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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGGAGTTACACTCGGACCGAAGGGAAGGAATGTCGTTTTGGAGAGCAAGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgcaatgctatcatggctgtacttggaatttgcttgctagctgataaattacataaaaaaggacagaccagtgctggcggttcccacatgaata...

Basic information

species Zea mays
transcript GRMZM2G083716_T04
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 3
AGTTGGAGTTACACTCGGACCGAAGGGAAGGAATGTCGTTTTGGAGAGCAAGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgcaatgct-atcatggctg--tacttggaatttgcttgctagctgataaattacataaaaaaggacagaccagtgctggcggttcccacatgaata
 |||||||||||||| ||||| |||||||||||||| ||||||||||||||||| || || || | |||||| || ||||| ||||||||||||||||||||| | | || || | ||   | |      | | |||||| ||| | |  || |   || |   |      ||   |            |       |     
TGTTGGAGTTACACTGGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGGTCCCCTAGGATTGTCAATGATGGTGTTACAGTTGCAAGAGAGgtatattacagtgtttattgcgtcaaatagcattgaatttccttacaatttgcttgtttgctgtatgctatacttccacagaaaaaaaatgtttgttttg---

upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 3
lower sequence: Vv09s0002g03930.t01 (Vitis vinifera), 5'ss of exon 2
AGTTGGAGTTACACTCGGACCGAAGGGAAGGAATGTCGTTTTGGAGAGCAAGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgcaatgctatcatggctgtacttggaatt-tgcttgctagctga-taaattacataaaaaaggacagaccagtgctggcggttcccacatgaata
||| || ||||| || || || || || |||||||| ||| ||||||||||||| || || || || |||||||| ||||| ||||| || |||||||||||| |    |    |          || ||  | || || | |   || || || |  |   || |||  |  |   |          ||  |  ||  |  
AGTGGGGGTTACTCTTGGTCCAAAAGGGAGGAATGTTGTTCTGGAGAGCAAGTATGGGTCCCCGAAAATTGTTAATGATGGTGTTACTGTGGCAAGAGAGgtataaattatcattgaataatgaatatttatacttctggtggtgggccgactagagcattaaagaaaatatgggttatgataatttatttacgtatata--
















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|148983129|gb|EE029060.2|EE029060
EST:     AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAG                         GTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
genomic: AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
EST: gi|148983089|gb|EE029008.2|EE029008
EST:     AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAG                         GTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
genomic: AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
EST: gi|32849132|gb|CD988813.1|CD988813
EST:     GCTCTCCCCAAGATTGTTAACGATGGCGTTACAGTTCCAAGAGAG                         GTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
genomic: GCTCT-CCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
EST: gi|149009207|gb|EE041320.2|EE041320
EST:     AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAG                         GTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
genomic: AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
EST: gi|148963973|gb|EE015101.2|EE015101
EST:     AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAG                         GTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
genomic: AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
EST: gi|32849348|gb|CD989029.1|CD989029
EST:     GTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAAGAGAG                         GTTGAGCTGGAGGAACCCTGTGGAAACCATTGGAGCTAAATTGGTCAGGC
genomic: GTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGC-AAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGG-ACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGC
EST: gi|149080249|gb|EE169273.2|EE169273
EST:     AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAG                         GTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
genomic: AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
EST: gi|32935083|gb|CF039895.1|CF039895
EST:     ACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAG                         GTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
genomic: ACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
EST: gi|149099158|gb|EE185183.2|EE185183
EST:     AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAG                         GTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
genomic: AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
EST: gi|148941096|gb|EC885959.2|EC885959
EST:     AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAG                         GTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
genomic: AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
EST: gi|211393798|gb|FL326098.1|FL326098
EST:     AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAG                         GTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
genomic: AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
EST: gi|148940496|gb|EC885295.2|EC885295
EST:     AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAG                         GTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
genomic: AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
EST: gi|78080918|gb|DV509330.1|DV509330
EST:     AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAG                         GTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
genomic: AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
EST: gi|32934340|gb|CF039152.1|CF039152
EST:     GTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAG                         GTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
genomic: GTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
EST: gi|148961770|gb|EE012547.2|EE012547
EST:     AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAG                         GTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
genomic: AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
EST: gi|33094317|gb|CF054311.1|CF054311
EST:     GATGGCGTTACAGTTGCAAGAGAG                         GTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
genomic: GATGGCGTTACAGTTGCAAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
EST: gi|32933718|gb|CF038530.1|CF038530
EST:     ACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAG                         GTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
genomic: ACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
EST: gi|149075815|gb|EE164351.2|EE164351
EST:     AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAG                         GTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
genomic: AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
EST: gi|32848870|gb|CD988551.1|CD988551
EST:     AGTATGGTTCTCCTAAAATTGTTAACGATGGCGTTACAGTTGCAAGAGAG                         GTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
genomic: AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
EST: gi|71764884|gb|DR962821.1|DR962821
EST:     AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAG                         GTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA
genomic: AGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAA

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), 49 (downstream exon)
Score: 397

AGTTGGAGTTACACTCGGACCGAAGGGAAGGAATGTCGTTTTGGAGAGCAAGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAAGCTGCAGCTAAGACCAACGATCTTGCTGGAGATGGGACAACCACCTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1233

AGTTGGAGTTACACTCGGACCGAAGGGAAGGAATGTCGTTTTGGAGAGCAAGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAAGCTGCAGCTAAGACCAACGATCTTGCTGGAGATGGGACAACCACCTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 146

AGTTGGAGTTACACTCGGACCGAAGGGAAGGAATGTCGTTTTGGAGAGCAAGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAAGCTGCAGCTAAGACCAACGATCTTGCTGGAGATGGGACAACCACCTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 631

AGTTGGAGTTACACTCGGACCGAAGGGAAGGAATGTCGTTTTGGAGAGCAAGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgca ... tgttctgtagGTTGAGCTGGAGGACCCTGTGGAAAACATTGGAGCTAAATTGGTCAGGCAAGCTGCAGCTAAGACCAACGATCTTGCTGGAGATGGGACAACCACCTCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGGAGTTACACTCGGACCGAAGGGAAGGAATGTCGTTTTGGAGAGCAAGTACGGCTCTCCCAAGATTGTTAACGATGGCGTTACAGTTGCAAGAGAGgtacagtgcaatgctatcatggctgtacttggaatttgcttgctagctgataaattacataaaaaaggacagaccagtgctggcggttcccacatgaata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaaaaa