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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcagagaaaaatattagagtttccttcttctctttctttcttcttgggagggtcctagacctcgaatgctaggaaacattgagctgattttcagttcataacaaataatcaagGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAGTGTTCAAGATAACAGGGAGGGGTTTGTTTTACTCGTGGATGCCA

Basic information

species Glycine max
transcript GLYMA04G24920.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G24920.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os09g20820.1 (Oryza sativa), 3'ss of exon 2
--gtagcagagaaaaatattagagtttccttcttctctttctttcttcttgggagggtcctagac-ctcgaatgctaggaaacattgagctgattttcagttcataacaa----------ataatcaagGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAGTGTTCAAGATAACAGGGAGGGGTTTGTTTTACTCGTGGATGCCA
   | |   | |   | ||  | |  |    ||| |  ||   |||  |        ||  | |   | |  | ||  ||   |     |    || ||||| |  |             || || ||||| |||||||| ||||||||||| ||||||||||||||||| || |||||||| | ||||||||| |||||                             
acattggcaacagttacatctgcgcatttgacttgtagtttgctctcgtcttttaattctcaaatgtttgtcttctgagatttacctgtccatgttacagTTTACCATGCCCTAAAGGGCATCATTAAGGCGAAATATGGTCAAGATGCATGCAATGTTGGAGATGAAGGTGGCTTTGCTCCTAATGTTCAAGACAACAG-----------------------------

upper sequence: GLYMA04G24920.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G034848_T01 (Zea mays), 3'ss of exon 2
---------gtagcagagaaaaatattagagtttccttcttctctttctt--tcttcttgggagggtcctagacctcgaatg-ctaggaaacattgagctgattttcagttcataacaaata--atcaagGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAGTGTTCAAGATAACAGGGAGGGGTTTGTTTTACTCGTGGATGCCA
           || | | |   ||||| | | ||  | |||||  |   |  ||   |          |   || | ||||  |   |  |   | | | | ||  ||  || | |     |  || |||||||||||||| ||||||||||| ||||| |||||||||||||| |||||||| | ||||||||| |||||                             
tttgttataaaagtaaacatctatatttgggatttttgcttcttctagctggtcacttcatcttctatcctcacttggaatatccttgttatggtaa-cagTTTACCATGTCCTGAAGGGCATCATTAAGGCAAAATATGGTCAAGATGCATGCAATGTCGGAGATGAAGGAGGTTTTGCTCCTAATGTTCAAGACAACAG-----------------------------

upper sequence: GLYMA04G24920.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G009030_T01 (Zea mays), 3'ss of exon 2
------gtagcagagaaaa---atattagagtttccttcttctctttctt--tcttcttgggagggtcctagacctcgaatgctaggaaacattgagctgattttcagttcataacaaata--atcaagGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAGTGTTCAAGATAACAGGGAGGGGTTTGTTTTACTCGTGGATGCCA
      ||| ||| ||| |   ||||| |   |   | |||||  |   |  ||   |          |   || | ||||         |    | | | ||  ||  || | |  |  |  || ||| |||||||||| ||||||||||| ||||| |||||||||||||| |||||||| | ||||||||| |||||                             
tatgttgtatcagtgaatagctatattgggactatttgcttctgctagctggtcacttcatcttctaacctcacttggaatatccttgttctggtaacagTTTACCATGTCCTGAAGAGCATCATTAAGTCAAAATATGGTCAAGATGCATGCAATGTCGGAGATGAAGGAGGTTTTGCTCCTAATGTTCAAGACAACAG-----------------------------

upper sequence: GLYMA04G24920.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------gtagcagagaaaaatattagagtttccttcttctctttct---ttcttcttgggagggtcctagacctcgaatgctaggaaacattgagctgattttcagttcataacaaataatcaagGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAGTGTTCAAGATAACAGGGAGGGGTTTGTTTTACTCGTGGATGCCA
            | |     |||  | ||  | | |     || ||        || || ||  ||  ||  |  |  |    | ||  |     |  || | ||  |   || | |    ||||||||  | || ||||| |||||||| |||||||| |||||||||||||| ||||| || | |||||||||||||||                             
catatttctcttttggttccaaagttcttctattctttggattatcacaaagaattgtttttctgatagtaatgcatttaatgtactttgttgattacagTTTATCATACATTGA-AGGGGATAATCAAAACTAAGTATGGTCAAGATGCTTGTAATGTCGGAGATGAAGGAGGGTTTGCGCCGAATGTTCAAGATAACAG-----------------------------

upper sequence: GLYMA04G24920.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 2
gtagcagagaaaaatattagagtttccttcttctctttctttcttcttgggagggtcctagacctcgaatgctaggaaacattga--gctgatttt------------cagttcataaca----------aataatcaagGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAGTGTTCAAGATAACAGGGAGGGGTTTGTTTTACTCGTGGATGCCA
              ||| |   |    |||||   ||    | || |||      |  |  | |   |||| ||||||| ||  |   |   ||||            ||||| || | |          ||| ||||||||||||||||||||||||||||| |||||||| ||||| || ||||||||||||| |||||| ||||| ||                             
-----------ttctatgattatgcagttctttagttgtgatattgttgatgcaataatccatcataaatgataggaaagataaataaccatttttaatttgtgggggcagTTTATCATACACTGAAGGGAATTATCAAGGCAAAATATGGACAAGATGCATGCAATGTTGGGGATGAGGGGGGATTTGCTCCCAATGTTCAGGATAATAG-----------------------------


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctcgaatgctaggaaacattgagctgattttcagttcataacaaataatcaagGCAAAATATGGACAAGATGCATGTAATGTTGGAGATGAAGGAGGATTTGCTCCCAGTGTTCAAGATAACAGGGAGGGGTTTGTTTTACTCGTGGATGCCA
                                     tcataac  putative branch site (score: 2)
                                    ttcataacaaataat  TA-rich tract