Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtatttcagaaccttcacattctactgatctgctctataaatgagatttatacaattcttaacaaagatgtcaaatataatgagattgatttatttataggaaactaactttgtattccatattttgttccatag

Basic information

species Glycine max
transcript GLYMA02G47460.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G47460.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os08g25734.1 (Oryza sativa), 5'ss of exon 6
TTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtatttcagaaccttcacattctact--gatctgctctataaatgagatt-tatacaattcttaacaaagatgtcaaatataatgagattgatttatttataggaaactaactttgtattccatattttgttccatag
 ||  ||||||| || || ||||| ||| | |||||||| || ||| | |||||||||||||| || || ||||| ||||||||||| ||||| ||||| |||||||| |  |    |  |  || || |   |      || ||  |   ||  | ||   || || |||      |||||   | | |   || |  |  | |          | |||||                    
GTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGTTGTGTTATTAAAgtaagtatgtt-gtgtttgtatgttataattcaaaacctcctgtagtttctatggtctatctttttttacatttccttcaaagtaatttatcatgctgcaactttcacttttcgtccttgtag-------------------

upper sequence: GLYMA02G47460.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os09g12660.2 (Oryza sativa), 5'ss of exon 6
TTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtat----ttcaga---accttcacatt--ctactgatctgctctataaatgagattta--tacaat-tcttaaca----aagatgtcaaatataatgagattgatttatttataggaaactaactttgtattccatattttgttc-catag-----------------------
|||  |  |||| || || ||||| ||||| |||||||| || ||  | |||||||||||||| || || ||||||||||||||||| ||||| ||||  ||||||||    ||||||   |   ||| |     | ||  | || ||| |  ||   |||     | ||  | |||  |     || | | |  | | |   ||    ||  |||  |       ||    |    ||  | ||||||  |||                         
TTCTGCCGCAATTTATACGCAACCTCGATACTTGCCTCCATCAAAAGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGTTGTGTTATTAGAgtaagtatccttttcagatgaattatcatagcgcttccttctatgatctgtggatagtattagatcataacatattaggaccttgagttattacttgttagtcgaacatttctttttcattgcttcaaaacagagaccctaaatttgttgacatgcctttccccctttattttggctag

upper sequence: GLYMA02G47460.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G163437_T01 (Zea mays), 5'ss of exon 6
TTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtatttcagaaccttcacattctactgatctgctctataaatgagatttatacaattcttaacaaagatgtcaaatataatgagattgatttatttataggaaactaactttgtattccatattttgttccatag
|||  |||||||||| || ||||| ||| || |||| || || ||| | |||||||||||||| || || |||||||||||||| |||||||| ||||| ||||||| |         |    || ||||         |  |||    || |||| | ||  || |    |    |  | |   |  ||| ||||| | | |      |  |||  | ||    |    |        
TTCTGCTCCAATCTATACACAACCTCGACATCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAGGGATGTGTTATTAAAgtaagtagtg--------ttttgttttactatagcatatttgaaaacctatatatagactttatatcctccaaagtatttttcccgtaattcatttactaaaacatttatgccttgatcttgtgcacacag--------

upper sequence: GLYMA02G47460.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G106213_T01 (Zea mays), 5'ss of exon 6
TTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtatttcagaaccttcacat-tctactgatctgctctataaatgagatttatacaattcttaacaaagatgtcaaatataatgagattgattta-tttataggaaactaactttgtattccatattttgttccatag
|||  ||||||| || || |||||  ||||||||||||| || ||| | |||||||||||||| || || ||||||||||| ||||| ||||| ||||| ||||| |    ||    ||||||| | | ||||| |  | | || |||   |||  | |    || | |      |  | | |   ||  || ||||| ||| | |                                   
TTCTGCTCCAATTTATACGCAACCTAGATATTTGCCTCCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGAGAAGGGTGTGTTATTAAAgtaagaa----agccttttcacatgttttctgatgtatt-tgtatatgttgttttcagaggctttcatatcagaatgcattttgg-gatcttaatttagtttgtgg-----------------------------------

upper sequence: GLYMA02G47460.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G068506_T03 (Zea mays), 5'ss of exon 6
TTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagta-tttcagaaccttcacattctactgatctgctctataaatgagatttatacaattcttaacaaagatgtcaaatataatgagattgatttatttataggaaactaactttgtattccatattttgttccatag
||   ||||||| || || ||||| ||| |  |||| || || ||| | |||||||||||||| || || ||||||||||||||||||||||| ||||| ||||| | |      ||  |  |||  |    | |   ||||||        || |   ||| |   |||||   |     |||||     | ||||| | | | |    |  |||  | ||    |    |        
TTTTGCTCCAATTTATACACAACCTCGACACCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGATGTGTTATTAAAgtaagcagtgcttttactgtagcatatttgaaaacctttctata-------cttcttttattttctccaaagtaatttctcataat-----tcatttactaaaacgtttatgccttgatcttgtgcacacag--------

upper sequence: GLYMA02G47460.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 5'ss of exon 6
TTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtatttcagaaccttcacat-tctactgatctgctctataaatgagatttatacaattcttaacaaagatgtcaaatataatgagattgatttatttataggaaactaactttgtattccatattttgttc-catag
||| |||||||||||||||||||| ||||||||||| || ||||||||||||||||||||||| || ||||||||||||||||| || ||||||||||||||||||    ||    |   |||  |||  || | || |  |||  ||     | |   || ||||  || | | |  |  ||  |  |||| ||  | ||| || ||  |  | ||||   || | || ||| |    ||
TTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCCATCTAAGATGCTTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGCTGTGTGATTAAGgtaagttacacatgggcaagacaggtctcttgctgtgtttcatagttgg----tgtcacatgcttatgaaggctttttataattgtt-gatt-atgcagtta-agtaagtt--ccttgttcacccttttctgtgcatgcag

upper sequence: GLYMA02G47460.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S2_392V6.1 (Physcomitrella patens), 5'ss of exon 6
TTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtatttcagaaccttcacattctactgatctgctctataaatgagatttatacaattcttaacaaagatgtcaaatataatgagattgatttatttataggaaactaactttgtattccatattttgttccatag
 ||| | || |||||||| ||  | || |   | |||||||| |||||| | ||||||||||| ||||| || || || || ||||||||||| ||||||||| |     ||||       ||  ||  |    ||   || ||||| ||||||      || | |     | |  |||   | || | || |   | | |  ||| | |   |                         
GTCAGCCCCTATCTACACACAGGCTCGCTTCCTCCCTCCCTCAAAGATGTTGGATGCTGATGTAACTGACAGCGTGATCGGAGAAGGATGTGTCATTAAGgtaggatccccagagatgcttcacccttgt----tgggtta-aaatgtgatttacttgcctcatcat----acgctaaa---attgggtttaacccactca--ggagattgtgt-------------------------

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|22929719|gb|BU546858.1|BU546858
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGNAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtattt ... tgttccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|193373035|gb|FK336083.1|FK336083
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtattt ... tgttccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|31465216|gb|CD407244.1|CD407244
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtattt ... tgttccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|9902053|gb|BE611021.1|BE611021
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtattt ... tgttccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|12489873|gb|BG043394.1|BG043394
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtattt ... tgttccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|51338121|gb|CO981987.1|CO981987
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtattt ... tgttccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|193375621|gb|FK340460.1|FK340460
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtattt ... tgttccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|15589858|gb|BI674474.1|BI674474
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtattt ... tgttccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|27424381|gb|CA935901.1|CA935901
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtattt ... tgttccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|298174060|gb|HO017396.1|HO017396
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtattt ... tgttccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|20498182|gb|BQ273112.1|BQ273112
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtattt ... tgttccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|192316610|gb|FK006817.1|FK006817
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtattt ... tgttccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|6070729|gb|AW100116.1|AW100116
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtattt ... tgttccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|16277058|gb|BI942182.1|BI942182
EST:     TGATGCTGATGTCACTGATAGTGTTATTGGTGAATGATGTGTGATGTA-G                         AACTGCGAAATTCACCATTCTGTGGTTGAGCTGCGATCTTGCATATCAGA
genomic: TGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGAT-TAAGgtaagtattt ... tgttccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGA
EST: gi|21637686|gb|BM107841.1|BM107841
EST:     TGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtattt ... tgttccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|20811566|gb|BQ296044.1|BQ296044
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtattt ... tgttccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|16278915|gb|BI943160.1|BI943160
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtattt ... tgttccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|13266691|gb|BG370154.1|BG370154
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtattt ... tgttccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|193316367|gb|FK282727.1|FK282727
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtattt ... tgttccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|193300968|gb|FK265475.1|FK265475
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGC-AAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtattt ... tgttccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|23728098|gb|BU762095.1|BU762095
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtattt ... tgttccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|15589806|gb|BI674422.1|BI674422
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtattt ... tgttccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|15814292|gb|BI786567.1|BI786567
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtattt ... tgttccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagtatttcagaaccttcacattctactgatctgctctataaatgagatttatacaattcttaacaaagatgtcaaatataatgagattgatttatttataggaaactaactttgtattccatattttgttccatag

- - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG