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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTGCAGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAATATATGGTCTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCATTTCTTTCAGgtacgttgacatttgctcttgatgcattgttggcaattatacatgtattaccatggcacaatgaatgatgtgtatgttcatatggtgataggtttggaca...

Basic information

species Glycine max
transcript GLYMA03G00470.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G00470.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os10g41960.1 (Oryza sativa), 5'ss of exon 10
AACTGCAGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAATATATGGTCTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCATTTCTTTCAGgtacgttgacatttgctcttgatgcattgttggcaattatacatgtattaccatggcacaatg-aatgatgtgtatgttcatatggtgataggtttggaca-
| ||||||| || ||||| ||||||||||||||||||||| | ||||||||||||| ||||||||| || ||   | |    ||||| || |||||||||||| |  ||  ||   || |      || | | |  | ||   |  ||| |  |    || || |||  | |||   || |  |  | ||    | | ||| 
ATCTGCAGTTACCTCAGTCCATGAAATGGAGAATGGTTTCCAAATATGGTCTTTCAGTGGCAAGCAACTTTACAAGGTGTCAAAGGACCACTTCTTTCAGgtatg--gaggttccatcctacccttttctggactctcatgtct-cattgctttacaccattgtaatcctttgt-catttactt--taatttactggtacag

upper sequence: GLYMA03G00470.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G174757_T01 (Zea mays), 5'ss of exon 10
AACTGCAGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAATATATGGTCTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCATTTCTTTCAGgta--cgttgacatttgctcttgatgcattgttggcaattatacatgtattaccatggcacaatgaatgatgtgtatgttcatatggtgataggtttggaca
 |||||||| || ||||||||||||||||||||||| ||  | |||||||| |||| |||||||||||| ||   | |    ||||||||||||| |||||||   ||| |    | ||| |  || ||      |||| ||| ||  | |    |       | | |    | ||  |  |      | | |||   |   
GACTGCAGTTACCTCAGTTCATGAAATGGAGAATGGCTTTCAAATATGGTCCTTCAGTGGCAAGCATCTTTACAAGGTGTCAAAGGATCATTTCTATCAGgtaaatgttcaatcattctccttttggatgcagttcaatgatatatacaattgtcttctgtggtaagtatcttttacatggactgaacggt-ggtacag---

upper sequence: GLYMA03G00470.1 (Glycine max), 5'ss of exon 10
lower sequence: AT5G27640.1 (Arabidopsis thaliana), 5'ss of exon 11
AACTGCAGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAATATATGGTCTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCATTTCTTTCAGgtacgttgacatttgctcttgatgcattgttggcaattatacatgtattaccatggcacaatgaatgatgtgtatgttcatatggtgataggtttggaca
||| |||||||| ||||| ||||| ||||||||||| ||||  |||||||||||||| || |     || || |||||  |||||||||||||||| |||||| ||    |      || | |      |   | |  || | |  ||| | ||| |  ||| ||  || | | |||     |||| | |          
AACCGCAGTGACATCAGTCCATGAGATGGAGAATGGGTTCACCATATGGTCTTTCAACGGGATTATGCTTTACCGGATATTGAAGGATCATTTCTTCCAGgtatgtaacaagaaaaactcggtct----taaacgagcat-cgtccattccgatgtc-taataaa--atatttgtgtatggttggttacacag-------

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|10843149|gb|BF066463.1|BF066463
EST:     ATTTCTTTCAG                         TTCTTATGGAGACCAAGGCCACCATCTTTCTTGACTCCCGAGAAAGAGGAA
genomic: ATTTCTTTCAGgtacgttgac ... tgctatatagTTCTTATGGAGACCAAGGCCACCATCTTTCTTGACTCCCGAGAAAGAGGAA
EST: gi|58021888|gb|CX708629.1|CX708629
EST:     CTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCATTTCTTTCAG                         TTCTTATGGAGACCAAGGCCACCATCTTTCTTGACTCCCGAGAAAGAGGAA
genomic: CTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCATTTCTTTCAGgtacgttgac ... tgctatatagTTCTTATGGAGACCAAGGCCACCATCTTTCTTGACTCCCGAGAAAGAGGAA
EST: gi|14125840|gb|BG790278.1|BG790278
EST:     CTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCATTTCTTTCAG                         TTCTTATGGAGACCAAAGCCACCATCTTTCTTGACTCCCGA
genomic: CTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCATTTCTTTCAGgtacgttgac ... tgctatatagTTCTTATGGAGACCAAGGCCACCATCTTTCTTGACTCCCGA
EST: gi|254345660|gb|GR855996.1|GR855996
EST:     CTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCATTTCTTTCAG                         TTCTTATGGAGACCAAGGCCACCATCTTTCTTGACTCCCGAGAAAGAGGAA
genomic: CTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCATTTCTTTCAGgtacgttgac ... tgctatatagTTCTTATGGAGACCAAGGCCACCATCTTTCTTGACTCCCGAGAAAGAGGAA
EST: gi|208189704|gb|GD990940.1|GD990940
EST:     CTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCATTTCTTTCAG                         TTCTTATGGAGACCAAGGCCACCATCTTTCTTGACTCCCGAGAAAGAGGAA
genomic: CTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCATTTCTTTCAGgtacgttgac ... tgctatatagTTCTTATGGAGACCAAGGCCACCATCTTTCTTGACTCCCGAGAAAGAGGAA
EST: gi|18717956|gb|BM523012.1|BM523012
EST:     CTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCATTTCTTTCAG                         TTCTTATGGAGACCAAGGCCACCATCTTTCTTGACTCCCGAGAAAGAGGAA
genomic: CTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCATTTCTTTCAGgtacgttgac ... tgctatatagTTCTTATGGAGACCAAGGCCACCATCTTTCTTGACTCCCGAGAAAGAGGAA
EST: gi|58016642|gb|CX703384.1|CX703384
EST:     CTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCATTTCTTTCAG                         TTCTTATGGAGACCAAGGCCACCATCTTTCTTGACTCCCGAGAAAGAGGAA
genomic: CTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCATTTCTTTCAGgtacgttgac ... tgctatatagTTCTTATGGAGACCAAGGCCACCATCTTTCTTGACTCCCGAGAAAGAGGAA
EST: gi|22932804|gb|BU549943.1|BU549943
EST:     ATTTCTTTCAG                         TTCTTATGGAGACCAAGGCCACCATCTTTCTTGACTCCCGAGAAAGAGGAA
genomic: ATTTCTTTCAGgtacgttgac ... tgctatatagTTCTTATGGAGACCAAGGCCACCATCTTTCTTGACTCCCGAGAAAGAGGAA
EST: gi|254345661|gb|GR855997.1|GR855997
EST:     CTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCATTTCTTTCAG                         TTCTTATGGAGACCAAGGCCACCATCTTTCTTGACTCCCGAGAAAGAGGAA
genomic: CTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCATTTCTTTCAGgtacgttgac ... tgctatatagTTCTTATGGAGACCAAGGCCACCATCTTTCTTGACTCCCGAGAAAGAGGAA
EST: gi|298179807|gb|HO025022.1|HO025022
EST:     CTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCATTTCTTTCAG                         TTCTTATGGAGACCAAGGCCACCATCTTTCTTGACTCCCGAGAAAGAGGAA
genomic: CTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCATTTCTTTCAGgtacgttgac ... tgctatatagTTCTTATGGAGACCAAGGCCACCATCTTTCTTGACTCCCGAGAAAGAGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTGCAGTGACTTCAGTTCATGAAATGGAGAATGGTTTCAATATATGGTCTTTCAATGGCAAGCATCTATATCGGATTCTGAAGGATCATTTCTTTCAGgtacgttgacatttgctcttgatgcattgttggcaattatacatgtattaccatggcacaatgaatgatgtgtatgttcatatggtgataggtttggaca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG