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

gtttgtctcacttttgccgtgtgcttttccatataaaaaacttactgtcacctttcagcctactgatttctaattcttctcccagGAGGCAATAAATGAATACGAGGGCACTGTTATCACAGTATCTCATGACCGATACTTTATAAAGCAAATAGTTAATAGAGTGATAGAAATTAAAGATGGCA

Basic information

species Glycine max
transcript GLYMA06G15200.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G15200.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os11g39020.1 (Oryza sativa), 3'ss of exon 6
-------------------------------------gtttgtctcacttttgccgtgtgcttttccatataaaaaacttactgtcacctttcagcctactgatttctaattcttctcc--------cagGAGGCAATAAATGAATACGAGGGCACTGTTATCACAGTATCTCATGACCGATACTTTATAAAGCAAATAGTTAATAGAGTGATAGAAATTAAAGATGGCA
                                     |    ||||     |  |      |||| | ||| |   |     |      ||      |||| |     ||| ||| |          |||||||||||    ||||||   ||||||||||| ||||| ||||||||||| || ||  |||||||||| ||||| ||||| || ||| | ||||||   |
gttagatgcaattctcgtatgttaaaaaaattgtaatgcagttctcctgcatagcaaaacttttttcttatgatccatcagttccttgtttagcatgtacttacagtaaatgcttgtgtgtgcatggcagGAGGCAATTTCAGAATACACAGGCACTGTTATAACAGTTTCTCATGACCGGTATTTCGTAAAGCAAATTGTTAACAGAGTTATTGAAGTGAAAGATCAGA

upper sequence: GLYMA06G15200.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0031g01640.t01 (Vitis vinifera), 3'ss of exon 6
-------------------------gtttgtctcact-tttgccgtgtgcttttccatataaaaaacttactgtcacctttcagcctactgatttctaattcttctcccagGAGGCAATAAATGAATACGAGGGCACTGTTATCACAGTATCTCATGACCGATACTTTATAAAGCAAATAGTTAATAGAGTGATAGAAATTAAAGATGGCA
                          ||    | ||| | | || ||||| ||      | ||    | | | |||| |       |  |||  |||  || ||||  |||||||||||||  || ||| ||||||||||| | ||||| |||||||| |||||||| ||||||||||||||||||||||| || ||| |||| ||||| |
gtttgattcatttgttcctatccatattgagattactatctaccatgtgcattatagctttaagt-ttaattatcacttcatgattttttgaactctgtttgttctatcagGAGGCAATAACGGAGTACAAGGGCACTGTTGTTACAGTGTCTCATGATCGATACTTCATAAAGCAAATAGTTAATAGAGTAATTGAAGTTAAGGATGGGA
















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|193322215|gb|FK284965.1|FK284965
EST:     TGGATGAACCAACCAATCACTTGGATATACCTTCTAAAGAAATGCTCGAG                         GAGGCAATAAATGAATACGAGGGCACTGTTATCACAGTATCTCATGACCGA
genomic: TGGATGAACCAACCAATCACTTGGATATACCTTCTAAAGAAATGCTCGAGgtttgtctca ... cttctcccagGAGGCAATAAATGAATACGAGGGCACTGTTATCACAGTATCTCATGACCGA
EST: gi|193518984|gb|FK472789.1|FK472789
EST:     TGGATGAACCAACCAATCACTTGGATATACCTTCTAAAGAAATGCTCGAG                         GAGGCAATAAATGAATACGAGGGCACTGTTATCACAGTATCTCATGACCGA
genomic: TGGATGAACCAACCAATCACTTGGATATACCTTCTAAAGAAATGCTCGAGgtttgtctca ... cttctcccagGAGGCAATAAATGAATACGAGGGCACTGTTATCACAGTATCTCATGACCGA
EST: gi|27446272|gb|CA953395.1|CA953395
EST:     TGGATGACCCANCCAATCACTTGGATATACCTTCTAAAGAAATGCTCGAG                         GAGGCAATAAATGAATACGAGGGCACTGTTATCACAGTATCTCATGACCGA
genomic: TGGATGAACCAACCAATCACTTGGATATACCTTCTAAAGAAATGCTCGAGgtttgtctca ... cttctcccagGAGGCAATAAATGAATACGAGGGCACTGTTATCACAGTATCTCATGACCGA
EST: gi|22540684|gb|BU090527.1|BU090527
EST:     TGGATGAACCAACCAATCACTTGGATATACCTTCTAAAGAAATGCTCGAG                         GAGGCAATAAATGAATACGAGGGCACTGTTATCACAGTATCTCATGACCGA
genomic: TGGATGAACCAACCAATCACTTGGATATACCTTCTAAAGAAATGCTCGAGgtttgtctca ... cttctcccagGAGGCAATAAATGAATACGAGGGCACTGTTATCACAGTATCTCATGACCGA
EST: gi|308099193|gb|HO761426.1|HO761426
EST:     TGGATGAACCAACCAATCACTTGGATATACCTTCTAAAGAAATGCTCGAG                         GAGGCAATAAATGAATACGAGGGCACTGTTATCACAGTATCTCATGACCGA
genomic: TGGATGAACCAACCAATCACTTGGATATACCTTCTAAAGAAATGCTCGAGgtttgtctca ... cttctcccagGAGGCAATAAATGAATACGAGGGCACTGTTATCACAGTATCTCATGACCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atataaaaaacttactgtcacctttcagcctactgatttctaattcttctcccagGAGGCAATAAATGAATACGAGGGCACTGTTATCACAGTATCTCATGACCGATACTTTATAAAGCAAATAGTTAATAGAGTGATAGAAATTAAAGATGGCA
                                     ttctaat  putative branch site (score: 2)
                                    tttctaattcttctcc  CT-rich tract
                                   atttctaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtctcacttttgccgtgtgcttttccatataaaaaacttactgtcacctttcagcctactgatttctaattcttctcccagGAGGCAATAAATGAATACGAGGGCACTGTTATCACAGTATCTCATGACCGATACTTTATAAAGCAAATAGTTAATAGAGTGATAGAAATTAAAGATGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG