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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAGgtgagatctactctattctctctcgttgtttcctctaaattcaactttttatgatgttttcgttattcaaactttgaaacatttagcctttgaaatttga...

Basic information

species Glycine max
transcript GLYMA04G11160.4
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G11160.4 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os07g43070.1 (Oryza sativa), 5'ss of exon 2
CCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAGgtgagatct-------actctattctctctcgttgtttcctctaaattcaactttttatgatgttttcgttattcaaactttgaaacatttagcctttgaaatttga
|||||||| | |||||| ||||||||||| || || ||||| ||||| || ||| |||||||| | || || |||||||||         |  ||  | | | |   ||| |  ||     |     |   |||||| || |||  |       |||     |||   |||   | ||   
CCGTCGGAGGCGATCAGTAAGGTGGTGTTCGGCGGGCAGGTGACCGAGGAGGAGTTCGAGAGCCTCAACAAGAGgtgagattgtgaagggaagctcgtgtgtgtgtgtgtgtgttcgtggctgtgaatgggatgatgattccgtgttcttgttcttgt----tttcttcttctgagtt---

upper sequence: GLYMA04G11160.4 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G107473_T01 (Zea mays), 5'ss of exon 2
CCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAGgtgagat------ctactcta---ttctctctcgttgtttcctctaaattcaactttttatgatgttttcgttattcaaactttgaaacatttagcctttga--aatttga---------------------------
|||||||| |  ||||||||||||||||| || |||||||||||||| || |||| ||| ||| | |  || |||| ||||      |  ||| |     |    || |   || ||||        || |      || |      ||||       |  |    |   | | ||   || |||                           
CCGTCGGAGGCTATCAGGAAGGTGGTGTTCGGGGGTCAGGTCACCGAGGAGGAGGCCGACAGCCTCACCAAGAGgtcagattccttcccgctccaaatccccgcttcttcacttgctcttggacgtgctctcgcgcgtggtccttcgattcgggtcaagggattcgttcgcctcgattgatatgacgctcaccctgatgaccgctcctccag

upper sequence: GLYMA04G11160.4 (Glycine max), 5'ss of exon 3
lower sequence: AT1G78150.2 (Arabidopsis thaliana), 5'ss of exon 3
CCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAGgtgagatctactctattctctctcgttgtttcctctaaattcaactttttatgatgttttcgttattcaaactttg---aaacatttagcctttgaaatttga----
|| ||||||||||| || || ||||||||||||||||| |||||||||||||| || |||||||| ||    |||| | |  ||||   || || ||  ||  || |    ||||| | || ||   |  ||       ||| || ||||   | | || |     ||||||  |      
CCATCGGATGGGATTAGCAAAGTGGTGTTTGGTGGTCAAGTCACCGATGAAGAAGTTGAGAGCTTGAACCGCAGgttaaacttacttccttatcactatttcatttcc---aattcgatttctttgaaaattagt----ttccaattttgtccatatatctgaaagttgaaaactttttgt

upper sequence: GLYMA04G11160.4 (Glycine max), 5'ss of exon 3
lower sequence: AT1G78150.3 (Arabidopsis thaliana), 5'ss of exon 2
CCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAGgtgagatctactctattctc----tctcgtt---------gtttcctctaaattcaactttttatgatgttttcgttattcaaactttgaaacatttagcctttgaaatttga-----------------------------------------------------------------
|| ||||||||||| || || ||||||||||||||||| |||||||||||||| || |||||||| ||    |||| | |  ||||   || ||    | || ||          |||| |  ||| | |  ||   ||  |||     |   | ||| ||  |||| ||| |    |  ||||                                                                    
CCATCGGATGGGATTAGCAAAGTGGTGTTTGGTGGTCAAGTCACCGATGAAGAAGTTGAGAGCTTGAACCGCAGgttaaacttacttccttatcactatttcatttccaattcgatttctttgaaaattagtttccaattttgtccatatatctgaaagttgaaaactttttgtgaattgaattcatactctgtttatgccatcaaaagttagatcatagagagtaatcttcaagtgtgacttgtatttaag

upper sequence: GLYMA04G11160.4 (Glycine max), 5'ss of exon 3
lower sequence: Vv18s0001g05480.t01 (Vitis vinifera), 5'ss of exon 2
CCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAGgtgagatctactctattctc----tctcgttgtttcctctaaattcaacttttta--tgatgttttcgttattcaaactttgaaacatttagcctttgaaatttga
|| || ||||||||||| |||||||||||||| || ||||| || ||||||||||  |||   ||    |||||||||||||||   | |  ||    | |||  ||||  |       | |||    |    |  ||   |  | | |||  |    |   |   | ||||        
CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAAGAGGCGGAGGCTTTGTCGAAAAGgtgagatctaggttttcttcatattttcgccgttttttaggttcacgactcaggagtcaacattcatggcaat-aaatgtccgtatgctcctcttttgtcc-----

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|193527753|gb|FK485943.1|FK485943
EST:     GTGTTTGGTGGTCAGGTCACCGATGAAGAGGTGGAGAGCTTAAATAAAAG                         AAAGCCTTGTTCGGATTATAAGATGAAGGAGATAACTGGAAGTGGAATATT
genomic: GTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAGgtgagatcta ... taatttccagAAAGCCTTGTTCGGATTATAAGATGAAGGAGATAACTGGTAGTGGAATATT
EST: gi|18848808|gb|BM567920.1|BM567920
EST:     GTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAG                         AAAGCCTTGTTCGGATTATAAGATGAAGGAGATAACTGGTAGTGGAATATT
genomic: GTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAGgtgagatcta ... taatttccagAAAGCCTTGTTCGGATTATAAGATGAAGGAGATAACTGGTAGTGGAATATT
EST: gi|209713150|gb|BW681684.1|BW681684
EST:     GTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAG                         AAAGCCTTGTTCGGATTATAAGATGAAGGAGATAACTGGTAGTGGAATATT
genomic: GTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAGgtgagatcta ... taatttccagAAAGCCTTGTTCGGATTATAAGATGAAGGAGATAACTGGTAGTGGAATATT
EST: gi|193677699|gb|FK614925.1|FK614925
EST:     TGTTTGGTGGTCAGGTCACCGATGAAGAGGTGGAGAGCTTAAATAAAAAG                         AAAGCCTTGTTCGGATTATAAGATGAAGGAGATAACCGGTAGTGGAATAT
genomic: TGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAA-Ggtgagatcta ... taatttccagAAAGCCTTGTTCGGATTATAAGATGAAGGAGATAACTGGTAGTGGAATAT
EST: gi|151400095|gb|EV269909.1|EV269909
EST:     GCGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAG                         AAAGCCTTGTTCGGATTATAAGATGAAGGAGATAACTGGTAGTGGAATATT
genomic: GTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAGgtgagatcta ... taatttccagAAAGCCTTGTTCGGATTATAAGATGAAGGAGATAACTGGTAGTGGAATATT
EST: gi|192324392|gb|FK015743.1|FK015743
EST:     GTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAG                         AAAGCCTTGTTCGGATTATAAGATGAAGGAGATAACTGGTAGTGGAATATT
genomic: GTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAGgtgagatcta ... taatttccagAAAGCCTTGTTCGGATTATAAGATGAAGGAGATAACTGGTAGTGGAATATT
EST: gi|17022986|gb|BM094020.1|BM094020
EST:     GTGTTTGGTGGTCAGGTCACCGATGAAGAGGTGGAGAGCTTAAATAAAAG                         AAAGCCTTGTTCGGATTATAAGATGAAGGAGATAACTGGTAGTGGAATATT
genomic: GTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAGgtgagatcta ... taatttccagAAAGCCTTGTTCGGATTATAAGATGAAGGAGATAACTGGTAGTGGAATATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAGgtgagatctactctattctctctcgttgtttcctctaaattcaactttttatgatgttttcgttattcaaactttgaaacatttagcctttgaaatttga

- - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT