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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTTTATCAATTGATGAGATGGCTGGAGGCACTCTTACAATATCCAATGGTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagttctactgagataaatattatttttttttttctttaattttgtaagacattctttgatatgttttgaagttgcttctttgtgtatatgata...

Basic information

species Glycine max
transcript GLYMA02G46200.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G46200.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 12
ATCTTTATCAATTGATGAGATGGCTGGAGGCACTCTTACAATATCCAATGGTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagttctactgagataaatattatttttttttttctttaattttgtaagacattctttgatatgttttgaagttgcttctttgtgtatatgata
  |  | ||||||||||||||||| ||||| ||  | || || || || ||||||||||| ||||||||| | || || ||||| |||||||| || |||||       ||  | |      | |   |    ||    ||  ||  ||     || |||| || || ||     | ||   |   |    |  |     
GGCACTCTCAATTGATGAGATGGCAGGAGGAACATTCACCATCTCTAACGGTGGTGTTTACGGAAGCCTTATCAGCACACCTATCATCAACCCCCCACAGgtcctt---tttcatttttgccacttgcaaaaattgccctcactaggtt-----gatattcattcatctgacacaatgtatatatatctaatgcag----

upper sequence: GLYMA02G46200.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os02g31040.1 (Oryza sativa), 5'ss of exon 11
ATCTTTATCAATTGATGAGATGGCTGGAGGCACTCTTACAATATCCAATGGTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgt--ttggaagttctactgagataaatattatttttttttttctttaattttgtaagacattctttgatatgttttgaagttgcttctttgtgtatatgata
  |    || ||  |  | ||||| ||||| ||  |||| || || |||||||||||||||||||||||| | ||||| ||||| || ||  |||| |||||  |     ||| |  |  | |   |  || |||| ||| |   |    |  ||| ||   |||| || |  | |                          
GGCACAGTCCATCAACAATATGGCAGGAGGGACCTTTACCATCTCAAATGGTGGTGTTTATGGAAGCCTTATCAGTACACCTATCATTAATTCTCCACAGgtgctcacttgtttttttttgctgccttgtaattttgtttgtaagttccctc-taacacgagcttt-atctaatgtag------------------------

upper sequence: GLYMA02G46200.1 (Glycine max), 5'ss of exon 14
lower sequence: AT5G55070.1 (Arabidopsis thaliana), 5'ss of exon 14
ATCTTTATCAATTGATGAGATGGCTGGAGGCACTCTTACAATATCCAATGGTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttgg---aagttctactgagataaatattatttttttttttctttaattttgtaagacattctttgatatgttttgaagttgcttctttgtgtatatgata
| |  ||||||| ||||||||||| |||||  |  | ||| |||| ||||||||||| |||||||| ||| | || || ||||| |||||||||||||||||| |     |    | |     |||| |  | |          | |  ||||||      || |||| ||    |  || |   |   |  |   ||     
AACCATATCAATCGATGAGATGGCAGGAGGATCATTCACAGTATCAAATGGTGGTGTCTATGGAAGTCTTATAAGCACTCCTATCATCAACCCTCCTCAGgttcgattcgatccttgcaatactaaaaaccaatcaaagaaaggtgtttttttgt------ttgtttgttactaatgcaaataaatctatcatacgtag----

upper sequence: GLYMA02G46200.1 (Glycine max), 5'ss of exon 14
lower sequence: PP1S2_220V6.1 (Physcomitrella patens), 5'ss of exon 8
ATCTTTATCAATTGATGAGATGGCTGGAGGCACTCTTACAATATCCAATGGTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttgg-aagttctactgagataaatattatttttttttttctttaattttgtaagacattctttgatat-gttttgaagttgcttctttgtgtatatgata--
     || | |||||||| ||||| ||||| ||| |||| || || ||||||||||||||||| || ||  | || || |||||||||||||||||||| ||| |  || ||||     || |   | | ||||   | | || |  || |     ||   |   || |  |   || |  || || |||  | | ||   |  
GAGCATAACCATTGATGATATGGCGGGAGGAACTTTTACTATCTCTAATGGTGGTGTTTATGGGAGTCTCATAAGCACTCCTATTATCAACCCTCCTCAAgttggtcaatttctttctcgaca---actcttttgaatatcctcttgttataattaactggcagcgaaaccgaaatgcaaatgtttatttccgaa-attccagg

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|192317500|gb|FK007538.1|FK007538
EST:     GTGGTGTTTATGGAAGCCTTTTGAGTACCC-TATTATCAACC-TC-TCAG                         TCTGCA-TCTTGGGTAT
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... ttcttggcagTCTGCAATCTTGGGTAT
EST: gi|120491282|gb|EH219449.1|EH219449
EST:     GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... ttcttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
EST: gi|17963680|gb|BM270426.1|BM270426
EST:     GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... ttcttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
EST: gi|151411405|gb|EV281216.1|EV281216
EST:     GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... ttcttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
EST: gi|209726696|gb|BW672450.1|BW672450
EST:     GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... ttcttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
EST: gi|209721888|gb|BW680047.1|BW680047
EST:     GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... ttcttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
EST: gi|6847358|gb|AW349648.1|AW349648
EST:     GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... ttcttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
EST: gi|16284571|gb|BI946159.1|BI946159
EST:     GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... ttcttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
EST: gi|193473527|gb|FK437144.1|FK437144
EST:     GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... ttcttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
EST: gi|31470743|gb|CD412771.1|CD412771
EST:     GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAG                         TCTGCAATCTNGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... ttcttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
EST: gi|16279466|gb|BI943451.1|BI943451
EST:     GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... ttcttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
EST: gi|192319333|gb|FK009875.1|FK009875
EST:     GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... ttcttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
EST: gi|298167625|gb|HO012888.1|HO012888
EST:     GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAG                         TCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA
genomic: GTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagt ... ttcttggcagTCTGCAATCTTGGGTATGCATTCCATAGTGAGCCGTCCAACGGTTGTTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTTTATCAATTGATGAGATGGCTGGAGGCACTCTTACAATATCCAATGGTGGTGTTTATGGAAGCCTTTTGAGTACCCCTATTATCAACCCTCCTCAGgtttggaagttctactgagataaatattatttttttttttctttaattttgtaagacattctttgatatgttttgaagttgcttctttgtgtatatgata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC