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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggttacttctctcacttgttccacttgaaatagttttcattttgcaattattttttagggtgaatctaatctaatgatctattaatattgtggacag

Basic information

species Glycine max
transcript GLYMA08G16770.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G16770.1 (Glycine max), 5'ss of exon 18
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 18
GTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggttacttctctcacttgttccacttg--aaatagttttcattttgcaattattttttag-ggtgaatctaatcta--atgatctattaatatt-gtggacag------------
|| ||||| |||||||||||||||||||||||||||||||| || |||||| | | |||  || |||| |    |||||   |||| | ||    ||     | ||   ||  |  ||| || ||| |   ||  |  |   || ||| || |  |  | ||    ||||||   | || ||             
GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCGgtatgt--ttacctgtcctggttaaataatttagtaaccaaatttaatcttgaacccatgatggaatagtaaatgtacttcagaacgagtacttaataaaagcggccatctaattacgcag

upper sequence: GLYMA08G16770.1 (Glycine max), 5'ss of exon 18
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 18
GTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggttacttctctcacttgttccacttgaaatagttttcattttgcaatt--attttttagggtgaatctaatctaatgatcta-ttaatattgtggacag-----------------
|| ||||| |||||||||||||||||||||||||| ||||| ||||||||| | | |||  || |||| |    |||||   |||  | | |   ||   | |  | |     | |  | |||    ||  | || | |  | | | | |||||||   |  |   | || |   || |                  
GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCGgtatgt--ttatctgtattggttaaacaatctaatgccatgtctaatttaatcttgaacttatgatagagtagcaaatctaactttagaacgagtacttaagaaaacttctctaactgcgcag

upper sequence: GLYMA08G16770.1 (Glycine max), 5'ss of exon 18
lower sequence: GRMZM2G063851_T05 (Zea mays), 5'ss of exon 4
GTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggttacttctctcacttgttccacttgaaa---tagt-----tttcattttgcaattattttttagggtgaat-ctaatctaatgatctattaatattgtggacag
|| || || |||||||| |||||||||||||||||||||||  | |||||| | | ||| ||| |||| | |  |||||   |||    | | | ||  || |  |   |   ||||     ||| | || |||| | |  ||  | ||||   ||||| |   || | | |||   ||  |    
GTCAAGAACCCATGGCCAAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgt--ttatgcttgtgatttagtctagatagcaatttagtcctctttttacttagcaaatctagttctgagtgagcactaatgtttggaac-actaactgtgcag----

upper sequence: GLYMA08G16770.1 (Glycine max), 5'ss of exon 18
lower sequence: GRMZM2G064023_T01 (Zea mays), 5'ss of exon 19
GTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggttacttctctcacttg--ttccacttga--aatagttt---tcattttgcaattattttttagggtgaat-ctaatctaatgatctattaatattgtggacag
|| || || || ||||| |||||||||||||||||||||||  | |||||| | | ||| ||| |||| | |  |||||    | ||| | ||| ||   ||||| || |   ||  |||   | | || | || ||   ||  |  |||   || || |   || | | |||   ||  |    
GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttatgctt-tgtcatttagattccaatttagtgatgtttttatttacttagtaaataaagttctgaatgagcactcatgtctggaac-actaactgtgcag----

upper sequence: GLYMA08G16770.1 (Glycine max), 5'ss of exon 18
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 5'ss of exon 17
GTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggttacttctctcacttgttccacttgaaatagttttcattttgcaattattttttagggtgaatctaatctaatgatctattaatattgtggacag
|| || || || |||||||| ||||||||||| || |||||||| |||||||| ||||||||||| || | || ||| ||   ||||| | |  |  |      ||||  | |||||  |    |     | || ||| ||||   |  | | |  || ||                
GTCAAGAACCCGTGGCCTAACGTTGATGCTCATAGCGGAGTGCTTCTGAACTACTATGGTCTAACCGAAGCAAGgta-ggaactacttgtgtatcgaggct---ttgaccttgttttgctgaatcttggttattatagagtgacattcctttca-aatatag---------------

upper sequence: GLYMA08G16770.1 (Glycine max), 5'ss of exon 18
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 5'ss of exon 18
GTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggttacttctctcacttgttccacttgaaatagttttcattttgcaattattttttagggtg--aatctaatctaatgatctattaatattgtggacag
|| || || || ||||| |||||||||||||||||||| ||  | |||||| | ||||||||||| || | || ||| |  ||     |   |           || || ||    |||||  ||         ||||| |   | || ||| |||| |||| |   | || | |    
GTGAAGAACCCGTGGCCAAATGTTGATGCTCACAGTGGGGTCTTGCTGAACCACTATGGTCTAACCGAAGCAAGgtaagaagtagacacctcc-----------ttcaagta----tcattgagc--------cttaggatagcactcaaatataat-atctgtgcgttttatag----

upper sequence: GLYMA08G16770.1 (Glycine max), 5'ss of exon 18
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 18
GTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggttacttctctcacttgttccacttgaaatagttttcattttgcaattattttttagggtgaatctaatctaatgatctattaatattgtggacag------
|||||||| |||||||| ||||| |||||||||||||| ||  | |||||| ||| |||| ||   || | |  |||  | |||   |||| || |  ||  | ||| |    | || |||| || |||   |  ||   ||  |  |   |||  |||  |||| | | ||  |        
GTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACGgtaaagagttctctctcacaatcattataattggagatttcttaatttggctatttaatagtatcttgggtagatggtaaaaatcctttaacaat-tgatcccttgcag

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|37995119|gb|CF806708.1|CF806708
EST:     GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA                         CTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
genomic: GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggtt ... ttgtggacagCTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
EST: gi|10710148|gb|BF009872.1|BF009872
EST:     GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA                         CTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
genomic: GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggtt ... ttgtggacagCTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
EST: gi|213604400|gb|DB983488.1|DB983488
EST:     GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA                         CTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
genomic: GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggtt ... ttgtggacagCTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
EST: gi|22934201|gb|BU551340.1|BU551340
EST:     GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA                         CTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
genomic: GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggtt ... ttgtggacagCTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
EST: gi|23057280|gb|BU577954.1|BU577954
EST:     GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA                         CTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
genomic: GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggtt ... ttgtggacagCTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
EST: gi|31460126|gb|CD402154.1|CD402154
EST:     GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA                         CTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
genomic: GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggtt ... ttgtggacagCTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
EST: gi|9440345|gb|BE440851.1|BE440851
EST:     GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA                         CTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
genomic: GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggtt ... ttgtggacagCTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
EST: gi|15287775|gb|BI471666.1|BI471666
EST:     GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA                         CTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
genomic: GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggtt ... ttgtggacagCTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
EST: gi|21994889|gb|BQ786417.1|BQ786417
EST:     GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA                         CTATTATACTGTTCTCTTTGGTGTATCAAGGAGC
genomic: GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggtt ... ttgtggacagCTATTATACTGTTCTCTTTGGTGTATCAAGGAGC
EST: gi|15664905|gb|BI702276.1|BI702276
EST:     GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA                         CTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
genomic: GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggtt ... ttgtggacagCTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
EST: gi|9820752|gb|BE556262.1|BE556262
EST:     GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA                         CTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
genomic: GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggtt ... ttgtggacagCTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
EST: gi|23733765|gb|BU765093.1|BU765093
EST:     GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA                         CTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA
genomic: GATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggtt ... ttgtggacagCTATTATACTGTTCTCTTTGGTGTATCAAGGAGCTTTGGAGTTGGCCCTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggttacttctctcacttgttccacttgaaatagttttcattttgcaattattttttagggtgaatctaatctaatgatctattaatattgtggacag

- - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - GTGGAG