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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgactgaccttgatttctccttaaacatgcagatatgactgtttgagtttttgttcttctcttcaagtatttcatatttttctttgtttctctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAGACCTGCACTTTTTTGTTACTGGAGGAGAAGAAGAGAATGAGCTTATTTT

Basic information

species Zea mays
transcript GRMZM2G431350_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G431350_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g38610.1 (Oryza sativa), 3'ss of exon 2
tgactgaccttgatttctccttaaacatgcagatatgactgtttgagt---ttttgttcttctc-ttcaagtatttcatatt-tttctttgtttctctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAGACCTGCACTTTTTTGTTACTGGAGGAGAAGAAGAGAATGAGCTTATTTT
    |    ||||   |  ||||    || |  | ||| ||    | |   |   ||   |||  |||||||| ||||  || | | | |||||| |  |  ||| |||||||||||||||||| || || |||||||| || ||||||||||||||||| || |||||||||||||||||||| || |||||||||||||||||
----tagtattgacagcgtcttatttgtg-acttgtgagtgaaaaattacataccgtatgtctagttcaagtaattcactttatgtatatgtttccccctttcagCTGAGATTGTAATGTTTGATGGCCACATTGTGGTGTATAAGTTCATCCAAGACCTCCATTTTTTTGTTACTGGAGGAGAGGAGGAGAATGAGCTTATTTT
















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|30591255|gb|CD052281.1|CD052281
EST:     CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAG                         TTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAGgtaatttaca ... tctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
EST: gi|211420227|gb|FL011433.1|FL011433
EST:     CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAG                         TTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAGgtaatttaca ... tctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
EST: gi|32863613|gb|CF003295.1|CF003295
EST:     CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAG                         TTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAGgtaatttaca ... tctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
EST: gi|22819983|gb|BU500073.1|BU500073
EST:     CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAG                         TTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAGgtaatttaca ... tctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
EST: gi|211420234|gb|FL011440.1|FL011440
EST:     CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAG                         TTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAGgtaatttaca ... tctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
EST: gi|211420230|gb|FL011436.1|FL011436
EST:     CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAG                         TTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAGgtaatttaca ... tctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
EST: gi|22545780|gb|BU098154.1|BU098154
EST:     CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAG                         TTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAGgtaatttaca ... tctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
EST: gi|30591528|gb|CD052418.1|CD052418
EST:     CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAG                         TTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAGgtaatttaca ... tctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
EST: gi|211270446|gb|FL011426.1|FL011426
EST:     CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAG                         TTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAGgtaatttaca ... tctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
EST: gi|71302986|gb|DR787604.1|DR787604
EST:     CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAG                         TTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAGgtaatttaca ... tctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
EST: gi|6020321|gb|AW065249.1|AW065249
EST:     CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAG                         TTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAGgtaatttaca ... tctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
EST: gi|211270449|gb|FL011429.1|FL011429
EST:     CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAG                         TTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAGgtaatttaca ... tctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
EST: gi|211420231|gb|FL011437.1|FL011437
EST:     CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAG                         TTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAGgtaatttaca ... tctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
EST: gi|86468241|gb|DY234611.1|DY234611
EST:     CGAAAAGTCGGTATTTACCAAAACCCAAAAAGCGAATGCTGGAACGGAAG                         TTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAGgtaatttaca ... tctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
EST: gi|211420229|gb|FL011435.1|FL011435
EST:     CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAG                         TTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAGgtaatttaca ... tctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
EST: gi|37622066|gb|CF675119.1|CF675119
EST:     CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAG                         TTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAGgtaatttaca ... tctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
EST: gi|211420226|gb|FL011432.1|FL011432
EST:     CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAG                         TTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAGgtaatttaca ... tctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
EST: gi|211420232|gb|FL011438.1|FL011438
EST:     CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAG                         TTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAGgtaatttaca ... tctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
EST: gi|30591531|gb|CD052420.1|CD052420
EST:     CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAG                         TTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAGgtaatttaca ... tctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
EST: gi|32929387|gb|CF034199.1|CF034199
EST:     CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAG                         TTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAGgtaatttaca ... tctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
EST: gi|33093855|gb|CF053849.1|CF053849
EST:     CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAG                         TTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG
genomic: CGAGAAGTCGGTATTTACCAAAACCCAGAAAGCGAATGCTGGAACGGAAGgtaatttaca ... tctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttttgttcttctcttcaagtatttcatatttttctttgtttctctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAGACCTGCACTTTTTTGTTACTGGAGGAGAAGAAGAGAATGAGCTTATTTT
                      tatttcatatttttct  CT-rich tract
                      tatttcatatttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgactgaccttgatttctccttaaacatgcagatatgactgtttgagtttttgttcttctcttcaagtatttcatatttttctttgtttctctttaacagTTGAGATTGTAATGTTTGACGGTCAAATTGTGGTATACAAGTTCATCCAAGACCTGCACTTTTTTGTTACTGGAGGAGAAGAAGAGAATGAGCTTATTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - acatgca
- - - - - - - - - - - - - - - - - - -actgttt
- - - - - - - - - - - - - - - - - - - - - - - gtttttg