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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaaaacaaacactttttttttatctctcagtttccattgatctaaagctttaaataaaacgttttgaatatgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA

Basic information

species Arabidopsis thaliana
transcript AT3G26440.4
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 7
--------------------------gtaacaaaacaaacactt-------tttttttatctctcagtttccattgatctaaagctttaaat------aaaacgttttgaat----atgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
                           | | |  | |||   |        |||||  |  |   ||| |  | || |       ||| |||      || || ||   |||     | ||||  |   ||||||||||| ||  |||||||||||||||| ||  | ||||||||||| ||||||||||| ||||||||||| || || |||||  | ||  | ||||||
gtaaggagctaagatgttcattattttttagaggataaattttcattgtagtttttgcaattaatagtgtttagtgcttacctaatttcaattatgtcaatacattgacaattttagtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCAGAA

upper sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 7
-------------------------------gtaacaaaaca--aacactttttttttatctctcagtttccattgatc-taaagctttaaataaaacgtt---ttgaatatgtt------tctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
                                ||| |||  |         |||||  |  | | ||| | || || |     |  || || ||     ||   ||||  || ||      ||  |   ||||||||||| ||  |||||||||||||||| ||  | ||||||||||| ||||||||||| ||||||||||| || || |||||  | ||  | || |||
gttaggagctaagcggttaattattttttagataataaattatcgttgtagtttttgcaagtattagtgttcaatgcttacctaatttcaattatgttattatattgacaattttggtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCGGAA

upper sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G14040.1 (Glycine max), 3'ss of exon 7
--------------------------------------------------gtaac----aaaacaaacactttttttttatctc---tcagt----ttccattgatctaa--agctttaaataaaacgttttgaatatgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
                                                  | |||    |  |  |  | | |||   || ||    |||      |||   | ||  ||  |  ||   |||  | |  || ||| | ||||  |   ||||||||||| ||  |||||||||||||||| ||  | ||||||||||| ||||| || || ||||||||||| || || |||||| | ||  | ||||| 
gtaagaatccattgcgctcgatcataaatattggatgacatattttccttgcaactcttaccatcattattgtttgcctaactaaagtcaaaagtgttctgctaattcaatcatgttatgatattaagcatttaatttttttccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAG

upper sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G30830.1 (Glycine max), 3'ss of exon 7
--------------------------------------------------gtaac----aaaacaaacactttttttttatctc---tcag--------tttccattgatctaaagctttaaataaaacgttttgaatatgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
                                                  | |||    |  |  |  | | |||   || ||    |||         |    ||| |||||     | | || || | |||  |||   ||||  |   ||||||||||| ||  |||||||||||||||| ||  | ||||||||||| ||||| || || ||||||||||| || || |||||| | ||  | ||||||
gtaagaatccattgcgctcgatcgtaaatattggatgacaaattttccttgcaacttttaccattattattgtttgcctaactaaaatcaaaagtgttctgcttattcatctatgttatgatattaagcattt--aattattttccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAA

upper sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G14050.1 (Glycine max), 3'ss of exon 5
gtaacaaaacaaacacttt---ttttttatctctcagtttccattgatctaaagctttaaa--taaaacgttttg--aatatgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
|||| |||     |   ||   || |   | | ||| || |  || || |        |||  ||||| | ||||  | |   |||   |   ||||||||||| || |||||||| ||||| || ||  | ||||||||||| ||||| ||||| ||||||||||| || || ||||| || ||| | ||||||
gtaaaaaagttctctgcttaaattctcattgtgtcatttccagttaatattgtttgccaaacttaaaatggtttgttatttctttttcctctcagGTGGTATGCCAAGAGGTTTCTACATCCAGACATTGTGGCACCATATGACTATATTTTCATGTGGGATGAAGACCTGGGGGTTGAGAATTTCAATGCAGAA

upper sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G30850.1 (Glycine max), 3'ss of exon 5
gtaacaaaacaa---acactttttttttatctctcagtttccattgatctaaagctttaaa--taaaacgttttga-atatgtttc-tattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
|||| ||  | |     |  ||||  || |  |  | ||||  || || |        |||  ||||| | ||||  || | ||||   |   ||||||||||| || |||||||| ||||| || ||  | | ||||||||| ||||| ||||| ||||||||||| || || ||||| || ||| | || |||
gtaaaaattctatgcttaaattttcattgtggcatattttcagttaatattgtttaccaaacttaaaatggtttgttatttctttcgcctcttagGTGGTATGCCAAGAGGTTTCTACATCCAGACATTGTGGTACCATATGACTATATTTTCATGTGGGATGAAGACCTGGGGGTTGAGAATTTCAATGCTGAA

upper sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------gtaacaaaacaaacactttttttt-tatctctcagtttccattgatctaaagctttaaataaaacgttttgaatatgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
                              |||| ||    |||||||| |  ||  | ||| |   |  || |||      ||   | ||     ||   |    || | |   ||||||||||| ||||| |||||||||||||| ||  | || |||||||| |||||||| || |||||||||||||| || |||||  | ||  | ||||||
gtaaggagcttctgcaaaggattatttttgaacagaagtttcactttttctggtaggtttcaataagctatggtctgttttattcttttaacttcattctttgcaattttgtcctagGTGGTATGCCAAAAGATTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA

upper sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 7
----------------------------gtaacaaaacaaacactttttttt-tatctctcagtttccattgatctaaagctttaaataaaacgttttgaatatgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
                              |||| ||    |||||||| |  ||  | ||| |   |  || |||      ||   | ||     ||   |    || | |   ||||||||||| |||||||||||||||||||| ||  | || |||||||| |||||||| || |||||||||||||| || |||||  | ||  | ||||||
gtaaggagcttctgcaaaggattatttttgaacagaagtttcactttttctggtaggtttcaataagctatggtctgttttattcttttaacttcattctttgcaattttgtcctagGTGGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA

upper sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S448_20V6.3 (Physcomitrella patens), 3'ss of exon 7
-----------------gtaacaaaacaaacactttttttttatctctcagtttccattgatctaaagctttaaataaaacgttttgaatatgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
                 ||     |     || | |   |  || |||   | | |  || | |  |  ||  | | ||  | ||| |    |   | |||| ||||||||||  ||  | ||| ||||||||||| |  | ||||  ||||||||||| |||||||||||||| |||||||   |     | ||| | ||    
atgcctgtttgttacttgtggtggattct-caatctgactacatttctggctctgctctgttgtcgaagttgtagttaactgatttta----ggggcaattgcagGTGGTATGTCAAGCGATTTTTGCATCCTGATGTGGTGGCACAGTATGAATATATCTTCATTTGGGATGAGGATCTTGATTTGACTCATTTCAATGCGCGG

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|124961155|gb|EL035730.1|EL035730
EST:     GAATGGTCTAAACGGGCGATACACGTCAGTGTACCTAAGCAAACCAAGTG                         GTGGTATGCTAAAAGGTTTCT
genomic: GAATGGTCTAAACGGGCGATACACGTCAGTGTACCTAAGCAAACCAAGTGgtaacaaaac ... tctattgaagGTGGTATGCTAAAAGGTTTCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttccattgatctaaagctttaaataaaacgttttgaatatgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
          atctaaa  putative branch site (score: 3)
                                           tttctatt  putative PPT
                   tttaaataaaacgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacaaaacaaacactttttttttatctctcagtttccattgatctaaagctttaaataaaacgttttgaatatgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA