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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccttggagctagcgttaatatgaggttagagtgtttatgtgcaccaagaactaacattctgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTTGTTGATCGCGAGTTCACTTACATGGTATGAAGCGTGATCAGTCTAAGTT

Basic information

species Zea mays
transcript GRMZM2G038588_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038588_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g12570.1 (Oryza sativa), 3'ss of exon 9
gtatgccttggagctagcg---ttaatatgagg---ttagagtgtttatg-tgcaccaagaactaacattctg-cattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTTGTTGATCGCGAGTTCACTTACATGGTATGAAGCGTGATCAGTCTAAGTT
|||  ||    | | |       ||  |||      ||   |  ||  || |    |   |  |||||| ||  ||||  ||||||||||| || ||||||||||| ||||| |||||| ||||||| | | |||| || ||||| ||  | || ||||| || || |||||||   | |  
gtacccccaacaaccaagaaaactagcatgtacctttttatggattcgtggtaagacctaacttaacatgctctcatttcagGAAGAAGCTCACATACATTGCACCATGCCCAGGGGACCTGCCAAGTAAGCTGTTAATTGCGAGCTCGTTAACGTGGTACGAGGCTTGATCAGCTCATGGC
















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|71756919|gb|DR954856.1|DR954856
EST:     CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG                         GAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|148960674|gb|EE011305.2|EE011305
EST:     CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG                         GAAGAAGGTGACGTACATTGCCCCTTGCCCGGGGGACTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|71763129|gb|DR961066.1|DR961066
EST:     CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG                         GAAGAAGCTGACGTACATTGCCCCTTGCCCGGGGGACTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|86471476|gb|DY237846.1|DY237846
EST:     CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG                         GAAGAAGCTGACGTACATTGCCCCTTGCCCGGGGGACTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|78075700|gb|DV504134.1|DV504134
EST:     CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG                         GAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|211229043|gb|FL456610.1|FL456610
EST:     CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG                         GAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|78081105|gb|DV509517.1|DV509517
EST:     CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG                         GAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|71323423|gb|DR798362.1|DR798362
EST:     CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG                         GAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|110518920|gb|EE023507.1|EE023507
EST:     CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG                         GAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|31405753|gb|CD484485.1|CD484485
EST:     CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG                         GAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCA-GCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|50338323|gb|CO533449.1|CO533449
EST:     CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG                         GAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|148965176|gb|EE015985.2|EE015985
EST:     CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG                         GAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|86471665|gb|DY238035.1|DY238035
EST:     CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG                         GAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|149010086|gb|EE041893.2|EE041893
EST:     CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG                         GAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|50338769|gb|CO533895.1|CO533895
EST:     CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG                         GAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|116827681|gb|EC871609.1|EC871609
EST:     CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG                         GAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|149073620|gb|EE161922.2|EE161922
EST:     CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG                         GAAGAAGGTGACGTACATTGCCCCTTGCCCGGGGGACTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|149034778|gb|EE155078.2|EE155078
EST:     CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG                         -AAG---CTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|93014406|gb|EB639926.1|EB639926
EST:     CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG                         GAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|148999969|gb|EE037044.2|EE037044
EST:     CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG                         GAAGAAGCTGACGTACATTGCCCCTTGCCCGGGGGACTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|211013387|gb|FL466952.1|FL466952
EST:     CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG                         GAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|60401015|gb|DN233822.1|DN233822
EST:     CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG                         GAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|71324526|gb|DR798964.1|DR798964
EST:     CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG                         GAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|60359327|gb|DN226300.1|DN226300
EST:     CAATGTTGCCGGATTCATTCATGTTATTGATGTTGACATCCAAAG                         GAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT
EST: gi|78122373|gb|DV540757.1|DV540757
EST:     CAATGTTGCCGGATTCATTCATGTTTCTGATGTTGACATCCAAAG                         GAAGAAGCTGACGTACATTGCCCCTTGCCCGGGGGGCTTGCCAAGCAGGTT
genomic: CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGgtatgccttg ... tgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatatgaggttagagtgtttatgtgcaccaagaactaacattctgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTTGTTGATCGCGAGTTCACTTACATGGTATGAAGCGTGATCAGTCTAAGTT
                                  aactaac  putative branch site (score: 1)
                 tgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgccttggagctagcgttaatatgaggttagagtgtttatgtgcaccaagaactaacattctgcattctagGAAGAAGCTGACGTACATTGCACCTTGCCCGGGGGACTTGCCAAGCAGGTTGTTGATCGCGAGTTCACTTACATGGTATGAAGCGTGATCAGTCTAAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC