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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtcttttacaatattttgagctcgttgagtccatctacacatgatatggaagtgattaccttatggaactacgccttgatgttccattttgcattaaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCAGCATTCACAGGAAAGAAATACTCACTGAAGGGCTGAATAAATAGGAAGA

Basic information

species Zea mays
transcript GRMZM2G037185_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037185_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g08480.1 (Oryza sativa), 3'ss of exon 9
gttggtcttttacaatattttgagctcgttgagtccatctacacatgatatggaagtgattaccttatggaactacgccttgatgttccattttgcattaaatgtgtagGCACCTGAAAAGGAAGCAGAGGAG---CCCAAGAAAGAAGACCCAAAATTCGCAGCATTCACAGGAAAGAAATACTCACTGAAGGGCTGAATAAATAGGAAGA
        | || || |  |    |   | |||      || | | | ||| |    |||    ||     |||     ||    |    | ||  |||     ||||||  |||||||||||| |  |||||   ||||||||||| || || |||||| |||| || ||||||| |||||||||| ||||||||||| ||   ||  |  
--------tctaaaacagctctgtcgattagagaaggcata-ataagttattgcttcgatgtgtttgacacacttttttttaccataatttgttttattttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTCTCAGCTTTTACAGGAAGGAAATACTCATTGAAGGGCTGA-TAGCCAGATA--
















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|60340795|gb|DN207768.1|DN207768
EST:     AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAG                         GCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
genomic: AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
EST: gi|29543953|gb|CB604333.1|CB604333
EST:     AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAG                         GCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
genomic: AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
EST: gi|211433047|gb|FL005816.1|FL005816
EST:     AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAG                         GCACCTGANAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
genomic: AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
EST: gi|13515727|gb|BG518003.1|BG518003
EST:     AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAG                         GCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
genomic: AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
EST: gi|16925940|gb|BM079008.1|BM079008
EST:     AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAG                         GCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
genomic: AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
EST: gi|23357513|gb|BU645162.1|BU645162
EST:     AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAGCCGAGCCGAAAAG                         GCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
genomic: AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
EST: gi|148985612|gb|EE029713.2|EE029713
EST:     AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAG                         GCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
genomic: AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
EST: gi|93281778|gb|EB674042.1|EB674042
EST:     AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAG                         GCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
genomic: AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
EST: gi|40334979|gb|CK369049.1|CK369049
EST:     AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAG                         GCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
genomic: AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
EST: gi|50332346|gb|CO527472.1|CO527472
EST:     AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAG                         GCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
genomic: AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
EST: gi|149106744|gb|EE188640.2|EE188640
EST:     AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAG                         GCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
genomic: AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
EST: gi|71766015|gb|DR963952.1|DR963952
EST:     AGGCCACAGGAAAACTTGTCTTTGGTTCTGGTGGTAACCGAGCCGAAAAG                         GCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
genomic: AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
EST: gi|37382129|gb|CF627990.1|CF627990
EST:     AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAG                         GCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
genomic: AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
EST: gi|116817619|gb|EC860494.1|EC860494
EST:     AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAG                         GCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
genomic: AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
EST: gi|7227799|gb|AW566440.1|AW566440
EST:     AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAGCCGAGCCGAAAAG                         GCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
genomic: AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
EST: gi|4775894|gb|AI664897.1|AI664897
EST:     AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAGCCGAGCCGAAAAG                         GCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
genomic: AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
EST: gi|13515728|gb|BG518004.1|BG518004
EST:     AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAG                         GCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
genomic: AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
EST: gi|16379636|gb|BI993068.1|BI993068
EST:     AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAG                         GCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
genomic: AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
EST: gi|33467511|gb|CF244560.1|CF244560
EST:     AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAG                         GCCCCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
genomic: AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
EST: gi|60355659|gb|DN222632.1|DN222632
EST:     AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAG                         GCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
genomic: AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
EST: gi|37401441|gb|CF638084.1|CF638084
EST:     AGGCCACACGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAG                         GCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
genomic: AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
EST: gi|30306883|gb|CD001556.1|CD001556
EST:     AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAG                         GCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
genomic: AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
EST: gi|31361823|gb|CD446180.1|CD446180
EST:     AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAGCCGAGCCGAAAAG                         GCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA
genomic: AGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 146

CGGTGTACAGCCTTCAACAGCCACCACATCACAGGGCAGTTCATCGCGTAAGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCAGCATTCACAGGAAAGAAATACTCACTGAAGGGCTGAATAAATAGGAAGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 160

CGGTGTACAGCCTTCAACAGCCACCACATCACAGGGCAGTTCATCGCGTAAGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCAGCATTCACAGGAAAGAAATACTCACTGAAGGGCTGAATAAATAGGAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 212

CGGTGTACAGCCTTCAACAGCCACCACATCACAGGGCAGTTCATCGCGTAAGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCAGCATTCACAGGAAAGAAATACTCACTGAAGGGCTGAATAAATAGGAAGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 150

CGGTGTACAGCCTTCAACAGCCACCACATCACAGGGCAGTTCATCGCGTAAGGCCACAGGAAAACTTGTCTTTGGCTCTGGTGGTAACCGAGCCGAAAAGgttggtcttt ... aaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCAGCATTCACAGGAAAGAAATACTCACTGAAGGGCTGAATAAATAGGAAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgattaccttatggaactacgccttgatgttccattttgcattaaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCAGCATTCACAGGAAAGAAATACTCACTGAAGGGCTGAATAAATAGGAAGA
                       ccttgat  putative branch site (score: 150)
                                   attttgcattaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtcttttacaatattttgagctcgttgagtccatctacacatgatatggaagtgattaccttatggaactacgccttgatgttccattttgcattaaatgtgtagGCACCTGAAAAGGAAGCAGAGGAGCCCAAGAAAGAAGACCCAAAATTCGCAGCATTCACAGGAAAGAAATACTCACTGAAGGGCTGAATAAATAGGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA