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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatgcttgctagttgtggcttataatatgtgcagccggtgctggtcgatgggctcagcatgtcgtctcccaattcctgaaacgaaaacgttatgaaaacttgcagGGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAGCAAGAACCCGTACGGGTACGCTGGGTCACGCGACAACAGCAAATGAACC

Basic information

species Zea mays
transcript GRMZM2G038598_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038598_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g51670.1 (Oryza sativa), 3'ss of exon 8
gtaagtatgcttgctagttgtg-gcttataatatgtgcagccggtgctggtcgatgggctcagcatgtcgtctcccaattcctgaaacgaaaacgttatgaaaacttgcagGGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAGCAAGAACCCGTACGGGTACGCTGGGTCACGCGACAACAGCAAATGAACC---
|||||||| |  | ||  | |     ||||  || |     |  | |   |  |  |       |||   | |   |||      | |    ||  | |  | ||   |||||| || |||||| | |||||||||||||| || |||||||| ||||||||||||||||| ||||||||   ||| || |  ||||  ||||| ||| ||   
gtaagtat-caggatatatatatatatatagcatctcacatcatttcatctgtactgtaatgaaatgaaatattaaaatc-----atcatgtactctcttcacac---cagGGCAAAATACGGGGTAGAGGAGATGTGCAGGGACCTGTGGAATTGGGCGAGCAAGAACCCCTACGGGTA---TGGATCGCCGGACAGTAGCAACTGATCCAGC
















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|111195381|gb|EE293516.1|EE293516
EST:     GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAA                         GGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
genomic: GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAAgtaagtatgc ... aaacttgcagGGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
EST: gi|71440043|gb|DR821093.1|DR821093
EST:     GAGATCGTTTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAA                         GGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
genomic: GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAAgtaagtatgc ... aaacttgcagGGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
EST: gi|148951201|gb|EC896889.2|EC896889
EST:     GAGATCGTTTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAA                         GGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
genomic: GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAAgtaagtatgc ... aaacttgcagGGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
EST: gi|31250360|gb|CD219384.1|CD219384
EST:     GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAAGAGCTCAAATGGAA                         GGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
genomic: GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAAgtaagtatgc ... aaacttgcagGGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
EST: gi|74240923|gb|DT648837.1|DT648837
EST:     GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAA                         GGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
genomic: GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAAgtaagtatgc ... aaacttgcagGGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
EST: gi|91053192|gb|EB163610.1|EB163610
EST:     GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAA                         GGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
genomic: GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAAgtaagtatgc ... aaacttgcagGGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
EST: gi|211169445|gb|FL037896.1|FL037896
EST:     GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAA                         GGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
genomic: GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAAgtaagtatgc ... aaacttgcagGGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
EST: gi|74237589|gb|DT645503.1|DT645503
EST:     GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAA                         GGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
genomic: GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAAgtaagtatgc ... aaacttgcagGGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
EST: gi|78085824|gb|DV514217.1|DV514217
EST:     GAGATCGTTTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAA                         GGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
genomic: GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAAgtaagtatgc ... aaacttgcagGGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
EST: gi|149087171|gb|EE176707.2|EE176707
EST:     GAGATCGTTTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAA                         GGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
genomic: GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAAgtaagtatgc ... aaacttgcagGGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
EST: gi|211169444|gb|FL037895.1|FL037895
EST:     GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAA                         GGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
genomic: GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAAgtaagtatgc ... aaacttgcagGGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
EST: gi|211091121|gb|FL440769.1|FL440769
EST:     GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAA                         GGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
genomic: GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAAgtaagtatgc ... aaacttgcagGGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
EST: gi|71429156|gb|DR810206.1|DR810206
EST:     GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAA                         GGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
genomic: GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAAgtaagtatgc ... aaacttgcagGGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
EST: gi|62525910|gb|DN828558.1|DN828558
EST:     GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAAGAGCTCAAATGGAA                         GGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
genomic: GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAAgtaagtatgc ... aaacttgcagGGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
EST: gi|116828756|gb|EC860854.1|EC860854
EST:     GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAAGAGCTCAAATGGAA                         GTCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
genomic: GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAAgtaagtatgc ... aaacttgcagGGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
EST: gi|50335983|gb|CO531109.1|CO531109
EST:     GAGATCGTTTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAA                         GGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
genomic: GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAAgtaagtatgc ... aaacttgcagGGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
EST: gi|18163517|gb|BM333356.1|BM333356
EST:     GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAA                         GGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
genomic: GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAAgtaagtatgc ... aaacttgcagGGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
EST: gi|78121122|gb|DV539506.1|DV539506
EST:     GAGATCGTTTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAA                         GGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
genomic: GAGATCGTCTACGCCGCAACTGCCAAGGCAGAGAAGGAGCTCAAATGGAAgtaagtatgc ... aaacttgcagGGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
EST: gi|18163490|gb|BM333329.1|BM333329
EST:     CTGCCAAGGCAGAGAAGGAGCTCAAATGGAA                         GGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG
genomic: CTGCCAAGGCAGAGAAGGAGCTCAAATGGAAgtaagtatgc ... aaacttgcagGGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggctcagcatgtcgtctcccaattcctgaaacgaaaacgttatgaaaacttgcagGGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAGCAAGAACCCGTACGGGTACGCTGGGTCACGCGACAACAGCAAATGAACC
                                       ttatgaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatgcttgctagttgtggcttataatatgtgcagccggtgctggtcgatgggctcagcatgtcgtctcccaattcctgaaacgaaaacgttatgaaaacttgcagGGCCAAGTACGGGATCGAGGAGATGTGCAGAGATCTGTGGAACTGGGCGAGCAAGAACCCGTACGGGTACGCTGGGTCACGCGACAACAGCAAATGAACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC