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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggggtctacttgtggcactagcactgtcatgtgtaataactattcgatgtttacagtttacttaatacttatactaactaatgcattatgacttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCATCGACCAGCAGCTTAGAGATCCGGTTGATCCAAAGCCAGGACGAGATCC

Basic information

species Zea mays
transcript GRMZM2G069758_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069758_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os12g40830.3 (Oryza sativa), 3'ss of exon 12
ggggtctacttgtggcactagcactgtcatgtgtaataactattcgatgtttacagtttactta-atacttatactaacta----atgcattatgactt-ctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCATCGACCAGCAGCTTAGAGATCCGGTTGATCCAAAGCCAGGACGAGATCC
 || |    |||   |  | | | | | | ||| ||  || ||||    ||   ||||||||   ||  |  ||  | ||     ||| |     | || ||||||||||| || |  ||||||||||||||||||||||  || || || ||||| || ||||||||| |||||||||| ||||| ||||||||||| || || |
-ggataagtttg---ctttcgaagtattaggtgcaa-gacaattcag-attcgaagtttactcgcattatcctagaagctttgatatgtacagaaattttctgcagGCACTCCTAAGGAGAACTGTGGAAGACTATAAAAGAGCTGGGTTTGACCCCTCCACCAGCAGCCTAGAGATCCGCTTGATTCAAAGCCAGGATGAAATTC
















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|18166331|gb|BM336170.1|BM336170
EST:     ATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTGCAG                         GCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
genomic: ATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
EST: gi|33097992|gb|CF057952.1|CF057952
EST:     ATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTGCAG                         GCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
genomic: ATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
EST: gi|32823768|gb|CD963490.1|CD963490
EST:     ATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTGCAG                         GCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
genomic: ATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
EST: gi|33096068|gb|CF056062.1|CF056062
EST:     ATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTGCAG                         GCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
genomic: ATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
EST: gi|8102609|gb|AW927412.1|AW927412
EST:     ATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTGCAG                         GCACTTTTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
genomic: ATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
EST: gi|17931888|gb|BM268848.1|BM268848
EST:     ATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAG                         GCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
genomic: ATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
EST: gi|67022839|gb|CO451588.1|CO451588
EST:     ATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTGCAG                         GCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
genomic: ATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
EST: gi|40303606|gb|CK347993.1|CK347993
EST:     ATCCTGATAGCCTCGAGAAAGCGGCAGAACTGGCAGTTTCCAGTTTGCAG                         GCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
genomic: ATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
EST: gi|16922789|gb|BM075781.1|BM075781
EST:     ATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAG                         GCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA
genomic: ATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 43

AAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCATCGACCAGCAGCTTAGAGATCCGGTTGATCCAAAGCCAGGACGAGATCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 176

AAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCATCGACCAGCAGCTTAGAGATCCGGTTGATCCAAAGCCAGGACGAGATCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 240

AAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCATCGACCAGCAGCTTAGAGATCCGGTTGATCCAAAGCCAGGACGAGATCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 89

AAATATCCTGATAGCCTCGAGAAAGCAGCAGAACTGGCAGTTTCCAGTTTGCAGgtataagagt ... acttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCATCGACCAGCAGCTTAGAGATCCGGTTGATCCAAAGCCAGGACGAGATCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgtttacagtttacttaatacttatactaactaatgcattatgacttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCATCGACCAGCAGCTTAGAGATCCGGTTGATCCAAAGCCAGGACGAGATCC
                                              cttctgc  CT-rich tract
           tttacttaatacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggggtctacttgtggcactagcactgtcatgtgtaataactattcgatgtttacagtttacttaatacttatactaactaatgcattatgacttctgcagGCACTTCTGAAAAGAACTGTGGAAGACTATAAAATGGCCGGCTTCGACCCATCGACCAGCAGCTTAGAGATCCGGTTGATCCAAAGCCAGGACGAGATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - -ctacttg
- - - - - - - - - - gcactgt
- - - - - - - - - - - - - -catgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgcatt