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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcgttatacagtgattgctttatgcattggttcatctctgacagaattggtatttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT

Basic information

species Arabidopsis thaliana
transcript AT3G06400.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 13
gtaagtgcgttatacagtgattgc---tttatgcattggttcat-ctctgacagaattggtatttatcttaactat---gcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
||| ||   |  | |    |||     |||| | |    ||||| |  |   |  ||  | |||||| ||     |    |||||||||||||||||||  || | ||||||||||||| |||||| || ||||| |||||||| || || |||||||| ||||| |||||||||||  | ||
gtatgtttttgctgcttgtattttatgtttaagaaggcattcatgcagtagtaagatatggatttattttgttcttctttcagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 13
-----gtaagtgcgttatacagtgattgctttatgcattgg--ttcatctctgacagaattggtatttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
      |   ||| | ||| | || |||||| |   ||     ||||    | |   |||     | | || |     | |||||||||||||||||||| |  | || ||||| |||| ||||||||| ||||| ||||| || || ||||||||||| ||||| || ||||||||  | ||
gttagttttttgcttcataaaatg-ttgcttgacaaatgaaaattcaaacatcaattaatgttcttctgtcgtggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 10
-----------gtaagtgcgttatacagtgatt----gctttatgcattggttcatctctgacagaattggtatttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
            ||  |||  | |  | |  ||    || || |  | | |||       ||  |   ||  |    ||| |  |||  ||||||||||||||||||  | || ||||||||  | | ||||||||| ||||| ||||||||||| || |||||||| || || ||||| |||||  | ||
gtatggttttgatatttgccatttctatttgttttaagcattttttactagtttgatctggattgttctgacaacattctcatttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 13
-----------gtaagtgcgttatacagtgattgc-------tttatgcattggttcatctctgacagaattggtatttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
            ||  ||| ||    | |  || |       ||| |  | | |||       ||      ||  |    ||||   | |  ||||||||||||||||||  | || ||||||||  | | ||||||||| ||||| ||||||||||| || |||||||| || || ||||| |||||  | ||
gtatggttatgatatttgcctttgctatttgtttcaagcatttttctttactagttggatatggattattctgacaacattcttttttgttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 13
-----------gtaagtgcgttatacagtgattgctttatgcattg-gttcatc-tctgacagaattggtatttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
            | | |   || |   ||   |    |     ||| ||  ||  ||| |     ||   ||| || || | | |||||| || ||||| |||||||||||||||||||| |||| ||| ||||| ||||| |||||||| || ||||| ||||| ||||| |||||||||||||||||
gtatggattcaatgaataatttttcttgtttctttgctgaaagttgtgtggattgtctaatgtggttc-cattgattttta-tgtgcagCGGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAGGATATTGATAGAAT

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 13
-------------gtaagtgcgttatacagtgattgctttatgcattggttcatctctgacagaat-tggtat--ttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
             |    |    | |    | |||  ||| |     | || ||   | | | ||  |||||   |    ||   ||||||||||| ||||| |||||||||||||||||||| |||| ||||||||| ||||| || ||||| || || || ||||| ||||| ||||||||||| |||||
gtaagggttttctgggttttatctttgtttttattattttgttgcaagattgatggattatataacatggtacaatctatttgtgtatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 13
------------gtaagtgcgttatacagtgattgctttatgcattggttcatctctgacagaat-tggtatttatcttaact----atgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
            | |  |    |      | |||  ||| |   | | || ||   | | | ||  |||||   |   ||  |    |||||||||| ||||| |||||||||||||||||||| |||| ||||||||| ||||| || ||||| || || || ||||| ||||| ||||||||||| |||||
gtaagggtttctggattttatcttcgtttttattattttgttgctagatttatggattatataacatggtacacaatctatttgtgtatgcagCTGTTAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 13
gtaagtgcgttatacagtgattgctttatgcattggttcatctctgacagaattg----gtat-------ttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
||| |      ||  |    ||   || |   || | | |    ||   | ||||     |||       ||  |||   | |||||| || ||||| ||||| |||||||||||||| |||| ||| ||||| ||||| |||||||| || ||||| ||||| ||||| || ||||||||||||||
gtaggaattcaatgaataacttttcttgtttctttgctgaaagttgtgtggattgtctaatatggttccattggcttttatgtgcagCGGTAAATAAAGATGAATTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAAGATATTGATAGAAT

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 13
------------------gtaag--tgcgttatacagtgattgctttatgcattggttcatctctgacagaatt--ggtatttatcttaactat-gcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
                    |||  ||| ||  ||  |||     | || ||| |    |   |    |  |||  | | ||| | |   || | |||||||| || || |||||| | || |||||||| || | ||||||||| ||||| ||||| || || ||||||||||| || || || || || || || ||
gtgagccatttctgcattacaagcttgctttgcactatgacatgctaattcatagaactagaaccactaacattttgttgtttttgtgggcttttgcagCTGTGAACAAAGATGAGCTACTGCAAATGGTCAGGTTTGGTGCTGAAATGGTTTTCAGCTCCAAGGATAGCACAATTACGGATGAAGACATAGACAGGAT

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ32950 (Selaginella moellendorffii), 3'ss of exon 12
gtaagtgcgttatacagtgattgctttatgcattggttcatctctgacagaattggtatttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
                     |   |  |  | || |||| |  || ||   || |    |  |||  |    ||||||| || ||||||||| | |||||||||||  |||| || || |||||||| ||||||||||||||||| || || || || || ||||| ||| | ||
--------------------gtatgtggttaaatgtttcaacgttgccactttttgacacttgcttggc---acagCTGTTAACAAGGATGAGCTTCTTCAAATGGTTCGATACGGCGCGGAGATGGTTTTCAGTTCTAAAGATAGTACCATAACCGATGAAGATATAGATCGTAT

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ15818 (Selaginella moellendorffii), 3'ss of exon 12
gtaagtgcgttatacagtgattgctttatgcattggttcatctctgacagaattggtatttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
                                  | |||| |  || ||   || |    |  |||  |    ||||||| || ||||||||| | |||||||||||  |||| || || |||||||| ||||||||||||||||| || || || || || ||||| ||| | ||
----------------------------------gtttcaacgttgccactttttgacacttgcttggc---acagCTGTTAACAAGGATGAGCTTCTTCAAATGGTTCGATACGGCGCGGAGATGGTTTTCAGTTCTAAAGATAGTACCATAACCGATGAAGATATAGATCGTAT

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|116473628|gb|EG516220.1|EG516220
EST:     AGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA                         CTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGG
genomic: AGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAAgtaagtgcgt ... aactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGG
EST: gi|116473629|gb|EG516221.1|EG516221
EST:     GTTATTCAACAAGGGAGATTGGCAGAACAGAAAA                         CTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGG
genomic: GTTATTCAACAAGGGAGATTGGCAGAACAGAAAAgtaagtgcgt ... aactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGG
EST: gi|125181844|gb|EL197762.1|EL197762
EST:     GCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAAACAGAAAA                         CTGTCAATAAGGATGAGTTG
genomic: GCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAA-CAGAAAAgtaagtgcgt ... aactatgcagCTGTCAATAAGGATGAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctttatgcattggttcatctctgacagaattggtatttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
                                         tcttaac  putative branch site (score: 2)
                                   tatttatcttaactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgcgttatacagtgattgctttatgcattggttcatctctgacagaattggtatttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT