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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactattatccacgacatttgcaactctattttttttaacagaaaccacagttctcttgataggccaatatatattttcaaaacttgcattagagctatccttaattctttatctattgttttatatcatgggagagaaggatagttttcagacatgcttctgatttttgcagATTTGGAAACTAATGAATGTTTGGAAAACAACGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGG

Basic information

species Arabidopsis thaliana
transcript AT3G52850.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G52850.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os11g02464.1 (Oryza sativa), 3'ss of exon 5
gtactattatccacgacatttgcaactctattttttttaacagaaaccacagttctcttgataggccaatatatattttcaaaacttgcattagagctatccttaattctttatctattgttttatatcatgggagagaaggatagttttcagacatgcttctgatttttgcagATTTGGAAACTAATGAATGTTTGGAAAACAACGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGG
                     |    |  |||  ||| || ||         |||| |   |  ||  ||  ||  |   |||| ||  |    ||| | | | | ||  ||     ||| ||| ||  ||  |              ||||  |||| | ||     ||| |||| |  |||| ||||| || ||||| ||||| ||||| || ||||||||||| ||||| |||||  ||||||||| |
---------------------gttggtgcattaatttcaataggt-------ttctatctgtttgctcattcatgata--aaaatttatac---agcaagcttaacttgcttgggccttgcttt-tagtatttg--------------ttcattcatgttacttcgaattgtagATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAG

upper sequence: AT3G52850.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os12g02390.1 (Oryza sativa), 3'ss of exon 5
gtactattatccacgacatttgcaactctattttttttaacagaaaccacagttctcttgataggccaatatatattttcaaaacttgcattagagctatccttaattctttatctattgttttatatcatgggagagaaggatagttttcagacatgcttctgatttttgcagATTTGGAAACTAATGAATGTTTGGAAAACAACGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGG
                     |    |  |||  ||| || |||        || | |   |  ||  ||  ||  |   |||| ||  |    ||| | | | | ||  ||     ||| ||| ||  ||  |          | |  | |  |||| | ||      || |||| |  |||| ||||| || ||||| ||||| ||||| || ||||||||||| ||||| |||||  ||||||||| |
---------------------gttggtgcattaatttcaatagat-------ttttatctgtttgctcattcatgata--aaaatttatac---agcaagcttaacttgcttgggccttgcttt-tagtatttgtt-------cattcatgattcatgttacttcgaactgtagATATACAAACAAATGAGTGCTTGGAGAACAATGGTGGCTGTTGGCAAGACAAGGCTGCTAACATCTCTGCATGCAAG

upper sequence: AT3G52850.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G347541_T01 (Zea mays), 3'ss of exon 5
gtactattatccacgacatttgcaactctattttttttaacagaaaccacagttctcttgataggccaatatatattttcaaaacttgcattagagctatccttaattctttatctattgttttatatcatgggagagaaggatagttttcagacatgcttctgatttttgc---agATTTGGAAACTAATGAATGTTTGGAAAACAACGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGG
                                                   | |  ||||||       | | ||||||    |  | || |   ||| | | | ||   | || || |      | | ||  |   |  | ||  | ||  ||  | |   | ||||  ||   |||| |  |||| || || ||  | || ||||| ||||| || |||||||| || ||||||||||| |||||||||| |
------------------------------------------------gttggtgccttgatt------tctctattttttttatgttcact---gct-tacatgatctatcatatacttccaagtgtgatttgtatgttgcatgctctt--gatgttcactttatttcggccttagATATACAAACAAACGAGTGCCTAGAGAACAATGGTGGCTGTTGGCAAGATAAGGCTGCCAACATCACTGCATGCAAG

upper sequence: AT3G52850.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G41070.3 (Glycine max), 3'ss of exon 5
gtactattatccacgacatttgcaactctattttttttaacagaaaccacagttctcttgataggccaatatatattttcaaaacttgcattagagctatccttaattctttatctattgttttatatcatgggagagaaggatagttttcagacatgcttctgatttttgcagATTTGGAAACTAATGAATGTTTGGAAAACAACGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGG
                                                                    || |  || |  | ||  |    |||   ||    ||  |   |   |    ||  || |  |   |||     ||  ||||   || || || |  | ||||||||  ||||||| ||||| |||||||||||||| ||||| || ||||| |||||| || | ||||||||||||||||||
-------------------------------------------------------------------gattttgatctagataaaatcatataggtgtactggtagctgactcattgaaattgaatcttgttc-agaagctaatgatttt---ac-tgattat--tctttgcagACCTGGAAACAAATGAGTGTTTGGAAAACAATGGTGGTTGTTGGCAGGACAAATCTTCTAACATTACTGCATGCAGG

upper sequence: AT3G52850.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G00510.1 (Glycine max), 3'ss of exon 5
gtactattatccacgacatttgcaactctattttttttaacagaaaccacagttctcttgataggccaatatatattttcaaaacttgcattagagctatccttaattctttatctattgttttatatcatgggagagaaggatagttttcagaca----tgcttctgatttttgcagATTTGGAAACTAATGAATGTTTGGAAAACAACGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGG
                                                                          | | | | | ||  || | | || ||   ||||   |    | |  |||  |||  ||| | | ||| || | | ||||  |    || || |  | ||||||||  ||||||| ||||| |||||| ||||||| ||||| || ||||| ||||||||| | ||||||||||||||||||
-------------------------------------------------------------------------caatcttatatctc-cacttg-gcaatgtgtaatgtgtg--ttgtcatttgctattttgg-ataaaagaattgatatcaggtaccattgattatattctttgcagACATGGAAACAAATGAGTGTTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTTCTAACATTACTGCATGCAGG

upper sequence: AT3G52850.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G14800.1 (Glycine max), 3'ss of exon 5
gtactattatccacgacatttgcaactctattttttttaacagaaaccacagttctcttgataggccaatatatattttcaaaacttgcattagagctatccttaattctttatctattgttttatatcatgggagagaaggatagttttcagacatgctt--ctgatttttgcagATTTGGAAACTAATGAATGTTTGGAAAACAACGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGG
                                                                      |   |  |    | ||| ||   | || ||   ||||      | | ||   |||| |    ||| | ||| || | | ||||  |   ||   |  | ||||||||  ||||||| ||||| || ||| ||||||| ||||| || ||||| ||||||||||| ||||||||||||||||||
---------------------------------------------------------------------caagcaactc---atctttcacctg-gcaatgtgtaatgtgcgttatcttcccttatttt---ggataaaagaattgatatcaggtaccattgattattctttgcagACATGGAAACAAATGAGTGCTTGCAAAACAATGGTGGTTGTTGGCAGGACAAAGCTGCTAACATTACTGCATGCAGG

upper sequence: AT3G52850.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G44580.1 (Glycine max), 3'ss of exon 5
gtactattatccacgacatttgcaactctattttttttaacagaaaccacagttctcttgataggccaatatatattttca-aaacttgcattagagctatccttaattctttatctattgttttatatcatgggagagaaggatagttttcagacatgcttctgatttttgcagATTTGGAAACTAATGAATGTTTGGAAAACAACGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGG
                                                                    || |  || |  | ||| ||  ||  | | ||     |  |   |   |    ||  || |  |   |||     || |||||   || || || |  | ||||||||  | ||||| ||||| |||||||||||||| ||||| || ||||| |||||| || | ||||||||||||||||| 
------------------------------------------------------------------ggattttgatctagataaaattatataggtg-tactggcagctgactcattgaaattgaatctttttc-agaagctaatggtttt---ac-tgattat--tctttgcaGACCTCGAAACAAATGAGTGTTTGGAAAACAATGGTGGTTGTTGGCAGGACAAATCTTCTAACATTACTGCATGCAG-

upper sequence: AT3G52850.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0058g01360.t01 (Vitis vinifera), 3'ss of exon 5
gtactattatccacgacatttgcaactctattttttttaacagaaaccacagttctcttgataggccaatatatatt-ttcaaaacttgcattagagctatccttaattctttatctattgttttatatcatgggagagaaggatagttttcagacatgcttctgatttttgcagATTTGGAAACTAATGAATGTTTGGAAAACAACGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGG
                                                                   |   |||||| || |  |  |  |||   |        || |   ||   |   || |        |||   |    |  | |||     |    ||| | | | ||||  | || || ||||| ||||||||||| || |||||||||||||| || || ||||| || ||||||||||||| |
------------------------------------------------------------------tatattatattatttaggaaataaattgtggtatgaagcaaatgagtacacacccttgt--------ggaatcagtattcatcttcttctgt-taactgttctctacagAGGTAGAGACAAATGAGTGTTTGGAAAATAATGGTGGATGCTGGCAGGATAAGGCTGCTAATATTACTGCATGCAAG

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|125169541|gb|EL193519.1|EL193519
EST:     TGTTCGGGTTTTCAAGAGTCAACGGAACCAGCTATCTGTCTTAACTGAAG                         ATTTGGAAACTAATGAATGTTTGGAA
genomic: TGTTCGGGTTTTCAAGAGTCAACGGAACCAGCTATCTGTCTTA-CTGAAGgtactattat ... atttttgcagATTTGGAAACTAATGAATGTTTGGAA
EST: gi|86037689|gb|DR333444.1|DR333444
EST:     GTGTTCGGGTTTTCAAGAGTCAACGGAACCAGCTATCTGTCTTACTGAAG                         ATTTGGAAACTAAT
genomic: GTGTTCGGGTTTTCAAGAGTCAACGGAACCAGCTATCTGTCTTACTGAAGgtactattat ... atttttgcagATTTGGAAACTAAT
EST: gi|86037688|gb|DR333443.1|DR333443
EST:     GTGTTCGGGTTTTCAAGAGTCAACGGAACCAGCTATCTGTCTTACTGAAG                         ATTTGGAAACTAATGAATGTTTGGAAAACAACGGTGGATGCTGGCAAGACA
genomic: GTGTTCGGGTTTTCAAGAGTCAACGGAACCAGCTATCTGTCTTACTGAAGgtactattat ... atttttgcagATTTGGAAACTAATGAATGTTTGGAAAACAACGGTGGATGCTGGCAAGACA
EST: gi|164219826|gb|ES175784.1|ES175784
EST:     GTGTTCGGGTTTTCAAGAGTCAACGGAACCAGCTATCTGTCTTACTGAAG                         ATTTGGAAACTAATGAATGTTTGGAAAAC
genomic: GTGTTCGGGTTTTCAAGAGTCAACGGAACCAGCTATCTGTCTTACTGAAGgtactattat ... atttttgcagATTTGGAAACTAATGAATGTTTGGAAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttatatcatgggagagaaggatagttttcagacatgcttctgatttttgcagATTTGGAAACTAATGAATGTTTGGAAAACAACGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGG
                                        ttctgat  putative branch site (score: 3)
                                              tttttgc  CT-rich tract
                       atagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactattatccacgacatttgcaactctattttttttaacagaaaccacagttctcttgataggccaatatatattttcaaaacttgcattagagctatccttaattctttatctattgttttatatcatgggagagaaggatagttttcagacatgcttctgatttttgcagATTTGGAAACTAATGAATGTTTGGAAAACAACGGTGGATGCTGGCAAGACAAAGCTGCCAACATTACTGCATGCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC