGTAGTTGCTGCAGCTGTGGACACCCGCACCGGTGAGCGGGT

upper sequence: AT2G01450.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G135904_T02 (Zea mays), 3'ss of exon 1
gtcttttggatctagggttttattatag--catttctgggttctttgttgaccaagaagaagatttgtattgatggaatgttgttgatgttgttgtgaacagTGAGAAATCAATAAGATGTTGGAGAAAGAGTTTTTCACGGAGTATGGTGAAGCAAGTCAATATCAGATCCAAGAAGTTGTTGGCAAAGGAAGCTACGGAG------------
   |||     |  |  |||| | | |   |||| || || |  |  |    |   |      |   ||        ||||  ||||  |||  ||   |    |||| ||| ||        || |  ||||| ||||| ||||| || || ||||| || || ||||||||||||||  |||| ||||| ||||||||||            
---tttcactacaggtattttgtaacaagtcattccttggatactcatcattctgtatatctctggttaacttcaatatgtacttgaaattgcggt---cttacagAACTCAGTA--------GAAATGGAGTTCTTCACAGAGTACGGAGAGGCAAGCCAGTACCAGATCCAAGAAGTCATTGGTAAAGGGAGCTACGGAGTAGTTGCTGCAG

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|164005098|gb|EL987631.1|EL987631
EST:     CTCTTTCTCTTCCATTATTATCTTAAAG                         TGAGAAATCAATAAGATGTTGGAGAAAGAGTTTTTCACGGAGTATGGTGAA
genomic: CTCTTTCTCTTCCATTATTATCTTAAAGgtccgtcttt ... ttgtgaacagTGAGAAATCAATAAGATGTTGGAGAAAGAGTTTTTCACGGAGTATGGTGAA
EST: gi|164120878|gb|EL967069.1|EL967069
EST:     ATTATTATCTTAAAG                         TGAGAAATCAATAAGATGTTGGAGAAAGAGTTTT-CACGGAGTATGGTGAA
genomic: ATTATTATCTTAAAGgtccgtcttt ... ttgtgaacagTGAGAAATCAATAAGATGTTGGAGAAAGAGTTTTTCACGGAGTATGGTGAA
EST: gi|19875322|gb|AU236153.1|AU236153
EST:     GCAGCTTCGTGGAAATTATTTTCTCTTTCTCTTCCATTATTATCTTAAAG                         TGAGAAATCAATAAGATGTTGGAGAAAGAGTTTTTCACGGAGTATGGTGAA
genomic: GCAGCTTCGTGGAAATTATTTTCTCTTTCTCTTCCATTATTATCTTAAAGgtccgtcttt ... ttgtgaacagTGAGAAATCAATAAGATGTTGGAGAAAGAGTTTTTCACGGAGTATGGTGAA
EST: gi|116408403|gb|EG450995.1|EG450995
EST:     GCAGCTTCGTGGAAATTATTTTCTCTTTCTCTTCCATTATTATCTTAAAG                         TGAGAAATCAATAAGATGTTGGAGAAAGAGTTTTTCACGGAGTATGGTGAA
genomic: GCAGCTTCGTGGAAATTATTTTCTCTTTCTCTTCCATTATTATCTTAAAGgtccgtcttt ... ttgtgaacagTGAGAAATCAATAAGATGTTGGAGAAAGAGTTTTTCACGGAGTATGGTGAA
EST: gi|86066694|gb|DR362451.1|DR362451
EST:     GCAGCTTCGTGGAAATTATTTTCTCTTTCTCTTCCATTATTATCTTAAAG                         TGAGAAATCAATAAGATGTTGGAGAAAGAGTTTTTCACGGAGTATGGTGAA
genomic: GCAGCTTCGTGGAAATTATTTTCTCTTTCTCTTCCATTATTATCTTAAAGgtccgtcttt ... ttgtgaacagTGAGAAATCAATAAGATGTTGGAGAAAGAGTTTTTCACGGAGTATGGTGAA
EST: gi|152035517|gb|BP856857.2|BP856857
EST:     GCAGCTTCGTGGAAATTATTTTCTCTTTCTCTTCCATTATTATCTTAAAG                         TGAGAAATCAATAAGATGTTGGAGAAAGAGTTTTTCACAGAGTATGGTGAA
genomic: GCAGCTTCGTGGAAATTATTTTCTCTTTCTCTTCCATTATTATCTTAAAGgtccgtcttt ... ttgtgaacagTGAGAAATCAATAAGATGTTGGAGAAAGAGTTTTTCACGGAGTATGGTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaccaagaagaagatttgtattgatggaatgttgttgatgttgttgtgaacagTGAGAAATCAATAAGATGTTGGAGAAAGAGTTTTTCACGGAGTATGGTGAAGCAAGTCAATATCAGATCCAAGAAGTTGTTGGCAAAGGAAGCTACGGAG
               atttgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcttttggatctagggttttattatagcatttctgggttctttgttgaccaagaagaagatttgtattgatggaatgttgttgatgttgttgtgaacagTGAGAAATCAATAAGATGTTGGAGAAAGAGTTTTTCACGGAGTATGGTGAAGCAAGTCAATATCAGATCCAAGAAGTTGTTGGCAAAGGAAGCTACGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - -ggtttta
- - - - - - - - - - - - - - - - - - - - - - - - accaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatttgt