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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAGCGCAAGTGTTGGTAAAGAACTGACGCTGTATTCGTATTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcctttcactacactccctttcctttttttcccttctctcatctcactttccactcacctttgcatacacatacag

Basic information

species Glycine max
transcript GLYMA17G00700.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G00700.2 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os02g35590.3 (Oryza sativa), 5'ss of exon 1
--------GCAAGCGCAAGTGTTGGTAAAGAA-CTGACGCTGTATTCGTATTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcctttcactacactccctttcctttttttcccttctctcatct---cactttccactcacctttgcatacacatacag--------------------------------------------------
        |   |||   |||  |     ||| |||   ||||| ||||| ||| ||||||| || || ||||| ||||| ||||| |||||||||||||||||  |     | |  | | |  || ||||  | ||       || |||   |    |   ||||     |   | |   |  |                                                  
GAGGCGGCGGGGGCGGCGGTGGCGCCGGCGAAGCTGGGTCTGTACTCGTACTGGCGGAGCTCGTGCTCGCACCGCGTCCGCATCGCCCTCAACCTCAAAGgtacgttgtgcccgcgccgcgcgattgccttcctctcgtcgtcatcttctatgcgtggttggctcatggccgggcagagtgagtgaacctggtgcgtgcgtgcgtgcgggtgattttgatgtctgtctcctgcag

upper sequence: GLYMA17G00700.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G064255_T02 (Zea mays), 5'ss of exon 1
--------GCAAGCGCAAGTGTTGGTAAAG-AACTGACGCTGTATTCGTATTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcctttca-ctacactccctttcctttttttcccttctctcat---ctcactt-tccactcacct---ttgcatacacatacag------------------
        | | ||| | | |  |||   |  ||||| |||||| ||||| ||| | ||||| || |||||||| | ||| ||||||||||| ||||||||| |   |  |||  | ||       |     |    || || |||  |   | || |  | || ||   |   |||  |  |  |   |                  
CAAATGGCGGAGGCGGAGGCGACGGTGGGGCGACTGATGCTGTACTCGTACTGGCGCAGCTCGTGCTCCCACCGTGCCCGCATCGCTCTCAATCTCAAAGgtgcgtgctgttcggccaccgctgaataagactcgggccattgtctattggacgcattgatgcattcgtttcgattgattcgatgtgtgggttgttttttttctgcag
















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|298182549|gb|HO031284.1|HO031284
EST:     TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAG                         GGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
genomic: TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcct ... acacatacagGGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
EST: gi|298164934|gb|HO010931.1|HO010931
EST:     TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAG                         GGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
genomic: TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcct ... acacatacagGGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
EST: gi|213618310|gb|DB961390.1|DB961390
EST:     TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAG                         GGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
genomic: TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcct ... acacatacagGGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
EST: gi|14011598|gb|BG726520.1|BG726520
EST:     TGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCAATCTCAACCTCAAAG                         GGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
genomic: TGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcct ... acacatacagGGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
EST: gi|23734319|gb|BU765384.1|BU765384
EST:     TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAG                         GGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
genomic: TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcct ... acacatacagGGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
EST: gi|14991218|gb|BI316891.1|BI316891
EST:     TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAG                         GGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
genomic: TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcct ... acacatacagGGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
EST: gi|14011899|gb|BG726821.1|BG726821
EST:     TGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAG                         GGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
genomic: TGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcct ... acacatacagGGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
EST: gi|209698696|gb|BW660697.1|BW660697
EST:     TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAG                         GGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
genomic: TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcct ... acacatacagGGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
EST: gi|298190896|gb|HO038375.1|HO038375
EST:     TTGGAGGAGCTCTTGTTCCCACCGAGTCCAAATCGCTCTCAACCTCAAAG                         GGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
genomic: TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcct ... acacatacagGGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
EST: gi|11689541|gb|BF597217.1|BF597217
EST:     TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAG                         GGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
genomic: TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcct ... acacatacagGGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
EST: gi|15337433|gb|BI498089.1|BI498089
EST:     TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAG                         GGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
genomic: TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcct ... acacatacagGGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
EST: gi|18711685|gb|BM522604.1|BM522604
EST:     TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAG                         GGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
genomic: TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcct ... acacatacagGGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
EST: gi|254316777|gb|GR828314.1|GR828314
EST:     TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAG                         GGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
genomic: TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcct ... acacatacagGGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
EST: gi|14011671|gb|BG726593.1|BG726593
EST:     TGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAG                         GGCTTAAATACGAATACAAGCCCGTCAATCTGTTCAAGGGAGAACAATCTC
genomic: TGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcct ... acacatacagGGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
EST: gi|17519554|gb|BM188596.1|BM188596
EST:     TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAG                         GGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
genomic: TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcct ... acacatacagGGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
EST: gi|17021881|gb|BM092915.1|BM092915
EST:     TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAG                         GGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
genomic: TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcct ... acacatacagGGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
EST: gi|23052836|gb|BU577327.1|BU577327
EST:     TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAG                         GGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
genomic: TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcct ... acacatacagGGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
EST: gi|151401424|gb|EV271238.1|EV271238
EST:     TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAG                         GGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
genomic: TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcct ... acacatacagGGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
EST: gi|298180061|gb|HO025276.1|HO025276
EST:     TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAG                         GGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
genomic: TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcct ... acacatacagGGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
EST: gi|298189960|gb|HO038363.1|HO038363
EST:     TTGGAGGAGCTCTTGTTCCCACCGAGTCCAAATCGCTCTCAACCTCAAAG                         GGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
genomic: TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcct ... acacatacagGGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
EST: gi|4294309|gb|AI442172.1|AI442172
EST:     TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAG                         GGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC
genomic: TTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcct ... acacatacagGGCTTAAATACGAATACAAGCCCGTCAATCTGCTCAAGGGAGAACAATCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAGCGCAAGTGTTGGTAAAGAACTGACGCTGTATTCGTATTGGAGGAGCTCTTGTTCCCACCGAGTCCGAATCGCTCTCAACCTCAAAGgtactctcctttcactacactccctttcctttttttcccttctctcatctcactttccactcacctttgcatacacatacag

- - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - GGAGCT