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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taagtacagaaacatatgttaatttgttgacagacgatgtgatcaaccttgagaaacctatgttggcttctaacattacctactctccttgcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGGAAGACGGCTCTCCAGAACCTGGAACAGTTCCAGGAGAAGGCAAAGAAGG

Basic information

species Zea mays
transcript GRMZM2G136296_T03
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 15
---------------------------------------------------------------------------------------taagtacag--aaacat-atgttaatttgttgacagacgatgtgatcaaccttg----agaaacctatg---ttggcttctaacattacctactctccttgcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGGAAGACGGCTCTCCAGAACCTGGAACAGTTCCAGGAGAAGGCAAAGAAGG
                                                                                       | | | |     |||||    |   ||||       | | ||    ||| || |    ||| |  | ||   ||| ||||     | |  | | |    ||  | | |||||||| |||||||||||||||||||||||||||||||| ||||||||||| ||| | ||||||||||| |||||||||||||||||||| ||||||||||
gttcgtgctacttgctacttaacattatgaattgtggtgatcttaaattagttgtcggttagcttctgcatagtctgctgtcacatatgaatgctactcaacattgcttctgtttgagattgaaggctgcttgcaaactagtcacagagatatgtgaaattgtcttcgttgctaatattcccattctgtttatgcagGAAGGGCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGATACTAGGGAGAGAAAGGCTGCTCTCCAGAATCTGGAACAGTTCCAGGAGAAAGCAAAGAAGG
















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|9461359|gb|BE453694.1|BE453694
EST:     AGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: AGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|18163487|gb|BM333326.1|BM333326
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGA
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|67017261|gb|CO446010.1|CO446010
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|4775850|gb|AI664855.1|AI664855
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|60396449|gb|DN229318.1|DN229318
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|211435102|gb|FL442353.1|FL442353
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|32847083|gb|CD986764.1|CD986764
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|211269150|gb|FL294986.1|FL294986
EST:     CAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|37393345|gb|CF633935.1|CF633935
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|40336444|gb|CK370514.1|CK370514
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|78025893|gb|DV494280.1|DV494280
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|5607972|gb|AI901639.1|AI901639
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|32944015|gb|CF048834.1|CF048834
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATACTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|29945603|gb|CB815724.1|CB815724
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|40334952|gb|CK369022.1|CK369022
EST:     AGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: AGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|20802346|gb|BQ293396.1|BQ293396
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTGCCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|211486828|gb|FL010663.1|FL010663
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|108953432|gb|EC364740.1|EC364740
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|33093747|gb|CF053741.1|CF053741
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGGGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|37382079|gb|CF627962.1|CF627962
EST:     AGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: AGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|5455714|gb|AI833404.1|AI833404
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|15080370|gb|BI389038.1|BI389038
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|32911048|gb|CF015860.1|CF015860
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
EST: gi|60357472|gb|DN224445.1|DN224445
EST:     CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAG                         GAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG
genomic: CTCTTGTTGATGCGGAGACAGAAAGTAGCATAAATGCTACCATGCTTGAGgtttgtgact ... gcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accttgagaaacctatgttggcttctaacattacctactctccttgcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGGAAGACGGCTCTCCAGAACCTGGAACAGTTCCAGGAGAAGGCAAAGAAGG
                      ttctaac  putative branch site (score: 1)
                                 cctactctccttgc  putative PPT
                         taacatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taagtacagaaacatatgttaatttgttgacagacgatgtgatcaaccttgagaaacctatgttggcttctaacattacctactctccttgcatctacagGAAGGCCTTGCTCGGCTTGAAAGAAGCAAGAGATGGGACACTAGGGAGAGGAAGACGGCTCTCCAGAACCTGGAACAGTTCCAGGAGAAGGCAAAGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - -aaacata
- - - - - - - - - - - tttgttg
- - - - - - - - - - - - - - - - - cgatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcttct