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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGGAGAACTGGGACAAGGTTAAGACTATCTTTCTTCCCACAGAGAAGCAAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctattggcttggaactctttattgctgacaattctcagattcttgattaaccatcagttctcagttgattctcattgatgatccgtgcttgaatttcag

Basic information

species Zea mays
transcript GRMZM2G034083_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G034083_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os12g37870.1 (Oryza sativa), 5'ss of exon 3
CGAGGAGAACTGGGACAAGGTTAAGACTATCTTTCTTCCCACAGAGAAGCAAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctattggcttggaactctttattgctgacaa---------ttctcagattcttgattaaccatcagttctcagttgattctcattgatgatccgtgcttgaatttcag--------------------------------------------------------------------
||||||||||||||| ||||| |||||  | ||||||||||| |||||   |||||||||||| || ||||||||||||||||||||||| || || |||||| |||  |   ||| | | | ||     || ||          || | |   | |||| |   |  |  ||||    | | |  |  |  || |  |  |||    || |                                                                     
CGAGGAGAACTGGGATAAGGTCAAGACAGTTTTTCTTCCCACCGAGAAAGCAATGACACCTGATGCGTGTGCTCCATTGATTGCCACCCTACCGTTAGAGgtacgcttatacattgtatcaccttccccatgtcacgttgttttttttttaacatgttgacttttctcccattctggactcaattcctctagtg-ttagaacttattattgatgatacctattttggtctgcattagccatcttgtgctcatgtcattcacgtcttctgtctgaatttcag

upper sequence: GRMZM2G034083_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv14s0060g00550.t01 (Vitis vinifera), 5'ss of exon 4
CGAGGAGAACTGGGACAAGGTTAAGACTATCTTTCTTCCCACAGAGAAGCAAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctattggcttggaactctttattgctgacaattctcagattcttgattaaccatcagttctcagttgattctcattgatgatccgtgcttgaatttcag
                   || ||||||||   |||||| || || ||||  |||||||||||  |||||||||||||||||||||| || ||  ||||||| || | |    || |   |||   ||   |    || ||    | || | |     | |  ||| ||   |   |   |    ||  |   ||   || || 
-------------------GTGAAGACTATTAATCTTCCAACTGAAAAGCCTATGACACCTGAGACATGTGCTCCATTGATTGCCACTCTTCCCCTGGAGgtgagttttgatatttgttttctaacttataggttcttttctctgtttttacttggattgacatctgagacaagagtttgt----atttgaatttcctttacaa

upper sequence: GRMZM2G034083_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S63_54V6.2 (Physcomitrella patens), 5'ss of exon 6
CGAGGAGAACTGGGACAAGGTTAAGACTATCTTTCTTCCCACAGAGAAGCAAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctattggcttggaactctttattgctgacaattctcagattcttgat----taaccatcagttctcagttgattctcattg---atgatccgtgcttgaatttcag
                   || | | |  ||||| | || || ||||||    ||||  | ||   ||||||||||||||||||||| || |||||||||||||    || |||      ||||| ||||  |   |  |||  | |   |     ||        || | |      ||||  ||   ||| | | || || |   |   
-------------------GTCAGGTCCGTCTTTATACCTACTGAGAAGACTCTGACGTCCGAGCTATGTGCTCCATTGATTGCCACACTTCCATTGGAGgtaa----ttagctc----ttctttcttgcccaggctcttcatgtgcgacacaatgtagtttgtgtttttgaaacagctctccctgtgaatggttcatgtttcatcat---

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|32848515|gb|CD988196.1|CD988196
EST:     AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAG                         GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
genomic: AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
EST: gi|31356652|gb|CD441009.1|CD441009
EST:     AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAG                         GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
genomic: AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
EST: gi|67010398|gb|CO439147.1|CO439147
EST:     AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAG                         GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
genomic: AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
EST: gi|149000525|gb|EE037708.2|EE037708
EST:     AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAG                         GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
genomic: AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
EST: gi|7238111|gb|AW573333.1|AW573333
EST:     CACCCTGCCATTGGAG                         GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
genomic: CACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
EST: gi|211020099|gb|FL063972.1|FL063972
EST:     AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAG                         GTCCGCNACAA-GATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCA
genomic: AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGC-ACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCA
EST: gi|31353311|gb|CD437668.1|CD437668
EST:     AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAG                         GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
genomic: AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
EST: gi|148951643|gb|EC897387.2|EC897387
EST:     AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAG                         GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
genomic: AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
EST: gi|149110454|gb|EE190425.2|EE190425
EST:     AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAG                         GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
genomic: AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
EST: gi|78103681|gb|DV522109.1|DV522109
EST:     AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAG                         GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
genomic: AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
EST: gi|149070778|gb|EE159189.2|EE159189
EST:     AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAG                         GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
genomic: AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
EST: gi|13381841|gb|BG458516.1|BG458516
EST:     AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAG                         GTCCGCACAAAGAT
genomic: AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGAT
EST: gi|13150055|gb|BG320377.1|BG320377
EST:     AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAG                         GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
genomic: AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
EST: gi|148947869|gb|EC893362.2|EC893362
EST:     AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAG                         GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
genomic: AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
EST: gi|31355046|gb|CD439403.1|CD439403
EST:     AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAG                         GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
genomic: AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
EST: gi|148935016|gb|EC879057.2|EC879057
EST:     AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAG                         GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
genomic: AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
EST: gi|148958422|gb|EC904655.2|EC904655
EST:     AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAG                         GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
genomic: AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
EST: gi|9566469|gb|BE475978.1|BE475978
EST:     AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAG                         GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
genomic: AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
EST: gi|67042517|gb|CO468772.1|CO468772
EST:     GTGCTCCATTGATTGCCACCCTGCCATTGGAG                         GTCCGCACAAAGATAGGTTGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
genomic: GTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
EST: gi|32859101|gb|CD998782.1|CD998782
EST:     AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAG                         GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
genomic: AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
EST: gi|33104123|gb|CF064083.1|CF064083
EST:     AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAG                         GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
genomic: AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
EST: gi|149113031|gb|EE295802.2|EE295802
EST:     AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAG                         GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
genomic: AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
EST: gi|148955951|gb|EC901669.2|EC901669
EST:     AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAG                         GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
genomic: AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
EST: gi|37401585|gb|CF638160.1|CF638160
EST:     TCCATTGA-TGCCACCCTGCCATT-GAG                         GTCCGCACAAAGATAGGTGG-TTCATTAGAGCTGTA-TTTCTG-TTTCCAA
genomic: TCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
EST: gi|148986293|gb|EE030028.2|EE030028
EST:     AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAG                         GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
genomic: AAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
EST: gi|67016541|gb|CO445290.1|CO445290
EST:     ATGACACCTGACGCATGTGCTCCATTGATGGCCACCCTGCCATTGGAG                         GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA
genomic: ATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAA

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: 361

CGAGGAGAACTGGGACAAGGTTAAGACTATCTTTCTTCCCACAGAGAAGCAAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 828

CGAGGAGAACTGGGACAAGGTTAAGACTATCTTTCTTCCCACAGAGAAGCAAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 669

CGAGGAGAACTGGGACAAGGTTAAGACTATCTTTCTTCCCACAGAGAAGCAAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 955

CGAGGAGAACTGGGACAAGGTTAAGACTATCTTTCTTCCCACAGAGAAGCAAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctatt ... tgaatttcagGTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAGGAGAACTGGGACAAGGTTAAGACTATCTTTCTTCCCACAGAGAAGCAAATGACACCTGACGCATGTGCTCCATTGATTGCCACCCTGCCATTGGAGgtaagctattggcttggaactctttattgctgacaattctcagattcttgattaaccatcagttctcagttgattctcattgatgatccgtgcttgaatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG