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

gtaaagtcattattcacttttccatctttggtttttaaatattggaccctgatgcatgacccattatgtggttttctgtattacagATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAGCGATTGCCTGAAGCAACAATTGGTGGAG

Basic information

species Glycine max
transcript GLYMA12G31740.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G31740.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G26530.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaaagtcattattcacttttccatctttggtttttaaatattggaccctgatgcatga---cccattatgtggttttctgtattacagATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAGCGATTGCCTGAAGCAACAATTGGTGGAG
||||||   ||| |    | |  ||  ||   ||| ||||    | |   ||| | ||       | | | |  || |  || ||| ||||||| ||||| ||||| |||||  | ||  |||||||||||||||| |||  | |||||||||||||||| |||||||
gtaaagatgttagtttgatatatatgctt---tttgaaatccatggctaggatccttggatgttaactttcttattgttcgt-ttatagATTCCTGGTGTACCAATCATGTATGTGACACAACGCAAGTACTCAATAGAGAAACTGCCTGAAGCAACAATCGGTGGAG

upper sequence: GLYMA12G31740.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 7
--------------gtaaag-tcattattc----acttttccatctttggtttttaaatattggaccctgatgcatga---cccattatgtgg----ttttctgtat-tacagATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAGCGATTGCCTGAAGCAACAATTGGTGGAG
               | | | |||| | |     | |  |     |   |||   | |||||       | ||||| |    | | ||  ||     | || |  || | ||| | || ||||| |||||||||||||| || |||| | |||| ||||||||||| ||||| ||||| |||||||||||||
gtaaaaatgaattgatgatgctcatgacttgataattactttgcatcaagttccaatatatttttgataggtgcatcaagttctaataaatgaaatttcttttcaatgtgcagGTCCCTGGTGTGCCAATAATGTACATTACAAAACACCAGTATTCAATTGAGCGGTTGCCCGAAGCGACAATTGGTGGAG

upper sequence: GLYMA12G31740.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S153_101V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------gtaaagtcattattcacttttccatctttggtttttaaatattggaccctgatgcatgacccattatgtggttttctgtattacagATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAGCGATTGCCTGAAGCAACAATTGGTGGAG
                               ||   |  || |   |  |  |   |||||  |     |   |     | | |  ||  |  |||   || ||  || | |  |||||||| ||||||||||||||||||||| |  | |   | || || || ||| |||| |||||||| |||||||| ||||
gttagactattgtttctcgcagagttctgttgttctgatatcacctaagtacctggctttgtgtcggcgaagctctgttcagctagatc-ctgatttaatgattcact-tgtcgcagATTCCTGGTGTTCCAATAATGTACATCTCACAGCATCAATATTCTATAGAGAGATTACCTGAAGCTACAATTGGGGGAG

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|17022905|gb|BM093939.1|BM093939
EST:     AGAATTCGGAAG                         ATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAG
genomic: AGAATTCGGAAGgtaaagtcat ... tgtattacagATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAG
EST: gi|192306233|gb|FG996847.1|FG996847
EST:     GCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGAATTCGGAAG                         ATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAG
genomic: GCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGAATTCGGAAGgtaaagtcat ... tgtattacagATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAG
EST: gi|192330326|gb|FK019876.1|FK019876
EST:     GCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGAATTCGGAAG                         ATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAG
genomic: GCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGAATTCGGAAGgtaaagtcat ... tgtattacagATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAG
EST: gi|21676190|gb|BQ628541.1|BQ628541
EST:     GCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGAATTCGGAAG                         ATTCCCGGTGTTCCAATAATGTACTTCTCCTTTCGCAAGNACTCAATTGAG
genomic: GCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGAATTCGGAAGgtaaagtcat ... tgtattacagATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAG
EST: gi|151411977|gb|EV281788.1|EV281788
EST:     GCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGAATTCGGAAG                         ATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAG
genomic: GCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGAATTCGGAAGgtaaagtcat ... tgtattacagATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAG
EST: gi|17022727|gb|BM093761.1|BM093761
EST:     AGAATTCGGAAG                         ATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAG
genomic: AGAATTCGGAAGgtaaagtcat ... tgtattacagATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAG
EST: gi|151407416|gb|EV277231.1|EV277231
EST:     GCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGAATTCGGAAG                         ATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAG
genomic: GCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGAATTCGGAAGgtaaagtcat ... tgtattacagATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAG
EST: gi|51345064|gb|CO985797.1|CO985797
EST:     GCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGAATTCGGAAG                         ATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAG
genomic: GCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGAATTCGGAAGgtaaagtcat ... tgtattacagATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAG
EST: gi|24205709|gb|BU964962.1|BU964962
EST:     GCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGAATTCGGAAG                         ATTCCCGGGTGTTCCAATAATGTACATCACCAAACGCA-GTACTCAATTGA
genomic: GCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGAATTCGGAAGgtaaagtcat ... tgtattacagATTCCCGG-TGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGA
EST: gi|298183933|gb|HO029146.1|HO029146
EST:     GCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGAATTCGGAAG                         ATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAG
genomic: GCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGAATTCGGAAGgtaaagtcat ... tgtattacagATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAG
EST: gi|209717530|gb|BW679664.1|BW679664
EST:     GCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGAATTCGGAAG                         ATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAG
genomic: GCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGAATTCGGAAGgtaaagtcat ... tgtattacagATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAG
EST: gi|151408961|gb|EV278769.1|EV278769
EST:     GCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGAATTCGGAAG                         ATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAG
genomic: GCTACATTGTTGCAACATGTGATCGGGACTTGAAGAGGAGAATTCGGAAGgtaaagtcat ... tgtattacagATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttaaatattggaccctgatgcatgacccattatgtggttttctgtattacagATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAGCGATTGCCTGAAGCAACAATTGGTGGAG
               ccctgat  putative branch site (score: 4)
                                        ttttctgt  putative PPT
     aaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagtcattattcacttttccatctttggtttttaaatattggaccctgatgcatgacccattatgtggttttctgtattacagATTCCCGGTGTTCCAATAATGTACATCACCAAACGCAAGTACTCAATTGAGCGATTGCCTGAAGCAACAATTGGTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG