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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcacctaccttatctcttttcatccattcggggagaaattcagctgaaagtttcatgtgatttgcactcactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC

Basic information

species Zea mays
transcript GRMZM2G081462_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 2
------------------------------------------------------------------------------------------------------------gtacgcacctacctta-----tctcttttcatccattcggg-gagaaattcagctgaaagtttcatgtgatttgcactcactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
                                                                                                             || ||  |    |||     ||  |||  |  || | | |  || |||||| |||||   |     ||||||   ||    ||| |||||||||||||||||||||||||| ||||||||||| |||||||| |||||| |||||||||||||||||||||||||||||||||||||||||||||||
gtaagtagtagtaacacactctaaattatttccttgcacaatgacacaatgtgattgcaagcagccattacaactcaaattgaactgtaccatgactagagaaaatatttaagcttcagttttagggcgtccatttcaactcaattgagtaagcaattcaactgaattgtctgcatgatttatgct----gttcagGTTCTTGAACAAGGGGCTGTCTGATTTCAACTTGGCACTGGACCTCGGGTTCTTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC

upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA03G27380.1 (Glycine max), 3'ss of exon 2
gtacgcacctaccttatctcttt-----tcatccattcgggga-gaaattcagctgaaagtttcatgtgatttgca----ctca--------ctgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
||| | |    |||| |  ||||     | |   || |      ||  |||   |  |  | |  | ||   ||||    ||||        ||||  ||||| |||||||||||  | ||||| ||||| ||||| |||||| |||| ||| ||||||| ||||| || ||||| || |||||||| ||||| ||||||
gtatggaaacgccttgtgcctttaatttttaattatccttctttgattttctatttgatatcttgtttgtagtgcatgacctcattttgattctgtgcagGTTTTTGAACAAGGGTTTATCTGATTTCAATTTGGCTCTGGACTTGGGTTTCTTGACCAAAGCTAGAAAATACACATTTTTCAAGCCAAAGTTTATCTTC

upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA19G30350.1 (Glycine max), 3'ss of exon 2
-------------gtacgcaccta--ccttatctctt-ttcatccatt--cggggagaaat-tcagctgaaagtttcatgtgatttgcactcactgttt-----------agGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
              |  ||   ||   ||||  |||  ||| | ||||  |     || || ||   |||| ||||  |||| | ||  |||| | |||           ||||| |||||||| ||  | ||||| || || ||||| |||||| |||| ||| ||||||| ||||| || ||||| || |||||||||||||| ||||||
gtatggacacaccttgtgcctttaattcttaattctcattctttcatttcctatttgatatctcgtttgaatgtttgttgtg-tatggcctcattattttgattctgtgcagGTTTTTGAACAAAGGTTTATCTGATTTTAATTTGGCTCTGGACTTGGGTTTCTTGACCAAAGCTAGAAAATACACATTTTTCAAGCCCAAGTTTATCTTC

upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT3G56940.2 (Arabidopsis thaliana), 3'ss of exon 3
gtacgcacctaccttatctcttttcatccattcggggagaaattcagctgaaagtttca--tgtgatt-tgcactcactgtt-tagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
               |||||||  ||   |            || | || |  ||||||  | ||||  |  |||   | |   |||||||||||||||||  ||||||| ||||||||||| || ||  |||| |||||||| ||||| ||||| ||||| ||||||||||| || |||||||||
----------gtaagatctcttaacactaaggacctctctttttaatctaagtgtttcaattttgatgataaactttttttggcagGTTCTTGAACAAGGGATTGTCTGATTTCAACTTGGCTCTTGATTTGGGTTTCCTGACAAAGGCAAGGAAATACACTTTCTTCAAGCCAAAATTCATCTTC

upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv08s0040g00390.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------gtacgcacc-taccttatct--cttttcatccattcggggagaaattcagct--------gaaagtttcatgtgatttgcactcactgtt----tagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
                                              || ||| | ||  ||      |   | || ||   |  |||   |  ||||         ||||| | |  | |  | ||    ||| |     || ||  ||||||| ||  | ||||| ||||| |||||  ||||| |||||||||| || |||||||| ||||||||||| || ||||||||||||||||||
gtatgcaaacaactctctgcccttctcccttcctcactcatggtcatatgcatcatagtttgcagaacaagtaatacagctgttgagttttatagcttttaactgaaaagtctgaaataaacttcatgttctgctgttgcagATTTCTGAACAAAGGTTTATCTGATTTCAATTTGGCTTTGGACTTGGGGTTCCTCACAAAGGCTAGAAAGTACACCTTTTTTAAGCCCAAGTTCATCTTC

upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 2
lower sequence: EDP04035 (Chlamydomonas reinhardtii), 3'ss of exon 4
--gtacgcacctaccttatctcttttcatccattcggggagaaattcagctgaaagtttcatg----tgatttgcactcactgtttagGTTCTTGAACAAGGGGCTGTC--TGACTT-CAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC---------
  ||  ||| |  | |     |   |   ||   |       ||  ||||   |   | ||        |    ||||| | |   | |  |    ||| |   |||    || ||  | |   ||| |   ||   || ||||||| ||||||   |  | ||  |  | |    |   |  |   ||||         
cggtcggcaacggcgtccctgcgcctttgcccacctcaccccaacccagcctcaccctccaccgcctcaaccctcactccccggcaacgcaccaacacagGTTCCTGCTCATGTCTCGCGATGAGGCCCGCCACGCCGGCTTCCTGAACAAGGCCCTGTCGGACTTCAACCTGGCCCTGGACCTGGGCTTCCTGACCAAG

upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S97_248V6.1 (Physcomitrella patens), 3'ss of exon 1
--gtacgcacctaccttatctcttttcatccattcggggagaaattcagctgaaagtttcatgtgat-ttgcactcactgttt---agGTTCTTGAACAAGGGGCTG--TCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTT---CAAGCCCAAGTTCATCTTC-------
    | |   | ||   |  | ||   | |   |   |       |   ||   |  |   ||| || ||| | |  ||   |   | |    ||||||   | |     |||   |      |    |   |||   ||    |    | || ||  |      ||||||   ||||     ||    ||||       
agaaatgttgccactccaattgttgcaaacagcttttgatctttcttctctccgatatgattgtaatgttgaaattgcttccttccatgaatgtgaacagAAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAAGCCAGACATGCTGGCTTCTTGAACAAGGGACTGTCAGACTTCAACTTGG

upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ28505 (Selaginella moellendorffii), 3'ss of exon 2
-----------------------------------------gtacgcacctaccttatctcttttcatccattcggggagaaattcagctgaaagtttcatgtgatttgcactcactgtttagGTTCTTGAACAAGGGGCTGTCT-GACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC--------------------------------------------------------------
                                          ||                                                                                                      ||||| |||||||| ||||| || || || |||||||| ||  ||||||||||||||||||||||  |||||||||||                                                              
gttctcagttactcagctggaaaaaaagcatcgatcatttcctatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncgactttaacttggctctggatcttggatttctgaccaaagCCCGGAAGTACACCTTCTTCAAGCCACAGTTCATCTTCTACGCGACGTATCTCTCGGAGAAGATCGGCTACTGGAGGTACATTACTATCTACAGGCACTT

upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ30397 (Selaginella moellendorffii), 3'ss of exon 2
gtacgcacctaccttatctcttttcatccattcggggagaaattcagctgaaagtttcatgtgatttgcactcactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
                |   || |||     || |   ||||   |||    |   |||| |  | |    |||     ||||||| ||||||| ||  | || ||||| |||||||| ||||| || || || |||||||| ||  ||||||||||||||||||||||  |||||||||||
---------------gtaagttctcagtttctcagttggaaaaaaagcatcga---tcatttcctatatgttca-----tagGTTCCTGAACAAAGGATTATCCGACTTTAACTTGGCTCTGGATCTTGGATTTCTGACCAAAGCCCGGAAGTACACCTTCTTCAAGCCACAGTTCATCTTC

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|78112391|gb|DV530785.1|DV530785
EST:     GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGG                         GTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
genomic: GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGGgtacgcacct ... cactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
EST: gi|149097284|gb|EE183107.2|EE183107
EST:     GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGG                         GTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
genomic: GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGGgtacgcacct ... cactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
EST: gi|84969707|gb|DW468136.1|DW468136
EST:     GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGG                         GTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
genomic: GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGGgtacgcacct ... cactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
EST: gi|76016942|gb|DT944112.1|DT944112
EST:     GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGG                         GTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
genomic: GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGGgtacgcacct ... cactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
EST: gi|15323476|gb|BI478494.1|BI478494
EST:     GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGG                         GTTCTTGAACAAGGGGCTGTCTGACTTCAACTGGGCGCTGGACCTGGGGTT
genomic: GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGGgtacgcacct ... cactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
EST: gi|211408498|gb|FL069298.1|FL069298
EST:     GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCAGG                         GTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
genomic: GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGGgtacgcacct ... cactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
EST: gi|50325243|gb|CO520369.1|CO520369
EST:     GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGG                         GTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
genomic: GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGGgtacgcacct ... cactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
EST: gi|13557965|gb|BG549321.1|BG549321
EST:     TCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGG                         GCTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGT
genomic: TCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGGgtacgcacct ... cactgtttagG-TTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGT
EST: gi|78107168|gb|DV525586.1|DV525586
EST:     GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGG                         GTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT
genomic: GTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGGgtacgcacct ... cactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccattcggggagaaattcagctgaaagtttcatgtgatttgcactcactgtttagGTTCTTGAACAAGGGGCTGTCTGACTTCAACTTGGCGCTGGACCTGGGGTTCCTGACCAAGGCTAGGAAGTACACCTTCTTCAAGCCCAAGTTCATCTTC
                                         cactcac  putative branch site (score: 2)
          agaaatt  TA-rich tract