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'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaattttatatcttcaatcagtttgagattaacttaattgcttctctaggctaatattgtcactccataactatgataactttggggttctataacatgatgtttctcacaatatgatatgatatgatgcagATAAAATGGATTTGCCCAACTGCTCCTACCCGTCCTGTGGCGATACTTGGTGGTTTTCCCTGCACTGCAT

Basic information

species Glycine max
transcript GLYMA15G01350.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G01350.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G15650.2 (Arabidopsis thaliana), 3'ss of exon 3
gtgagaattttatatcttcaatcagtttgagattaacttaattgcttctctaggctaatattgtcactccataactatgataactttggggttctataacatgatgtttctcacaatatgatatgatatgatgcagATAAAATGGATTTGCCCAACTGCTCCTACCCGTCCTGTGGCGATACTTGGTGGTTTTCCCTGCACTGCAT
                          |   |||  |   ||       |  | | |||| || |   ||  ||| |||  | | |    ||||||   | | |||          ||||| |||  | |    ||||| ||||||||||| |||||||||||| | ||||||||  || | || ||||| ||||| |||||||| |
-------------------------gtaaggatccatggaaacaaacttggaag-taattttttgtatcactaaatattcttagtg-aaggttctgataaaagat----------atatggtattctgt----cagATCAAATGGATTTGTCCAACTGCTCCTTCGCGTCCTGTTTCGCTTCTCGGTGGATTTCCTTGCACTGCCT

upper sequence: GLYMA15G01350.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G52700.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagaattttatatcttcaatcagtttgagattaacttaattgcttctctaggctaatattgtcactccataactatgataactttggggttctataacatgatgtttctcacaatatgatatg-atatgatgca--gATAAAATGGATTTGCCCAACTGCTCCTACCCGTCCTGTGGCGATACTTGGTGGTTTTCCCTGCACTGCAT
                        ||  ||   || | ||  || ||           | || | | ||||  | ||  || |   ||    |||||    ||| || | | | || |  ||||| ||   |||||  ||||||||||||||| ||||| |||||| | ||||||||  | |  |||||||| ||| | |||||||| |
------------------------gtaagaatctatcatacatgttt-----------tgttataagtccaccatta-aatgaaagtgcatctctat----tgaagtctttaataaaaacatatgtatgctatgcacagATAAAATGGATTTGTCCAACCGCTCCTTCGCGTCCTGTTACAAGTCTTGGTGGATTTACATGCACTGCTT

upper sequence: GLYMA15G01350.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0002g06010.t01 (Vitis vinifera), 3'ss of exon 4
gtgagaattttatatcttcaatcagtttgagattaacttaattgcttctctaggctaatattgtcactccataactatgataactttggggttctataacatgatgtttctcacaatatgatatgatatgatgcagATAAAATGGATTTGCCCAACTGCTCCTACCCGTCCTGTGGCGATACTTGGTGGTTTTCCCTGCACTGCAT
                                                            |    | |   |   |   ||  |||| ||| | ||||| |  |    ||| ||  |   | ||  |||||||||||||||||||||||| |||||||||||||| |||||||| ||  |||| ||||| ||||| ||||||||||
-----------------------------------------------------------gtaaggatttgtttttttaaattgcttttgggct-tataaaaccacaaatcttactgttcaa-attctatgatgcagATAAAATGGATTTGTCCAACTGCTCCTACTCGTCCTGTTGCAGTACTCGGTGGATTTCCTTGCACTGCAT

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|209717358|gb|BW659048.1|BW659048
EST:     CTCATCTCAGCTCCTGGAATCCCTTCCACTTCCAAAT                         ATAAAATGGATTTGCCCAACTGCTCCTACCCGTCCTGTGGCGATACTTGGT
genomic: CTCATCTCAGCTCCTGGAATCCCTTCCACTTCCAAATgtgagaattt ... tatgatgcagATAAAATGGATTTGCCCAACTGCTCCTACCCGTCCTGTGGCGATACTTGGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactttggggttctataacatgatgtttctcacaatatgatatgatatgatgcagATAAAATGGATTTGCCCAACTGCTCCTACCCGTCCTGTGGCGATACTTGGTGGTTTTCCCTGCACTGCAT
                          ttctcac  putative branch site (score: 2)
                                 aatatgatatgatat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaattttatatcttcaatcagtttgagattaacttaattgcttctctaggctaatattgtcactccataactatgataactttggggttctataacatgatgtttctcacaatatgatatgatatgatgcagATAAAATGGATTTGCCCAACTGCTCCTACCCGTCCTGTGGCGATACTTGGTGGTTTTCCCTGCACTGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG