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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtttcttttcatttaagtttgaacattgttgatgaagaacagatttagcttccacgtttctaaatttccagagatgacactatttcgcattttttgcagCTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCACCACCTTCAG

Basic information

species Arabidopsis thaliana
transcript AT1G79210.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79210.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G16660.1 (Glycine max), 3'ss of exon 1
ggtttcttttcatttaagtttgaacattgttgatgaagaacagatttagcttccacgtttctaaatttccagagatgacactatttcgcattttttgcagCTTGATTTAGT-TGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCACCACCTTCAG
| | | |||| || || || | | | |||| | ||| | || | || | || | || | | || ||||| |||||||| |||||||| ||||||||||||||||| || ||
---tcaagtgcttttactttccaatataaaataaaacaatatgattgttttgttttgttattgtgattgtgattgtaacttgcaagtaaagttgtgattgcagATTCTTGTGCGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG

upper sequence: AT1G79210.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G17810.1 (Glycine max), 3'ss of exon 1
-----------ggtttcttttcatttaagtttgaacattgttgatgaagaacagatttagcttccacgtttctaaatttccagagatgacactattt----cgcattttt---tgcagCTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCACCACCTTCAG
||||| | ||| || || | | | | | | | | | | || | | | | ||| | | | | || | ||||| || || | ||||| |||||||| |||||||| ||||||||||||||||| || ||
tgaagataaaaaaccctctttcaagtgttttt-aattttctataaatatagtaaactgattatttttggtttgttttgtgctgtgattgtaacttgcaaagTGAAGTTGTGAGTGCAGATTTCTTGCGC-GGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG

upper sequence: AT1G79210.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G17810.3 (Glycine max), 3'ss of exon 1
----ggtttcttttcatttaagtttgaacattgttgatgaagaacagatttagcttccacgtttctaaatttccagagatgacactatttcgcattttttgcagCTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCACCACCTTCAG
| |||| | || | | || || || | || | ||| | || | || || | | || | | | ||||| || || | ||||| |||||||| |||||||| ||||||||||||||||| || ||
ctttcaagtgtttttaattttctataaatatagtaaact--gattatttttggtttgttttgtgctgtgattgtaac--ttgcaaagtgaagttgtgagtgcagATTTCTTGCGC-GGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG

upper sequence: AT1G79210.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G25940.1 (Glycine max), 3'ss of exon 1
-------ggtttcttttcattta--agtttgaacattgttgatgaagaacagatttagcttccacgtttctaaatttccagagatgacactatttcgcattt--tttgcagCTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCACCACCTTCAG
|||||||||| || ||||| | || | | |||| ||| || || || || | | || | || ||||||| || || ||||| |||||||| |||||||| ||||||||||||||||| || ||
ttttctttttttcttttcaactactgaagtgaacccttttatttctatat---tttaaattcgtatttgctttcgtttcaatttctgcggtgttgggtataagGTTTGCAGTTT--CTTGTGCGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG

upper sequence: AT1G79210.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G17810.5 (Glycine max), 3'ss of exon 1
------ggtttcttttcatttaagtttgaacattgttgatgaagaacagatttagcttccacgtttctaaatttccagagatgacactattt----cgcattttt---tgcagCTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCACCACCTTCAG
||||| | ||| || || | | | | | | | | | | || | | | | ||| | | | | || | ||||| || || | ||||| |||||||| |||||||| ||||||||||||||||| || ||
ataaaaaaccctctttcaagtgttttt-aattttctataaatatagtaaactgattatttttggtttgttttgtgctgtgattgtaacttgcaaagtgaagTTGTGAGTGCAGATTTCTTGCGC-GGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG

upper sequence: AT1G79210.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G25940.3 (Glycine max), 3'ss of exon 1
ggtttcttttcattta--agtttgaacattgttgatgaagaacagatttagcttccacgtttctaaatttccagagatgacactatttcgcattt--tttgcagCTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCACCACCTTCAG
|||||||||| || ||||| | || | | |||| ||| || || || || | | || | || ||||||| || || ||||| |||||||| |||||||| ||||||||||||||||| || ||
-ttttcttttcaactactgaagtgaacccttttatttctatat---tttaaattcgtatttgctttcgtttcaatttctgcggtgttgggtataaggtttgcagTTT--CTTGTGCGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG

upper sequence: AT1G79210.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G41330.1 (Glycine max), 3'ss of exon 1
ggtttcttttcatttaagt-ttgaacattgttgatgaa--gaacagatttagcttccacgtttctaaatttccagagatgacactatttcgcattttt-tgcagCTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCACCACCTTCAG
| || || |||| || ||| | || || || ||| || | |||| ||| || ||| || | || | | ||||| || || ||||| |||||||| |||||||| ||||||||||||||||| || ||
-aaaccccctctttcaagtgtttttaattttcaataaatagagtagaattgctatttttgtttt---gttttatgatgtgattgtaacttgcttgtgagtgcagATT--CTTGCGCGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG

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|86065881|gb|DR361638.1|DR361638
EST:     CTTCTCTTGCGACCATTCCGTTGTTCGATCCATATATCAAAG                         CTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCA
genomic: CTTCTCTTGCGACCATTCC---GTTCGATCCATATATCAAAGgtatgttgct ... ttttttgcagCTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCA
EST: gi|86065884|gb|DR361641.1|DR361641
EST:     TGCGACCATTCCGTTGTTCGATCCATATATCAAAG                         CTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCA
genomic: TGCGACCATTCC---GTTCGATCCATATATCAAAGgtatgttgct ... ttttttgcagCTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCA
EST: gi|86065879|gb|DR361636.1|DR361636
EST:     CTTCTCTTGCGACCATTCCGTTGTTCGATCCATATATCAAAG                         CTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCA
genomic: CTTCTCTTGCGACCATTCC---GTTCGATCCATATATCAAAGgtatgttgct ... ttttttgcagCTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCA
EST: gi|47831532|gb|CK121216.1|CK121216
EST:     GTTCGATCCATATATCAAAG                         CTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCA
genomic: GTTCGATCCATATATCAAAGgtatgttgct ... ttttttgcagCTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCA
EST: gi|86065878|gb|DR361635.1|DR361635
EST:     CTTCTCTTGCGACCATTCCGTTGTTCGATCCATATATCAAAG                         CTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCA
genomic: CTTCTCTTGCGACCATTCC---GTTCGATCCATATATCAAAGgtatgttgct ... ttttttgcagCTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCA
EST: gi|86065891|gb|DR361648.1|DR361648
EST:     TGCGACCATTCCGTTGTTCGATCCATATATCAAAG                         CTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCA
genomic: TGCGACCATTCC---GTTCGATCCATATATCAAAGgtatgttgct ... ttttttgcagCTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCA
EST: gi|86065890|gb|DR361647.1|DR361647
EST:     GCGACCATTCCGTTGTTCGATCCATATATCAAAG                         CTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCA
genomic: GCGACCATTCC---GTTCGATCCATATATCAAAGgtatgttgct ... ttttttgcagCTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCA
EST: gi|86065889|gb|DR361646.1|DR361646
EST:     CTTCTCTTGCGACCATTCCGTTGTTCGATCCATATATCAAAG                         CTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCA
genomic: CTTCTCTTGCGACCATTCC---GTTCGATCCATATATCAAAGgtatgttgct ... ttttttgcagCTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagcttccacgtttctaaatttccagagatgacactatttcgcattttttgcagCTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCACCACCTTCAG
             ttctaaa  putative branch site (score: 2)
 catttttt  putative PPT
 tttctaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtttcttttcatttaagtttgaacattgttgatgaagaacagatttagcttccacgtttctaaatttccagagatgacactatttcgcattttttgcagCTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCACCACCTTCAG

- - - - - - - - agtttga
- - - - - - - - - - - - - - - - - gaagaac
- - - - - - - - - - - - - - - - - - - - - gatttag