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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctagatttatgcttaaatcgtgattggtttaatctgaggaatgaatcgaggagaaaatgtgtctgatgcatattttgtcttttcaatttgttatctgcagTGGGTTTTGTCCTCTAAGGAAATTAACTTCCCTTATCCTTTGGGCTTGACTCTACTTCACATGGTCTTCTCCTCTGTTCTGTGTTTTGTGTTAACCAAGA

Basic information

species Glycine max
transcript GLYMA15G40160.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G40160.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g04110.2 (Oryza sativa), 3'ss of exon 1
-ctagatttatgcttaaatcgtgattggtttaatctgaggaatgaatcgaggaga-aaatgtgtctgatgcatattttgtcttttcaatttgttatctgcagTGGGTTTTGTCCTCTAAGGAAATTAACTTCCCTTATCCTTTGGGCTTGACTCTACTTCACATGGTCTTCTCCTCTGTTCTGTGTTTTGTGTTAACCAAGA
  |  |   |  |     | ||    ||     || |   | |   |      || ||||||  |   |   ||  | || |  |  |||||     ||||||||||||| ||||| || || || |||||||| |||||| |||  || ||||| || |||||||| ||||| |||||  |||| || |   | || ||||
tttcaacacactccatcgttgttcccggagatgtccgcaaattctttttccttgataaatgtaacc--ttgttaactagtatcatgtatttgcctgatgcagTGGGTTTTATCCTCAAAAGAGATCAACTTCCCCTATCCTGTGGCATTAACTCTGCTGCACATGGTTTTCTCATCTGTAGTGTGCTTCGCAATTACAAAGA

upper sequence: GLYMA15G40160.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G53660.1 (Arabidopsis thaliana), 3'ss of exon 1
-ctagatttatgcttaaatcgtgattggtttaatctgaggaatgaatcgaggagaaaatgtgtctgatgcatattttgtcttttcaatttgttatc-tgcagTGGGTTTTGTCCTCTAAGGAAATTAACTTCCCTTATCCTTTGGGCTTGACTCTACTTCACATGGTCTTCTCCTCTGTTCTGTGTTTTGTGTTAACCAAGA
   | | || ||  |||||  || ||  ||  || |       |  ||    ||    | | |   |    || ||| | |||   | |   | |  |||||||||| ||||| ||||||||||| ||||||||||||||  | || |||||  |||||||||||   || ||||||||| |||||||| |  | || ||| 
ttcaaacttttg--taaattttggttcattccatttctctttagcttctttcagtttcttttttccagcactaatttttatttctgactcaatctgatgcagTGGGTATTGTCATCTAAGGAAATAAACTTCCCTTATCCACTTGGATTGACATTACTTCACATGACTTTTTCCTCTGTTTTGTGTTTTCTCCTCACGAAGG

upper sequence: GLYMA15G40160.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G14410.1 (Arabidopsis thaliana), 3'ss of exon 1
ctagatttatgcttaaatcgtgattggtttaatctgaggaatgaatcgaggagaaaatgtgtc-----tgatgcatattttgtcttttcaatttgttatctgcagTGGGTTTTGTCCTCTAAGGAAATTAACTTCCCTTATCCTTTGGGCTTGACTCTACTTCACATGGTCTTCTCCTCTGTTCTGTGTTTTGTGTTAACCAAGA
     || |   ||  |   |   | |        ||   ||  || | ||      | | |      |||   |  ||||    ||| ||||  |   ||||||||||||||||| |||||||||||||| |||||||||||| | || |||||| |||| || ||| |||| ||||||||  |||| ||| |  | |||||  
-----ttcaccgttttacaatctgtagcaagtaacgattcatagattgtggtttctctcttttcgtcatgactaacgtttttgtctttgaattgctctgctgcagTGGGTTTTGTCATCTAAGGAAATTAATTTCCCTTATCCTCTTGGATTGACTTTACTCCATATGATCTTTTCCTCTGTCTTGTGCTTTCTTCTTACCAAAG

upper sequence: GLYMA15G40160.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0046g00460.t01 (Vitis vinifera), 3'ss of exon 1
-ctagatttatgcttaaatcgtgattggt-ttaatctgaggaatgaatcgaggagaaaatgtgtctgatgcatattttgtcttttcaatttgttatctgcagTGGGTTTTGTCCTCTAAGGAAATTAACTTCCCTTATCCTTTGGGCTTGACTCTACTTCACATGGTCTTCTCCTCTGTTCTGTGTTTTGTGTTAACCAAGA
  |   ||| |  |||  ||    ||    || || |      |  | |   |    |   || || |   ||  ||| |||| | || |||| |  || ||||||||||||| || |||||||| || ||||| || ||  | ||  ||||||| |||||||||||||||||||||||  |||| ||| |  | ||||   
tttttttttttctttacctctctcttatccttgatatctctgtttgagctttgcttca-catggctaacagatgattt-tcttctaaaattgtaaaatgtagTGGGTTTTGTCATCAAAGGAAATAAATTTCCCCTACCCACTTGGACTGACTCTGCTTCACATGGTCTTCTCCTCTGTATTGTGCTTTATTCTCACCAGAG

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|208212258|gb|GE015363.1|GE015363
EST:     ACATTCTTCTCTACATTGCTCTCTCCAGCGGCCAAATCTTCTTCAACAAG                         TGGGTTTTGTCCTCTAAGGAAATTAACTTCCCTTATCCTTTGGGCTTGACT
genomic: ACATTCTTCTCTACATTGCTCTCTCCAGCGGCCAAATCTTCTTCAACAAGgttaccgtcg ... ttatctgcagTGGGTTTTGTCCTCTAAGGAAATTAACTTCCCTTATCCTTTGGGCTTGACT
EST: gi|298164008|gb|HO013653.1|HO013653
EST:     ACATTCTTCTCTACATTGCTCTCTCCAGCGGCCAAATCTTCTTCAACAAG                         TGGGTTTTGTCCTCTAAGGAAATTAACTTCCCTTATCCTTTGGGCTTGACT
genomic: ACATTCTTCTCTACATTGCTCTCTCCAGCGGCCAAATCTTCTTCAACAAGgttaccgtcg ... ttatctgcagTGGGTTTTGTCCTCTAAGGAAATTAACTTCCCTTATCCTTTGGGCTTGACT
EST: gi|213597725|gb|DB964173.1|DB964173
EST:     ACATTCTTCTCTACATTGCTCTCTCCAGCGGCCAAATCTTCTTCAACAAG                         TGGGTTTTGTCCTCTAAGGAAATTAACTTCCCTTATCCTTTGGGCTTGACT
genomic: ACATTCTTCTCTACATTGCTCTCTCCAGCGGCCAAATCTTCTTCAACAAGgttaccgtcg ... ttatctgcagTGGGTTTTGTCCTCTAAGGAAATTAACTTCCCTTATCCTTTGGGCTTGACT
EST: gi|15287909|gb|BI471800.1|BI471800
EST:     ACATTCTTCTCTACATTGCTCTCTCCAGCGGCCAAATCTTCTTCAACAAG                         TGGGTTTTGTCCTCTAAGGAAATTAACTTCCCTTATCCTTTGGGCTTGACT
genomic: ACATTCTTCTCTACATTGCTCTCTCCAGCGGCCAAATCTTCTTCAACAAGgttaccgtcg ... ttatctgcagTGGGTTTTGTCCTCTAAGGAAATTAACTTCCCTTATCCTTTGGGCTTGACT
EST: gi|208206706|gb|GE004611.1|GE004611
EST:     ACATTCTTCTCTACATTGCTCTCTCCAGCGGCCAAATCTTCTTCAACAAG                         TGGGTTTTGTCCTCTAAGGAAATTAACTTCCCTTATCCTTTGGGCTTGACT
genomic: ACATTCTTCTCTACATTGCTCTCTCCAGCGGCCAAATCTTCTTCAACAAGgttaccgtcg ... ttatctgcagTGGGTTTTGTCCTCTAAGGAAATTAACTTCCCTTATCCTTTGGGCTTGACT
EST: gi|7640658|gb|AW734955.1|AW734955
EST:     ACATTCTTCTCTACATTGCTCTCTCCAGCGGCCAAATCTTCTTCAACAAG                         TGGGTTTTGTCCTCTAAGGAAATTAACTTCCCTTATCCTTTGGGCTTGACT
genomic: ACATTCTTCTCTACATTGCTCTCTCCAGCGGCCAAATCTTCTTCAACAAGgttaccgtcg ... ttatctgcagTGGGTTTTGTCCTCTAAGGAAATTAACTTCCCTTATCCTTTGGGCTTGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgaggagaaaatgtgtctgatgcatattttgtcttttcaatttgttatctgcagTGGGTTTTGTCCTCTAAGGAAATTAACTTCCCTTATCCTTTGGGCTTGACTCTACTTCACATGGTCTTCTCCTCTGTTCTGTGTTTTGTGTTAACCAAGA
               gtctgat  putative branch site (score: 4)
                                  ttttcaatttgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctagatttatgcttaaatcgtgattggtttaatctgaggaatgaatcgaggagaaaatgtgtctgatgcatattttgtcttttcaatttgttatctgcagTGGGTTTTGTCCTCTAAGGAAATTAACTTCCCTTATCCTTTGGGCTTGACTCTACTTCACATGGTCTTCTCCTCTGTTCTGTGTTTTGTGTTAACCAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - -tttatgc
- - - - - - - - - -gtgattg
- - - - - - - - - - - - - - - - - - -ggaatga
- - - - - - - - - - - - - - - - - - - - - - - - -ggagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatgc