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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtgatattgtgctactttaagagagatgatgtctatggcatccaactcttcgtaatgttaatgatatcactaagaggtgtatggactaatttttcttttcccttttgtcggtgtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGTTTTGGTAATCATTACCCAAAACATGTTCACCATAGAGGAGCATCTATAC

Basic information

species Glycine max
transcript GLYMA15G13080.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G13080.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G147849_T01 (Zea mays), 3'ss of exon 5
gtgtgtgatattgtgctactttaagagagatgatgtctatggcatccaactcttcgtaa-tgttaatgatatcactaagag-gtgtatggactaatttttcttttcccttttgtcggtgtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGTTTTGGTAATCATTACCCAAAACATGTTCACCATAGAGGAGCATCTATAC
                               |       |       |||||| | ||  ||   |   |  || ||  || |    |||     |  ||    ||   |   |        |||||| |||| |||||||||||||| ||||||  ||| |||||||| ||||| ||||| || ||  | ||||| || |    |||||| ||||| || || ||||
-------------------------------gtaaatcgttcttcttaactctccttaggtgcccaaccttacattagcagagaaagtgggtcggtagttaaaatctgctcgat--------ttgcagCTTGACTACATCCTTGGAAAGAACCCATTGAAGATGAGCTACGTTGTGGGTTTCGGAAACAAGTACCCGAAGCGCCCTCACCACAGAGGTGCGTCGATAC

upper sequence: GLYMA15G13080.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0035g02180.t01 (Vitis vinifera), 3'ss of exon 5
gtgtgtgatattgtgctactttaagagagatgatgtctatggcatccaactcttcgtaatgttaatgatatcactaagaggtgtatggactaatttttcttttcccttttgtcggtgtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGTTTTGGTAATCATTACCCAAAACATGTTCACCATAGAGGAGCATCTATAC
|| || |||||  || | | | ||   |  |  ||       |||    ||  || |   || |   ||||   |   |     | ||  | | ||   |||| | | |    |   || | |||||||||||||||||| || || || ||  | || ||||||||| ||| ||||||||| |||||||| |||| |||||| ||||||||||| |||||||| |
gtatgcgatatc-tgattcctcaattaaagttgtgag-ggaacatgagtctgctcatgtagtaataaatattgttggaaccaacaagg--tcacttaaatttttcatatctctgaccttctggcagATTGATTACATCCTCGGCAAAAATCCTCGAAAGATGAGCTATATTGCAGGTTTTGGCAATCATTATCCAAGACATGTCCACCATAGAGGTGCATCTATCC
















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|14009233|gb|BG725837.1|BG725837
EST:     GTAATTTTGCCAAGACCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGT
genomic: GTAATTTTGCCAAGACCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGT
EST: gi|6502372|gb|AW203745.1|AW203745
EST:     GACCTAATTTCTTTTCAACTGATGTGCTCCGTAATTTTGCCAAGACCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGGAAATGAGCTATGTTGTAGGT
genomic: GACCTAATTTCTTTTCAACTGATGTGCTCCGTAATTTTGCCAAGACCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGT
EST: gi|14012135|gb|BG727057.1|BG727057
EST:     GACCTAATTTCTTTTCAACTGATGTGCTCCGTAATTTTGCCAAGACCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGT
genomic: GACCTAATTTCTTTTCAACTGATGTGCTCCGTAATTTTGCCAAGACCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGT
EST: gi|26058724|gb|CA801638.1|CA801638
EST:     ATTTTGCCAAGACCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGT
genomic: ATTTTGCCAAGACCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGT
EST: gi|58019165|gb|CX705907.1|CX705907
EST:     CGTAATTTTGCCAAGACCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGT
genomic: CGTAATTTTGCCAAGACCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGT
EST: gi|7640040|gb|AW734349.1|AW734349
EST:     GACCTAATTTCTTTTCAACTGATGTGCTCCGTAATTTTGCCAAGACCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGT
genomic: GACCTAATTTCTTTTCAACTGATGTGCTCCGTAATTTTGCCAAGACCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGT
EST: gi|58017124|gb|CX703866.1|CX703866
EST:     GACTTAATTTCTTTTCAACTGATGTGCTCCGTAATTTTGCCAAGACCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGT
genomic: GACCTAATTTCTTTTCAACTGATGTGCTCCGTAATTTTGCCAAGACCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGT
EST: gi|13789346|gb|BG651937.1|BG651937
EST:     GACCTAATTTCTTTTCAACTGATGTGCTCCGTAATTTTGCCAAGACCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGT
genomic: GACCTAATTTCTTTTCAACTGATGTGCTCCGTAATTTTGCCAAGACCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGT
EST: gi|16347793|gb|BI973388.1|BI973388
EST:     GACCTAATTTCTTTTCAACTGATGTGCTCCGTAATTTTGCCAAGACCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGT
genomic: GACCTAATTTCTTTTCAACTGATGTGCTCCGTAATTTTGCCAAGACCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGT
EST: gi|6072595|gb|AW101982.1|AW101982
EST:     GACCTAATTTCTTTTCAACTGATGTGCTCCGTAATTTTGCCAAGACCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGT
genomic: GACCTAATTTCTTTTCAACTGATGTGCTCCGTAATTTTGCCAAGACCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGT
EST: gi|15813092|gb|BI785367.1|BI785367
EST:     GACCTAATTTCTTTTCAACTGATGTGCTCCGTAATTTTGCCAAGACCCAG                         ATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGT
genomic: GACCTAATTTCTTTTCAACTGATGTGCTCCGTAATTTTGCCAAGACCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGT
EST: gi|58022357|gb|CX709098.1|CX709098
EST:     CTAATTTCTTTTCAACTGATGTGCTCCGTAATTTTGCCAAGACCCAG                         ATTGATTACATCCTTGGAAATACCCCAAGGAAAATGAGCTATGTTGTAGGT
genomic: CTAATTTCTTTTCAACTGATGTGCTCCGTAATTTTGCCAAGACCCAGgtgtgtgata ... gtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactaagaggtgtatggactaatttttcttttcccttttgtcggtgtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGTTTTGGTAATCATTACCCAAAACATGTTCACCATAGAGGAGCATCTATAC
                gactaat  putative branch site (score: 2)
                      tttttcttttcccttt  CT-rich tract
                 actaatttttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtgatattgtgctactttaagagagatgatgtctatggcatccaactcttcgtaatgttaatgatatcactaagaggtgtatggactaatttttcttttcccttttgtcggtgtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGCTATGTTGTAGGTTTTGGTAATCATTACCCAAAACATGTTCACCATAGAGGAGCATCTATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA