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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtttttttgttttactcaaaaactctgcttttcaattcaatttcagcaatctaaatctcaattaaaaaaatcaacacagTATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATGAAGGAACTCAGGGAAGTGACAGCAAAACATCCATGGAACATAATGACCACATCAG

Basic information

species Arabidopsis thaliana
transcript AT4G34050.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G34050.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G33780.1 (Glycine max), 3'ss of exon 1
--------------------------------------------------gtctgtttttttgttttactcaaaaactctgcttttcaattcaatttcagcaatctaa--atctcaattaaaaaaatca------acacagTATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATGAAGGAACTCAGGGAAGTGACAGCAAAACATCCATGGAACATAATGACCACATCAG
                                                   | | | |||| | |||     ||||   |  | || ||   ||  ||     | |     | |    |||||   | |          ||||||| |||||||||||||| || || |||||||| ||||| ||||| ||||| || ||  ||||||||||||| |||||                    
gtaccaccccaattgcattcctttgataaaaagaaaaagaaaaaaaatctttttctcttttgggtttttgataaaatggttatgttgaaaaaaaaatctattttttgggggtttttgataaaatggttatgctgtgtttagTATATTCTGGAGACAAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAACTGAGAGAGTTGACAGCAAAACACCCATG--------------------

upper sequence: AT4G34050.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G11530.2 (Glycine max), 3'ss of exon 1
----------------------------------------------------------gtctgtttttttgttttactcaaaaactctgctt----ttcaattcaatttcagcaatctaaatctcaattaaaaaaatca------acacagTATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATGAAGGAACTCAGGGAAGTGACAGCAAAACATCCATGGAACATAATGACCACATCAG
                                                          |  | || |||| |||||   || |  | || |        || ||  |||            | |    |||||   | |          ||||||| |||||||| ||||| || || |||||||| ||||| ||||| ||||| || ||  ||||||||||||| |||||                    
gtaccaccccaattacattcctttgttaaaaaagaaaaaaaaaatctttttttcttttggtttttattttattttatataatagttatgttgaaaacaaaaatctttttttttcgggggggtgtttgataaaatggttatgttgtgtttagTATATTCTGGAGACCAGTGTCTACCCAAGAGAACCTGAATCCATGAAAGAACTGAGAGAGTTGACAGCAAAACACCCATG--------------------
















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|47829433|gb|CK119117.1|CK119117
EST:     ATCAAGAAGTTGGTCACAAGAGTCTCTTACAGAGCGATGATCTCTACCAG                         TATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATGAAGGAA
genomic: ATCAAGAAGTTGGTCACAAGAGTCTCTTACAGAGCGATGATCTCTACCAGgtctgttttt ... atcaacacagTATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATGAAGGAA
EST: gi|125222855|gb|EL236940.1|EL236940
EST:     AAGAGTCTCTTACAGAGCGATGATCTCTACCAG                         TATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGA
genomic: AAGAGTCTCTTACAGAGCGATGATCTCTACCAGgtctgttttt ... atcaacacagTATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGA
EST: gi|124822616|gb|EH907482.1|EH907482
EST:     CTTACAGAGCGATGATCTCTACCAG                         TATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATGAAGGAA
genomic: CTTACAGAGCGATGATCTCTACCAGgtctgttttt ... atcaacacagTATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATGAAGGAA
EST: gi|86020813|gb|DR316559.1|DR316559
EST:     ATCAAGAAGTTGGTCACAAGAGTCTCTTACAGAGCGATGATCTCTACCAG                         TATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATGAAGGAA
genomic: ATCAAGAAGTTGGTCACAAGAGTCTCTTACAGAGCGATGATCTCTACCAGgtctgttttt ... atcaacacagTATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATGAAGGAA
EST: gi|86020787|gb|DR316533.1|DR316533
EST:     ATCAAGAAGTTGGTCACAAGAGTCTCTTACAGAGCGATGATCTCTACCAG                         TATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATGAAGGAA
genomic: ATCAAGAAGTTGGTCACAAGAGTCTCTTACAGAGCGATGATCTCTACCAGgtctgttttt ... atcaacacagTATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATGAAGGAA
EST: gi|124730985|gb|EH822387.1|EH822387
EST:     ATCAAGAAGTTGGTCACAAGAGTCTCTTACAGAGCGATGATCTCTACCAG                         TATATACTGGAGACAAGTGTGTAT
genomic: ATCAAGAAGTTGGTCACAAGAGTCTCTTACAGAGCGATGATCTCTACCAGgtctgttttt ... atcaacacagTATATACTGGAGACAAGTGTGTAT
EST: gi|124773910|gb|EH864039.1|EH864039
EST:     AAGTTGGTCACAAGAGTCTCTTACAGAGCGATGATCTCTACCAG                         TATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATG
genomic: AAGTTGGTCACAAGAGTCTCTTACAGAGCGATGATCTCTACCAGgtctgttttt ... atcaacacagTATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATG
EST: gi|116475760|gb|EG518352.1|EG518352
EST:     ATCAAGAAGTTGGTCACAAGAGTCTCTTACAGAGCGATGATCTCTACCAG                         TATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATGAAGGAA
genomic: ATCAAGAAGTTGGTCACAAGAGTCTCTTACAGAGCGATGATCTCTACCAGgtctgttttt ... atcaacacagTATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATGAAGGAA
EST: gi|124924253|gb|EL002367.1|EL002367
EST:     AGTCTCTTACAGAGCGATGATCTCTACCAG                         TATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATGAAGGAA
genomic: AGTCTCTTACAGAGCGATGATCTCTACCAGgtctgttttt ... atcaacacagTATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATGAAGGAA
EST: gi|47832008|gb|CK121692.1|CK121692
EST:     ATCAAGAAGTTGGTCACAAGAGTCTCTTACAGAGCGATGATCTCTACCAG                         TATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATGAAGGAA
genomic: ATCAAGAAGTTGGTCACAAGAGTCTCTTACAGAGCGATGATCTCTACCAGgtctgttttt ... atcaacacagTATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATGAAGGAA
EST: gi|116475771|gb|EG518363.1|EG518363
EST:     CAAGAAAGTTGGTCACAAGAGTCTCTTACAGAGCGATGATCTCTACCCAG                         TATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATGAAAGG
genomic: CAAG-AAGTTGGTCACAAGAGTCTCTTACAGAGCGATGATCTCTA-CCAGgtctgttttt ... atcaacacagTATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATG-AAGG
EST: gi|124743995|gb|EH835157.1|EH835157
EST:     TTGGTCACAAGAGTCTCTTACAGAGCGATGATCTCTACCAG                         TATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGA
genomic: TTGGTCACAAGAGTCTCTTACAGAGCGATGATCTCTACCAGgtctgttttt ... atcaacacagTATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGA
EST: gi|116377761|gb|EG420353.1|EG420353
EST:     ATCAAGAAGTTGGTCACAAGAGTCTCTTACAGAGCGATGATCTCTACCGG                         TATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATGAAGGAA
genomic: ATCAAGAAGTTGGTCACAAGAGTCTCTTACAGAGCGATGATCTCTACCAGgtctgttttt ... atcaacacagTATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATGAAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcttttcaattcaatttcagcaatctaaatctcaattaaaaaaatcaacacagTATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATGAAGGAACTCAGGGAAGTGACAGCAAAACATCCATGGAACATAATGACCACATCAG
                        atctaaa  putative branch site (score: 3)
                       aatctaaatctcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtttttttgttttactcaaaaactctgcttttcaattcaatttcagcaatctaaatctcaattaaaaaaatcaacacagTATATACTGGAGACAAGTGTGTATCCTAGAGAACCAGAATCAATGAAGGAACTCAGGGAAGTGACAGCAAAACATCCATGGAACATAATGACCACATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA