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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtcaccattttacttgtctttcatcatttccttgtccgataacttccatctcttacagagctttctgattaaacaaacttctatccagATTTGCTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACTGGAAAGGAGGACATCAGAGCAATTACAAAAATGGCTCGTTCTGCG

Basic information

species Arabidopsis thaliana
transcript AT3G13870.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: LOC_Os01g39310.1 (Oryza sativa), 3'ss of exon 17
gtgtcaccattttacttgtctttcatcatttccttgtccgataacttccatctcttacagagctttctgattaaacaaacttctatccagATTTGCTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACTGGAAAGGAGGACATCAGAGCAATTACAAAAATGGCTCGTTCTGCG
                 |     || ||  |  |  | | |    |      | | | |||     || |||  |  ||   | ||  || ||  | ||| | ||||||| |||| |||| ||||||||| | || ||||| |||||||||||||| |  || ||||| ||||  |||||||| || 
-------------gtgagctgcacaccaaatgttgattcaaatgatatgtgttttcagaga-----ctaattggatgaaaaac-atgaagGTTCTCAACACTATTCAGCCGTGATGCTGACTCAATGCCAAGAGTGTGGACCGGAAAGGAGGACATAAAGGCCATTACTAAAACTGCTCGTTCAGCT

upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA08G20610.1 (Glycine max), 3'ss of exon 17
gtgtcaccattttacttgtctttcatcatttccttgtccgataacttccatctcttacagagctttctgattaaacaaacttctatccagATTTGCTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACTGGAAAGGAGGACATCAGAGCAATTACAAAAATGGCTCGTTCTGCG
|||| |   || | |   |  |   |    |  ||  | | |   ||   | |     |||      |   | |||    ||  |  ||| ||| | |   | || ||||||||||||||||||||||| ||||||||||| || || || || ||  |||| || || || |  ||||| ||| | 
gtgtgaatcttctgcaacttctaagttgactt-ttacctgttcgattgagttttacttagatgcacttaccttaac---tttgaaagcagGTTTACAATGTTGTTTAGCCATGATTCTGATTCAATGCCTCGTGTTTGGACGGGGAAAGAAGATATACGAGCCATCACCAAGACTGCTCGCTCTTCT

upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA07G01230.1 (Glycine max), 3'ss of exon 17
gtgtcaccatttt---acttgtctttcatcatttccttgtccgat-aacttccatctcttacagagctttctgattaaacaaacttctatccagATTTGCTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACTGGAAAGGAGGACATCAGAGCAATTACAAAAATGGCTCGTTCTGCG
|| | |   || |   |||| |   |   | ||| | ||| || |  | ||  |  |  ||   |  |  ||        ||  ||  || ||| ||| | |   | || ||||||||||||||||||||||| ||||||||||| || || || || ||  |||| || || || |  ||||| ||| | 
gtatgaatcttctgcaacttctaagttgacttttacctgttcgtttgagttttactttatatgcacttacct-------taactttgaatgcagGTTTACGATGTTGTTTAGCCATGATTCTGATTCAATGCCTCGTGTTTGGACGGGTAAAGAAGATATACGAGCCATCACCAAGACTGCTCGCTCTTCT

upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA15G02780.1 (Glycine max), 3'ss of exon 17
gtgtcaccattttacttgtctttcatcatttccttgtccgataacttccatctc-ttacagagctttctgattaaacaaacttctatccagATTTGCTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACTGGAAAGGAGGACATCAGAGCAATTACAAAAATGGCTCGTTCTGCG
|| | |  |  |||     | || |   ||  |||||  ||    ||   | |   |  ||||     |   |    ||| ||| |  ||| |||   ||| | || || |||||||||||||||||||| ||| ||||||| ||||| || ||  |  ||||||| || ||    || || ||| ||
gtatga--aacttatgcaacatttaa-gttgacttgttagacttgttgagttttgctttagaggcacttatct---taaatttcaaagcagGTTTTTGACATTGTTTAGTCATGATTCTGATTCAATGCCTCGTATTTGGACGGGAAAAGAAGATGTTCGAGCAATCACCAAGTCTGCCCGCTCTTCG

upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA13G42650.1 (Glycine max), 3'ss of exon 18
gtgtcaccattttacttgtctttcatcatttccttgtccgataacttccatctcttacagagctttctgattaaacaaacttctatccagATTTGCTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACTGGAAAGGAGGACATCAGAGCAATTACAAAAATGGCTCGTTCTGCG
            ||     |||  |  |  |    ||    |   |    | |  |  ||||     |   |    ||| ||| |  ||| |||   ||| | || || |||||||||||||||||||| ||| ||||||| ||||| || ||  |  |||| || || ||    || || ||| | 
-----------gtatgaaccttatacaacatgtaagtttacttgttgagttttactttagaggcacttatct---taaatttcaaagcagGTTTATGACATTGTTTAGTCATGATTCTGATTCAATGCCTCGTATTTGGACGGGAAAAGAAGATGTTCGAGCCATCACCAAGTCTGCCCGCTCTTCC

upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv09s0002g02200.t01 (Vitis vinifera), 3'ss of exon 17
-------------------gtgtcaccattttacttgtctttcatcatttccttgtccgataact-----tccatctcttacagagctttctgattaa-acaaacttc----tatccagATTTGCTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACTGGAAAGGAGGACATCAGAGCAATTACAAAAATGGCTCGTTCTGCG
                    ||  |   ||||| ||  | ||  |  |||     | | | || |     || |   |||       | ||  ||    |   | ||      || ||| ||||| ||| | || |||||||||||||| |||||||||||||| |||||||| || || || ||  | ||||| || ||||  ||||||||| | 
gttgcaactgttacattatttgaaattcttttattttccctttttatttttagattacaagaaatcgggatctactgctttggactgtatcaaatggggatggattttactgcatgcagGTTTGCGACATTGTTTAGCCATGATTCTGACTCAATGCCACGTGTCTGGACTGGGAAAGAAGATATTCGTGCAATCACCAAAACTGCTCGTTCTTCT

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|124927421|gb|EL005161.1|EL005161
EST:     AAGGAAGAGGCTGGAAGAGCGATGATGCGCATGAAGGATAG                         ATTTGCTACAATCTTCAGCCATGATTCTGATTCAATGCCA
genomic: AAGGAAGAGGCTGGAAGAGCGATGATGCGCATGAAGGATAGgtgtcaccat ... ttctatccagATTTGCTACAATCTTCAGCCATGATTCTGATTCAATGCCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccgataacttccatctcttacagagctttctgattaaacaaacttctatccagATTTGCTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACTGGAAAGGAGGACATCAGAGCAATTACAAAAATGGCTCGTTCTGCG
                             ttctgat  putative branch site (score: 3)
                                            cttctatcc  putative PPT
                                  attaaacaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtcaccattttacttgtctttcatcatttccttgtccgataacttccatctcttacagagctttctgattaaacaaacttctatccagATTTGCTACAATCTTCAGCCATGATTCTGATTCAATGCCACGTGTTTGGACTGGAAAGGAGGACATCAGAGCAATTACAAAAATGGCTCGTTCTGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA