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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctgctcaccgataatacctttcagatggtttaagttccaaaaaaaaaaaataacttcagaattcagatggagccacaacgcaacctgctgcgctgccagcttcttttaagtaaactctgaactaatctcgttcgtctctctctcccccacagAATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGACCGAAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAG

Basic information

species Zea mays
transcript GRMZM2G075333_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075333_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g08100.1 (Oryza sativa), 3'ss of exon 4
gtaagctgctcaccgataatacctttcagatggtttaagttccaaaaaaaaaaaataacttcagaattcagatggagccacaacgcaacctgctgcgctgccagcttcttttaagtaaactctgaactaatctcgtt-cgtctctctctcccccacagAATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGACCGAAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAG
                                                       | | | ||    || |||| |       ||| |     |     || ||    | |  ||| |||| | | || ||   ||| |   |    ||      ||| ||||| ||||| ||||| |||||| | || ||||||||||| || ||||| ||||| ||  || |||||||||||||||||||| ||||||| || || 
------------------------------------------------------gtgagtccat--ctctgatgaaatt----cgccattgatta-atcgcgagagaatgt--agtgaactgtca-ctgattcagttgctggtgaaacttgttttcagGATGAAGGATGATCTTGCCGGTGAAGTGCCAGTCGCCTTCATTGTCCGGACAGAAGGCTCAGAAATCACCGAGGATGAGATCAAGAAATTCGTTGCAAAA
















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|37385300|gb|CF629786.1|CF629786
EST:     GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATC                         AATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
genomic: GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATCgtaagctgct ... tcccccacagAATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
EST: gi|37378779|gb|CF626098.1|CF626098
EST:     GCCGCCGTCGTATC                         AATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
genomic: GCCGCCGTCGTATCgtaagctgct ... tcccccacagAATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
EST: gi|5740686|gb|AI948376.1|AI948376
EST:     GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATC                         AATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
genomic: GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATCgtaagctgct ... tcccccacagAATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
EST: gi|91053777|gb|EB164195.1|EB164195
EST:     GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATC                         AATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
genomic: GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATCgtaagctgct ... tcccccacagAATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
EST: gi|14208215|gb|BG841893.1|BG841893
EST:     GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATC                         AATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
genomic: GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATCgtaagctgct ... tcccccacagAATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
EST: gi|149084820|gb|EE174324.2|EE174324
EST:     GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATC                         AATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
genomic: GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATCgtaagctgct ... tcccccacagAATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
EST: gi|78021777|gb|DV490164.1|DV490164
EST:     GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATC                         AATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
genomic: GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATCgtaagctgct ... tcccccacagAATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
EST: gi|45568048|gb|CK985876.1|CK985876
EST:     GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATC                         AATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
genomic: GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATCgtaagctgct ... tcccccacagAATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
EST: gi|78109184|gb|DV527601.1|DV527601
EST:     GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATC                         AATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
genomic: GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATCgtaagctgct ... tcccccacagAATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
EST: gi|86473141|gb|DY239511.1|DY239511
EST:     GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATC                         AATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
genomic: GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATCgtaagctgct ... tcccccacagAATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
EST: gi|14243060|gb|BG840786.2|BG840786
EST:     AAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATC                         AATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
genomic: GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATCgtaagctgct ... tcccccacagAATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
EST: gi|37385990|gb|CF630164.1|CF630164
EST:     GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATC                         AATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
genomic: GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATCgtaagctgct ... tcccccacagAATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
EST: gi|113701577|gb|EE679081.1|EE679081
EST:     GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATC                         AATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
genomic: GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATCgtaagctgct ... tcccccacagAATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
EST: gi|149109199|gb|EE293185.2|EE293185
EST:     GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATC                         AATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
genomic: GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATCgtaagctgct ... tcccccacagAATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
EST: gi|24934544|gb|CA452762.1|CA452762
EST:     GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATC                         AATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
genomic: GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATCgtaagctgct ... tcccccacagAATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
EST: gi|148949766|gb|EC895249.2|EC895249
EST:     GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATC                         AATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
genomic: GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATCgtaagctgct ... tcccccacagAATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
EST: gi|148970850|gb|EE021626.2|EE021626
EST:     GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATC                         AATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
genomic: GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATCgtaagctgct ... tcccccacagAATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
EST: gi|74242637|gb|DT650551.1|DT650551
EST:     GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATC                         AATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
genomic: GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATCgtaagctgct ... tcccccacagAATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
EST: gi|148953986|gb|EC899377.2|EC899377
EST:     GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATC                         AATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC
genomic: GAGGCGCTCCTCATCACGCACCCGGAGATCAAGGACGCCGCCGTCGTATCgtaagctgct ... tcccccacagAATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcttcttttaagtaaactctgaactaatctcgttcgtctctctctcccccacagAATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGACCGAAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAG
                      aactaat  putative branch site (score: 2)
                        ctaatctcgttcgtct  CT-rich tract
      ttttaagtaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctgctcaccgataatacctttcagatggtttaagttccaaaaaaaaaaaataacttcagaattcagatggagccacaacgcaacctgctgcgctgccagcttcttttaagtaaactctgaactaatctcgttcgtctctctctcccccacagAATGAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGACCGAAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA