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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAGgtagattcttttgatgttacaatctacaaatttattttcaatcattaactacttgggactctatgcttttttgtccttgtggggaacttttaatcatcat...

Basic information

species Glycine max
transcript GLYMA20G34940.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G34940.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os10g17990.1 (Oryza sativa), 5'ss of exon 10
GATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAGgtagatt-cttttgatgttacaatctac---aaatttattttcaatcattaactacttgggactctatgcttttttgtccttgtggggaacttttaatcatcat
|||||||||||||| || || || ||||||||| |||| ||||| |||||||| || |||  || ||||| | ||||   | |     ||   | |||  |||  |       |  |     ||  | | | | | | ||   |     |   |  ||   
GATTTTGGTGATAGCATACCTGGCCATGGTGGATTTACTGACAGGATGGATTGTCAAgtaagttactttttaagttaatttttttctgaaggctgtttataatggt--gtctttcagatgagtaaacctctgtatacctgctagtgctctcgtagtata--

upper sequence: GLYMA20G34940.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G452529_T03 (Zea mays), 5'ss of exon 2
GATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAGgtagattcttttgatgttacaatctacaaat-ttatt--ttcaatcattaactacttggg-actctatgcttttttgtccttgtggggaacttttaatcatcat
||||||||||| || || || || |||||||||||||| |||||||||||||| || |||  |   |           ||    |||| ||| |   | |    |   | |||||   | |  | |||||||   | || |       ||  ||| ||   
GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAAgtaagtatctcaagaaacgttatagggaaatgttagtgacttatgggtatgcaacttgaataatgcaagctttttaa-cattctcattctgttgaaataat---

upper sequence: GLYMA20G34940.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM5G825110_T02 (Zea mays), 5'ss of exon 10
GATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAGgtagattcttttg---atgttacaatc-tacaaatttattttcaatcattaactacttgggactctatgcttttttgtccttgtggggaacttttaatcatcat
||||||||||| || || || || |||||||||||||| || |||||||||||||| |||  |   |      | |||  |    ||   |  | |     |    |   ||        | ||  | || |  | ||  ||    | | | ||       
GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatctcaaggaacgttttagctatagggaaatgtcactgacttatggttatccaaactttta-acattctcattctattgaaataatataaaagga---

upper sequence: GLYMA20G34940.1 (Glycine max), 5'ss of exon 10
lower sequence: AT4G22340.3 (Arabidopsis thaliana), 5'ss of exon 9
GATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAGgtagat---tcttttgatgt---tacaatct-acaaattt-------attttcaatcatta--actacttgggactctatgcttttttgtccttgtggggaacttttaatcatcat
|| ||||||||||||||||| |||||||| |||||||| || ||||||||||| |||||| ||       ||||  |   |||| ||| |  | |||       | |||||| ||| |  |    || | ||| |||    | |  |   ||    |   |||   |    | 
GACTTTGGTGATAGTATTCCCGGACATGGCGGAATTACAGATAGAATGGATTGTCAGgtatataggcgcattgacttcaatacattcttattactttcttaaagactttcaaacatcactatggtttagaactgtattagatctgata--tgatatgtcttttgggtttctag

upper sequence: GLYMA20G34940.1 (Glycine max), 5'ss of exon 10
lower sequence: AT1G62430.1 (Arabidopsis thaliana), 5'ss of exon 10
GATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAGgtagattcttttgatgttacaatct----acaaatttattttcaatcattaactacttgggactctatgcttttttgtccttgtggggaacttttaatcatcat-----------------------------------------------
|| |||||||||||||||||||||||||||||||| || || |||||||| ||||||||| | |||  |||   ||  ||||      ||  ||||  | |    || |    ||        | | ||     | | | |        | |||   ||||                                               
GACTTTGGTGATAGTATTCCAGGACATGGTGGAATCACAGATAGAATGGACTGCCAGgta-actctaatgaaactagtatctcttcgtaagattatgattaggtctttagagttttcattcacaagattcgcattgcatattcttcttctctaactctcatctttaagcatatacataaaccagacctaatgttatctattgttacag

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|6483173|gb|AW202361.1|AW202361
EST:     GTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAG                         ATGGTTATGGCGGTGTTTGCATATATATATCATCAATCATTTGTTGTGCCG
genomic: GTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAGgtagattctt ... tggtgtgtagATGGTTATGGCGGTGTTTGCATATATATATCATCAATCATTTGTTGTGCCG
EST: gi|151412323|gb|EV282135.1|EV282135
EST:     GTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAG                         ATGGTTATGGCGGTGTTTGCATATATATATCATCAATCATTTGTTGTGCCG
genomic: GTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAGgtagattctt ... tggtgtgtagATGGTTATGGCGGTGTTTGCATATATATATCATCAATCATTTGTTGTGCCG
EST: gi|207826711|gb|GD800200.1|GD800200
EST:     GTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGACTGCCAG                         ATGGTTATGGCGGTGTTTGCATATATATATCATCAATCATTTGTTGTGCCG
genomic: GTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAGgtagattctt ... tggtgtgtagATGGTTATGGCGGTGTTTGCATATATATATCATCAATCATTTGTTGTGCCG
EST: gi|10252704|gb|BE820470.1|BE820470
EST:     GTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAG                         ATGGTTATGNNGGTGTTTGCATATATATATCATCAATCATTTGTTGTGCCG
genomic: GTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAGgtagattctt ... tggtgtgtagATGGTTATGGCGGTGTTTGCATATATATATCATCAATCATTTGTTGTGCCG
EST: gi|208290556|gb|GE087618.1|GE087618
EST:     GTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGACTGCCAG                         ATGGTTATGGCGGTGTTTGCATATATATATCATCAATCATTTGTTGTGCCG
genomic: GTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAGgtagattctt ... tggtgtgtagATGGTTATGGCGGTGTTTGCATATATATATCATCAATCATTTGTTGTGCCG
EST: gi|207731465|gb|GD706140.1|GD706140
EST:     GTATTAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGACTGCCAG                         ATGGTTATGGCGGTGTTTGCATATATATATCATCAATCATTTGTTGTGCCG
genomic: G-A-TAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAGgtagattctt ... tggtgtgtagATGGTTATGGCGGTGTTTGCATATATATATCATCAATCATTTGTTGTGCCG
EST: gi|120534022|gb|EH262155.1|EH262155
EST:     GTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAG                         ATGGTTATGGCGGTGTTTGCATATATATATCATCAATCATTTGTTGTGCCG
genomic: GTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAGgtagattctt ... tggtgtgtagATGGTTATGGCGGTGTTTGCATATATATATCATCAATCATTTGTTGTGCCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAGgtagattcttttgatgttacaatctacaaatttattttcaatcattaactacttgggactctatgcttttttgtccttgtggggaacttttaatcatcat

- - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgggga