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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatatgtattgctagtgacaactaatttaatgtttgctttgctactggaaattctttccattgcaaataacagactcataaatactttatgtgtgctcagACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTGAATGAAAAACAGTTCAGTCCTGATGTGGTTGTGGATCTCATACATCTTA

Basic information

species Zea mays
transcript GRMZM2G039711_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039711_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g44560.1 (Oryza sativa), 3'ss of exon 2
--tatatgtattgctagtg-acaactaatttaatgtttgctttgctactggaaattctttccattgcaaataacagactcataaatactttatgtgtgctcagACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTGAATGAAAAACAGTTCAGTCCTGATGTGGTTGTGGATCTCATACATCTTA
   |||| || | ||  |  |  | | |||| |||  |   |   || ||| ||  ||  | |   ||   |    |||  |   |  ||    |||  |||||||||||||||||||||||||||||||||||||||||| || |||||||||||||||||||  ||||  |||||||| || |||||||||||||||||||
atgatatctacttctgtttcaggaatgatttgatgcctttgtatttagtggcaaagctaccaaccacatg-atttaactgttg--tttttggcatgtattcagACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATTCGATACACACTGAATGAAAAACCATTCAACCCTGATGTAGTCGTGGATCTCATACATCTTA
















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|89246890|gb|DY618676.1|DY618676
EST:     AGGGCAGGGAGGCAATAAATTATCCTGCTCTTCAGGACCTAATGCAAAAG                         ACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTG
genomic: AGGGCAGGGAGGCAATAAATTATCCTGCTCTTCAGGACCTAATGCAAAAGgtatgttgcc ... gtgtgctcagACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTG
EST: gi|76010570|gb|DT937740.1|DT937740
EST:     AGGGCAGGGAGGCAATAAATTATCTTGCTCTTCAGGACCTAATGCAAAAG                         ACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTG
genomic: AGGGCAGGGAGGCAATAAATTATCCTGCTCTTCAGGACCTAATGCAAAAGgtatgttgcc ... gtgtgctcagACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTG
EST: gi|78122387|gb|DV540771.1|DV540771
EST:     AGGGCAGGGAGGCAATAAATTATCCTGCTCTTCAGGACCTAATGCAAAAG                         ACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTG
genomic: AGGGCAGGGAGGCAATAAATTATCCTGCTCTTCAGGACCTAATGCAAAAGgtatgttgcc ... gtgtgctcagACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTG
EST: gi|71763142|gb|DR961079.1|DR961079
EST:     AGGGCAGGGAGGCAATAAATTATCCTGCTCTTCAGGACCTAATGCAAAAG                         ACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTG
genomic: AGGGCAGGGAGGCAATAAATTATCCTGCTCTTCAGGACCTAATGCAAAAGgtatgttgcc ... gtgtgctcagACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTG
EST: gi|18166312|gb|BM336151.1|BM336151
EST:     AGGGCAGGGAGGCAATAAATTATCCTGCTCTTCAGGACCTAATGCAAAAG                         ACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTG
genomic: AGGGCAGGGAGGCAATAAATTATCCTGCTCTTCAGGACCTAATGCAAAAGgtatgttgcc ... gtgtgctcagACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTG
EST: gi|13237142|gb|BG355156.1|BG355156
EST:     CAATAAATTATCCTGCTCTTCAGGACCTAATGCAAAAG                         ACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTG
genomic: CAATAAATTATCCTGCTCTTCAGGACCTAATGCAAAAGgtatgttgcc ... gtgtgctcagACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTG
EST: gi|110221084|gb|EC902982.1|EC902982
EST:     GGGCAGGGAGGCAATAAATTTTCCTTTTCTTCAGGGCCTAATGCAAAAG                         CCAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTG
genomic: GGGCAGGGAGGCAATAAATTATCCTGCTCTTCAGGACCTAATGCAAAAGgtatgttgcc ... gtgtgctcagACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTG
EST: gi|94475013|gb|EB703971.1|EB703971
EST:     AGGGCAGGGAGGCAATAAATTATCTTGCTCTTCAGGACCTAATGCAAAAG                         ACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTG
genomic: AGGGCAGGGAGGCAATAAATTATCCTGCTCTTCAGGACCTAATGCAAAAGgtatgttgcc ... gtgtgctcagACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTG
EST: gi|71431017|gb|DR812067.1|DR812067
EST:     AGGGCAGGGAGGCAATAAATTATCCTGCTCTTCAGGACCTAATGCAAAAG                         ACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTG
genomic: AGGGCAGGGAGGCAATAAATTATCCTGCTCTTCAGGACCTAATGCAAAAGgtatgttgcc ... gtgtgctcagACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTG
EST: gi|71333251|gb|DR803680.1|DR803680
EST:     AGGGCAGGGAGGCAATAAATTATCCTGCTCTTCAGGACCTAATGCAAAAG                         ACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTG
genomic: AGGGCAGGGAGGCAATAAATTATCCTGCTCTTCAGGACCTAATGCAAAAGgtatgttgcc ... gtgtgctcagACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTG

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), 46 (downstream exon)
Score: 117

GTGAGTAAGAATATATTCTTGTTGAAGTCACTAGATGATCTGTTTCAGAAGGGCAGGGAGGCAATAAATTATCCTGCTCTTCAGGACCTAATGCAAAAGgtatgttgcc ... gtgtgctcagACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTGAATGAAAAACAGTTCAGTCCTGATGTGGTTGTGGATCTCATACATCTTA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 107

GTGAGTAAGAATATATTCTTGTTGAAGTCACTAGATGATCTGTTTCAGAAGGGCAGGGAGGCAATAAATTATCCTGCTCTTCAGGACCTAATGCAAAAGgtatgttgcc ... gtgtgctcagACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTGAATGAAAAACAGTTCAGTCCTGATGTGGTTGTGGATCTCATACATCTTA


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 61

GTGAGTAAGAATATATTCTTGTTGAAGTCACTAGATGATCTGTTTCAGAAGGGCAGGGAGGCAATAAATTATCCTGCTCTTCAGGACCTAATGCAAAAGgtatgttgcc ... gtgtgctcagACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTGAATGAAAAACAGTTCAGTCCTGATGTGGTTGTGGATCTCATACATCTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 118

GTGAGTAAGAATATATTCTTGTTGAAGTCACTAGATGATCTGTTTCAGAAGGGCAGGGAGGCAATAAATTATCCTGCTCTTCAGGACCTAATGCAAAAGgtatgttgcc ... gtgtgctcagACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTGAATGAAAAACAGTTCAGTCCTGATGTGGTTGTGGATCTCATACATCTTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaaattctttccattgcaaataacagactcataaatactttatgtgtgctcagACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTGAATGAAAAACAGTTCAGTCCTGATGTGGTTGTGGATCTCATACATCTTA
                   aaataac  putative branch site (score: 118)
                              tcataaatactttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatatgtattgctagtgacaactaatttaatgtttgctttgctactggaaattctttccattgcaaataacagactcataaatactttatgtgtgctcagACAGGATTTGACATGGATGATGTAGTAAGGAAGTACATCCGTTACACACTGAATGAAAAACAGTTCAGTCCTGATGTGGTTGTGGATCTCATACATCTTA

-atatgta
- - - - - gctagtg
- - - - - - - - - caactaa
- - - - - - - - - - - - - - - tgtttgc
- - - - - - - - - - - - - - - - - - - - gctactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aataaca