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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggttactgggtttactctttaatcaccatgtcattgatattcaaactgaattacttgcttgaaaaatctattgttgaaattttgccaaaaaaacccggcggtaatcgaagggcatccactacttgaataatccattttcagaagtttgcttccttcttatatttcatctgttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGACGATTCTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTT

Basic information

species Zea mays
transcript GRMZM2G083546_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083546_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g63710.1 (Oryza sativa), 3'ss of exon 5
gtgggttactgggtttactctttaatcaccatgtcattgatattcaaactgaattacttgcttgaaaaatctattgttgaaattt-tgccaaaaaaacccggcggtaatcgaagggcatccactacttgaataatccattttcagaagtttgcttccttcttatatttcatctgttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGACGATTCTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTT
                                                                        |||||| |  ||| ||| |  |   |       || ||    |   |       ||| ||  |   ||| |      || |     || | | |||   |  |||    ||||||||||| |||||||||||  ||||||||||||||||   | |  |||| || || || |||||  |||| ||||| |||||||||||||||||||| |
------------------------------------------------------------------------attgtttatgtttgtgctagtacttcatttgaatattctgtagaagt-------ttgcatcttttttttcc-----cttacggttctccttttttttccccctttaattcagGGTTCTTCGTCCATTTCAAGTGCTGATCTTTTTGGCCGCCGCGACATGGATGACTCGAATCTGGATTTAAGTGCTGCGGATCTCATCAACAGAATATCAT
















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|148994701|gb|EE034198.2|EE034198
EST:     CTCAAAACAGAGAAGAGAAAGAGGTTCAGCTATCCCTTCAGAAATTCGCG                         GGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
genomic: CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCGgtgggttact ... ttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
EST: gi|18162325|gb|BM332164.1|BM332164
EST:     GAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCG                         GGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
genomic: GAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCGgtgggttact ... ttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
EST: gi|37379430|gb|CF626459.1|CF626459
EST:     CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCG                         GGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
genomic: CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCGgtgggttact ... ttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
EST: gi|78092043|gb|DV520417.1|DV520417
EST:     CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCG                         GGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
genomic: CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCGgtgggttact ... ttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
EST: gi|110209090|gb|EC890987.1|EC890987
EST:     CAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCG                         GGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGCCCGTACCAATGTGGAC
genomic: CAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCGgtgggttact ... ttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
EST: gi|88746794|gb|DY530935.1|DY530935
EST:     CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCG                         GGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
genomic: CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCGgtgggttact ... ttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
EST: gi|76924552|gb|DV170001.1|DV170001
EST:     CCCTTCAGAAATTCGCG                         GGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
genomic: CCCTTCAGAAATTCGCGgtgggttact ... ttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
EST: gi|1498115|gb|AA030725.1|AA030725
EST:     CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCG                         GGTTCTTCATCCATTTCAAGCTCTGATCTTTTT
genomic: CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCGgtgggttact ... ttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTT
EST: gi|149086706|gb|EE176245.2|EE176245
EST:     CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCG                         GGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
genomic: CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCGgtgggttact ... ttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
EST: gi|60358412|gb|DN225385.1|DN225385
EST:     CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCG                         GGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
genomic: CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCGgtgggttact ... ttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
EST: gi|6022125|gb|AW067053.1|AW067053
EST:     CTCANAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCG                         GGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
genomic: CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCGgtgggttact ... ttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
EST: gi|109179344|gb|EC379938.1|EC379938
EST:     CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCG                         GGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
genomic: CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCGgtgggttact ... ttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
EST: gi|37381689|gb|CF627745.1|CF627745
EST:     CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCG                         GGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
genomic: CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCGgtgggttact ... ttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
EST: gi|60358232|gb|DN225205.1|DN225205
EST:     CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCG                         GGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
genomic: CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCGgtgggttact ... ttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
EST: gi|74237116|gb|DT645030.1|DT645030
EST:     CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCG                         GGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
genomic: CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCGgtgggttact ... ttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
EST: gi|89757145|gb|DY686866.1|DY686866
EST:     CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCG                         GGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
genomic: CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCGgtgggttact ... ttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
EST: gi|60342316|gb|DN209289.1|DN209289
EST:     CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCG                         GGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
genomic: CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCGgtgggttact ... ttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
EST: gi|60348664|gb|DN215637.1|DN215637
EST:     CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCG                         GGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
genomic: CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCGgtgggttact ... ttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
EST: gi|148940300|gb|EC885085.2|EC885085
EST:     CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCG                         GGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
genomic: CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCGgtgggttact ... ttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
EST: gi|78024255|gb|DV492642.1|DV492642
EST:     CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCG                         GGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
genomic: CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCGgtgggttact ... ttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
EST: gi|60355340|gb|DN222313.1|DN222313
EST:     CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCG                         GGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC
genomic: CTCAAAACAGAGAAGAGAAAGAGGCTCAGCTATCCCTTCAGAAATTCGCGgtgggttact ... ttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataatccattttcagaagtttgcttccttcttatatttcatctgttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGACGATTCTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTT
                                         tctgtttt  CT-rich tract
                            ttcttatatttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggttactgggtttactctttaatcaccatgtcattgatattcaaactgaattacttgcttgaaaaatctattgttgaaattttgccaaaaaaacccggcggtaatcgaagggcatccactacttgaataatccattttcagaagtttgcttccttcttatatttcatctgttttgaacagGGTTCTTCATCCATTTCAAGCTCTGATCTTTTTGGCCGTACCAATGTGGACGATTCTAACCTGGACCTAAGCGCTGCAGATCTCATCAACAGAATATCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT