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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggggcattattaatttattatgcatcagggaacacattctatttttttcactgatactataaaagttttaatttcttatttgcttttaatcctagtgcagGAGTTGATCCTCCATCATCTCGTGATCCTCCTGTGCTGCTTGCAGCACCAGCATCAAATGTTCTATCATTGCAGAACTCAGCACTGTTGGACTCATCCCT

Basic information

species Zea mays
transcript GRMZM2G052078_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os04g42840.1 (Oryza sativa), 3'ss of exon 13
------------------------------------------------ggggcattatta---atttattatgcatcagggaaca-cattct-atttttttcactgatactataaaagttttaatttcttatttgcttttaatcctagtgcagGAGTTGATCCTCCATCATCTCGTGATCCTCCTGTGCTGCTTGCAGCACCAGCATCAAATGTTCTATCATTGCAGAACTCAGCACTGTTGGACTCATCCCT
                                                ||    |||| |   ||||  |   |||      |||  ||| | || ||  |     ||  || ||||  |  | |||||||||| ||||||||||||||||||| |||||||||||||| ||||||||||||||||| | |||||||||| |||| ||||||  ||| || || ||||| ||||||||| | ||||||||  |
gtattcttttaactgcttagttgtcaattactgttaagtaatagaaatggccttttatcatgtatttcctggtcattgactgacaatattatcatcttagttttctatgataaaaaaaatc-agtttcttatttccttttaatcctagtgcagGGGTTGATCCTCCATCGTCTCGTGATCCTCCTGTTCCGCTTGCAGCAACAGCTTCAAATCATCTGTCCTTACAGAATTCAGCACTGCTCGACTCATCTGT

upper sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA19G35460.1 (Glycine max), 3'ss of exon 13
------------------------ggggcattattaatttattatgcatcagg----gaacacattctatt-----tttttcactgatactataaaagttttaatttctta---tttgcttttaat---cctagtgcagGAGTTGATCCTCCATCATCTCGTGATCCTCCTGTGCTGCTTGCAGCACCAGCATCAAATGTTCTATCA-------TTGCAGAACTCAGCACTGTTGGACTCATCCCT
                              |||||  |   | |    |||||    ||   ||||| ||      | | | | || |  | ||||   ||| |    |||   ||| || ||| |   ||||||||||||||||| |||||||||||||||||||| ||| | |    ||| |  || ||||| |||  |||  ||       |  |||||   |  |||  |||  |       
gtaccacataagttttcctgttagttatttttatttgtacctcaattttcaggactagatgtcattcaatggttgatctgttagtgtttttttaaactatttgagcggttaaatttttctcttattgcccctagtgcagGAGTTGACCCTCCATCATCTCGTGATCCACCTTTCCCTGCTGCTGTCCCCGCATCTAATCATCTGACAAGCTCTTTAACAGAATCAACTACTTCTGGCAT-------

upper sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA13G19230.1 (Glycine max), 3'ss of exon 13
----------------------------------------------------ggggcattattaatttattatgcatcagggaacacattctatttttttcactgatactataaaagttttaatttcttatttgcttttaatcctagtgcagGAGTTGATCCTCCATCATCTCGTGATCC----TCCTGTGCTGCT--TGCAGCACC--AGCATCAAAT--GTTCTATCATTGCAGAACTCAGCACTGTTGGACTCATCCCT
                                                      ||  || ||    |   |    | | | | |   |  |||  |||| |   |   | | |  |  | |||   |||| |  | ||   ||||||||||||||||| ||||| ||||||||||||||    | |  |||||||    ||||| |  | ||||  |   | ||| | |  ||||||   |   | | |||          
gtaccaaataagtttacttgttaaatatatatattttttctaccacattgttctggacttgttgccattcaacaattgatgaagctagtgatatggttttta--aactttgtgagcggctaaat---ttatctcttattgcccctagtgcagGAGTTGACCCTCCCTCATCTCGTGATCCACCATTCCCTGCTGCTGTCACAGCATCTAATCATCTGACTAGCTCTTTAACGGCAGAATCAACTGCAGCTGG----------

upper sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA03G32710.1 (Glycine max), 3'ss of exon 13
------------------------------------------ggggcattattaatttattatgcatcagggaacacattctatttttttcactgatactataaaagttttaatttcttatttgcttttaatcctagtgcagGAGTTGATCCTCCATCATCTCGTGATCCTCCTGTGCTGCTTGCAGCACCAGCATCAAATGTTCTATCATTGCAGAACTCAGCACTGTTGGACTCATCCCT
                                                | |  | || ||        | ||   |  |  || | ||||  |  |   | | |  |  | ||||| |   ||    ||   ||||||||||||||||| |||||||||||||||||||| ||| | |     || |  || ||||| |||  |||  ||          || ||   |      | |||  
gtacaacataagttttcctgttatatatttttatttttacctcaattttcaggacttgatgccattcaatggttgatctgttagtgttttttcaaactatttgagcggctaaatttttctctta---ttgcccctagtgcagGAGTTGACCCTCCATCATCTCGTGATCCACCTTTCCCTGCAGCTGTCCCCGCATCTAATCATCTGACAAGCTCTTTAACAACAGAATCAACTACTTCCGG

upper sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA10G04850.1 (Glycine max), 3'ss of exon 13
----------------------------------------------------ggggcattattaatttattatgcatcagggaacacattctatttttttcactgatactataaaagttttaatttcttatttgcttttaatcctagtgcagGAGTTGATCCTCCATCATCTCGTGATCCTCCTGTGCTGCTTGCAGCACCAGCATCAAATGTTCTATCATTGCAGAACTCAGCACTGTTGGACTCATCCCT
                                                      ||  || ||    |   |    | | |   |   |  |||  |||| |   |   | | |  |  | |||   |||| |  | ||   ||||||||||||||||| ||||| |||||||||||||| ||  | |    ||| |   ||||||| |||  |||| |           |  ||   |      ||||   
gtaccaaataagtttacttgttaaatatatatattttttctacctcattgttctggacttgttgccattcaacaattgatgatgctagtgatatggttttta--aactttgtgagcggctaaat---ttatctcttattgcccctagtgcagGAGTTGACCCTCCCTCATCTCGTGATCCACCATTCCCTGCTGCTGTCACAGCATCTAATCATCTAACTAGCTCTTTAACGACAGAATCAACTGCATCTGG

upper sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 13
lower sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 13
ggggcattattaatttattatgcatcagggaacacattctattttt------ttcactgatactataaaagttttaatttc---------ttatttgcttttaatcctagtgcagGAGTTGATCCTCCATCATCTCGTGATCCTCCTGTGCTGCTTGCAGCACCAGCATCAAATGTTCTATCATTGCAGAACTCAGCACTGTTGGACTCATCCCT-----
       |||| | ||  | | | |  |  |  ||| | | |||||      | |  | | |  |   ||| | |  || |         || | | |||||   ||||||||||||||||| |||||||| ||||||||||||||| | |    ||  || |||||||| |||  ||   ||      | | ||||  || || |   |  | |     
------gtattgagtttctttccttatgaaagtacagtttgtttttgaaacgtcctttaacatgagctaagatatccttgcgcagctaaattgtcttctttttcccctagtgcagGAGTTGACCCTCCATCGTCTCGTGATCCTCCTTTCCATGCTGTTGCTCCAGCATCCAATAGTCACACA---AGTAGCGCAGC--TGCTGAATCAACACATAGTAT

upper sequence: GRMZM2G052078_T02 (Zea mays), 3'ss of exon 13
lower sequence: Vv07s0005g05030.t01 (Vitis vinifera), 3'ss of exon 10
----------------------------------------------------------------------------------------ggggcattattaatttattatgcatcagggaacac-attctatttttttcactgatac----tataaaagttttaatttcttatttgcttttaatcctagtgcagGAGTTGATCCTCCATCATCTCGTGATCCTCCTGTGCTGCTTGCAGCACCAGCATCAAAT-GTTCTATCATTGCAGAACTCAGCACTGTTGGACTCATCCCT
                                                                                        |  | || | ||  | |||   ||   |  || || |  || | |||     |   ||    ||| || |  | | ||| |   ||    ||   ||||| ||||||||||| |||||||||||||||||||||||  | |  ||||| |  ||||||||||||     ||  |   |     |  | |   |   |  | ||   
gtattgaatggttttgtcaattagattattatctttgatcataatattaatttgactgtcaatctatgaagctattcaatggtttactgttgaatcactatctgattgaccaatggtcaaaacgaagctgtctttaatgtttgaacaatttatgaacggctaagtttttctctta---ttgcccctagcgcagGAGTTGACCCTCCATCATCTCGTGATCCTCCATTTCCTCTTGCTGTTCCAGCATCAAATCAACTTACAAACACTTCGAT-GGTAGAATCAAATGCTTCTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcactgatactataaaagttttaatttcttatttgcttttaatcctagtgcagGAGTTGATCCTCCATCATCTCGTGATCCTCCTGTGCTGCTTGCAGCACCAGCATCAAATGTTCTATCATTGCAGAACTCAGCACTGTTGGACTCATCCCT
                                      ttttaat  putative branch site (score: 3)
        atactataaaagtttt  TA-rich tract