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

ACAGCTGGATCCGGAATTTGCTAAGAACATTGGGCAGATTCTGATTCTTGGTGGTGCTTTTGCAGTAAATGGCAATGTGAATCCAGCTGCTGAAGCCAATgtgagtatttccattctgcatcaaattcttaatcttcaatataaatattatatcattcacaactcaatctgtctaactctttggttggatttgttccag

Basic information

species Glycine max
transcript GLYMA0048S00280.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA0048S00280.2 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os03g31170.1 (Oryza sativa), 5'ss of exon 5
ACAGCTGGATCCGGAATTTGCTAAGAACATTGGGCAGATTCTGATTCTTGGTGGTGCTTTTGCAGTAAATGGCAATGTGAATCCAGCTGCTGAAGCCAATgtgagtat--ttccattctgcatc--aaattcttaatcttcaatataaatattatatcattcacaactcaatctgtctaactctttggttggatttgttccag---
| | || |||||    ||  | ||||| |||||||||||| |||| ||||||||||| | | |||| ||||| ||||| || || || ||||| || ||||||||      || ||| |   ||  ||||     || ||| ||     | |  || |||   ||     |||   || |||  | |  |   ||| |   |    
AGAACTTGATCCTTCTTTCCCGAAGAAGATTGGGCAGATTGTGATCCTTGGTGGTGCGTATTCAGTTAATGGAAATGTCAACCCTGCAGCTGAGGCAAATgtgagggaggctctattttttctctgaaatggaacattttctattcctttctggtaacatgttca---tgatcctgcttactgatggaatatgtttatattaacag

upper sequence: GLYMA0048S00280.2 (Glycine max), 5'ss of exon 5
lower sequence: AT1G05620.2 (Arabidopsis thaliana), 5'ss of exon 4
ACAGCTGGATCCGGAATTTGCTAAGAACATTGGGCAGATTCTGATTCTTGGTGGTGCTTTTGCAGTAAATGGCAATGTGAATCCAGCTGCTGAAGCCAATgtgagtatttccattctgcatcaaattcttaatcttcaatataaatattatatcattcacaactcaatctgtctaactctttggttggatttgttccag--------------------
 ||||| ||||| || ||| | || ||  | || || ||| |  |||||||||| || ||||||||||| || ||||| ||||||||| | ||||| ||||| |||   | ||  |   |    | | |  || |||| || | |||  | |||| |  | |   ||      |   |   |  |   || ||||  |                     
TCAGCTTGATCCAGAGTTTTCGAAAAATGTCGGACAAATTGTTCTTCTTGGTGGAGCATTTGCAGTAAACGGAAATGTAAATCCAGCTTCGGAAGCTAATgtaagttccttcacccgttaaagtaatgt-gatattca-tacacataacacatcactttctatcaaaaactcttcttttagttttcacatctgtttaaccaattttttggttagggtag

upper sequence: GLYMA0048S00280.2 (Glycine max), 5'ss of exon 5
lower sequence: Vv05s0094g01420.t01 (Vitis vinifera), 5'ss of exon 5
ACAGCTGGATCCGGAATTTGCTAAGAACATTGGGCAGATTCTGATTCTTGGTGGTGCTTTTGCAGTAAATGGCAATGTGAATCCAGCTGCTGAAGCCAATgtgagtatttccattctgcat---caaattcttaat--cttcaatataaatattatatcattcacaactcaatctgtc-taactctttggttggatttgttccag
  | || ||||| |  ||| | || ||||||||||||||| |  ||||||||||||||||||| |||||||| |||||||||||||| ||||| |||||||| ||| |||| | ||||  |      || |  |||  | ||||| | |    || |     |||||       |    || |       ||     | ||    
TGAACTAGATCCTGGGTTTTCCAAAAACATTGGGCAGATTGTTCTTCTTGGTGGTGCTTTTGCTGTAAATGGGAATGTGAATCCAGCAGCTGAGGCCAATgtaagtttttcaaatctgtgtgcatggatacaaaatggcatcaatgtgacctctaaag-gcccacaatatgtcttactatagcatccccattatgcatttt----

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|192319150|gb|FK006906.1|FK006906
EST:     GTGGTGCTTTTGCAGTAAATGGCAATGTGAATCCAGCTGCTGAAGCCA-T                         ATATTTGGTGATCCAGAGGCTGCAGATGTTGTATTTACAAGTGGGGCAGAT
genomic: GTGGTGCTTTTGCAGTAAATGGCAATGTGAATCCAGCTGCTGAAGCCAATgtgagtattt ... tttgttccagATATTTGGTGATCCAGAGGCTGCAGATGTTGTATTTACAAGTGGGGCAGAT
EST: gi|254326906|gb|GR836515.1|GR836515
EST:     GTGGTGCTTTTGCAGTAAATGGCAATGTGAATCCAGCTGCTGAAGCCAAT                         ATATTTGGTGATCCAGAGGCTGCAGATGTTGTATTTACAAGTGGGGCAGAT
genomic: GTGGTGCTTTTGCAGTAAATGGCAATGTGAATCCAGCTGCTGAAGCCAATgtgagtattt ... tttgttccagATATTTGGTGATCCAGAGGCTGCAGATGTTGTATTTACAAGTGGGGCAGAT
EST: gi|254346378|gb|GR856100.1|GR856100
EST:     GTGGTGCTTTTGCAGTAAATGGCAATGTGAATCCAGCTGCTGAAGCCAAT                         ATATTTGGTGATCCAGAGGCTGCAGATGTTGTATTTACAAGTGGGGCAGAT
genomic: GTGGTGCTTTTGCAGTAAATGGCAATGTGAATCCAGCTGCTGAAGCCAATgtgagtattt ... tttgttccagATATTTGGTGATCCAGAGGCTGCAGATGTTGTATTTACAAGTGGGGCAGAT
EST: gi|192317206|gb|FK009793.1|FK009793
EST:     GTGGTGCTTTTGCAGTAAATGGCAATGTGAATCCAGCTGCTGAAGCCAAT                         ATATTTGGTGATCCAGAGGCTGCAGATGTTGTATTTACAAGTGGGGCAGAT
genomic: GTGGTGCTTTTGCAGTAAATGGCAATGTGAATCCAGCTGCTGAAGCCAATgtgagtattt ... tttgttccagATATTTGGTGATCCAGAGGCTGCAGATGTTGTATTTACAAGTGGGGCAGAT
EST: gi|254346379|gb|GR856101.1|GR856101
EST:     GTGGTGCTTTTGCAGTAAATGGCAATGTGAATCCAGCTGCTGAAGCCAAT                         ATATTTGGTGATCCAGAGGCTGCAGATGTTGTATTTACAAGTGGGGCAGAT
genomic: GTGGTGCTTTTGCAGTAAATGGCAATGTGAATCCAGCTGCTGAAGCCAATgtgagtattt ... tttgttccagATATTTGGTGATCCAGAGGCTGCAGATGTTGTATTTACAAGTGGGGCAGAT
EST: gi|254326907|gb|GR836516.1|GR836516
EST:     GTGGTGCTTTTGCAGTAAATGGCAATGTGAATCCAGCTGCTGAAGCCAAT                         ATATTTGGTGATCCAGAGGCTGCAGATGTTGTATTTACAAGTGGGGCAGAT
genomic: GTGGTGCTTTTGCAGTAAATGGCAATGTGAATCCAGCTGCTGAAGCCAATgtgagtattt ... tttgttccagATATTTGGTGATCCAGAGGCTGCAGATGTTGTATTTACAAGTGGGGCAGAT
EST: gi|16997071|gb|BM086443.1|BM086443
EST:     GTGGTGCTTTTGCAGTAAATGGCAATGTGAATCCAGCTGCTGAAGCCAAT                         ATATTTGGTGATCCAGAG
genomic: GTGGTGCTTTTGCAGTAAATGGCAATGTGAATCCAGCTGCTGAAGCCAATgtgagtattt ... tttgttccagATATTTGGTGATCCAGAG
EST: gi|192325277|gb|FK019148.1|FK019148
EST:     GTGGTGCTTTTGCAGTAAATGGCAATGTGAATCCAGCTGCTGAAGCCAAT                         ATATTTGGTGATCCAGAGGCCGCAGATGTTGTATTTACAAGTGGGGCAGAT
genomic: GTGGTGCTTTTGCAGTAAATGGCAATGTGAATCCAGCTGCTGAAGCCAATgtgagtattt ... tttgttccagATATTTGGTGATCCAGAGGCTGCAGATGTTGTATTTACAAGTGGGGCAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAGCTGGATCCGGAATTTGCTAAGAACATTGGGCAGATTCTGATTCTTGGTGGTGCTTTTGCAGTAAATGGCAATGTGAATCCAGCTGCTGAAGCCAATgtgagtatttccattctgcatcaaattcttaatcttcaatataaatattatatcattcacaactcaatctgtctaactctttggttggatttgttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC