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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttctgtgttacgatatttttatgaccgatgttgctgattgtccggattatagttttggtgctcattttataaccagatctaccgtaaatatgtttccagCTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCATTGGTGACCCGCCAGAAGTGCGCTTCGATTTGGATTTCTGCGCCAAGTTG

Basic information

species Zea mays
transcript GRMZM2G094978_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094978_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g36750.1 (Oryza sativa), 3'ss of exon 7
-cttctgtgttacgatatttttatgaccgatgt-tgctgattgtccggattatagttttggtgctcattttataaccagatctaccgtaaatatgtttccagCTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCATTGGTGACCCGCCAGAAGTGCGCTTCGATTTGGATTTCTGCGCCAAGTTG
  |||||   |   | || |  || |   ||   ||   ||| | |   | || |||    ||     |   | |    || |            | | ||| |||||||||||||||||||| |  ||||| ||||| ||||||||||||||||||||||| |||||||| ||||| |||||||| |||||||||||  | 
tgttctgatctttca-atctaaataaataatacgtgagaattattcacctcat-gttccaatgaaatgtacgtgatattatgtttttgggggcgctgtgcagATACACTGCAGAAGAGGACTTTGCAACAGCTGATGCTGTGTTCGATTGCATTGGTGACCCTCCAGAAGTACGCTTTGATTTGGAGTTCTGCGCCAACCTC
















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|211136606|gb|FL156037.1|FL156037
EST:     TCGCAAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCAG                         CTACACTGCAGAAGAGGACTTCGA
genomic: TCGCA-GCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGGgtacagattt ... atgtttccagCTACACTGCAGAAGAGGACTTCGA
EST: gi|88753379|gb|DY537520.1|DY537520
EST:     CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG                         CTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
genomic: CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGGgtacagattt ... atgtttccagCTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
EST: gi|86467368|gb|DY233738.1|DY233738
EST:     CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG                         CTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
genomic: CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGGgtacagattt ... atgtttccagCTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
EST: gi|13388479|gb|BG462185.1|BG462185
EST:     CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG                         CTACACTGCAGAAGA
genomic: CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGGgtacagattt ... atgtttccagCTACACTGCAGAAGA
EST: gi|86470646|gb|DY237016.1|DY237016
EST:     CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG                         CTACCCTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
genomic: CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGGgtacagattt ... atgtttccagCTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
EST: gi|13558959|gb|BG550314.1|BG550314
EST:     CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG                         CTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
genomic: CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGGgtacagattt ... atgtttccagCTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
EST: gi|211329033|gb|FL456230.1|FL456230
EST:     CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG                         CTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
genomic: CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGGgtacagattt ... atgtttccagCTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
EST: gi|71764322|gb|DR962259.1|DR962259
EST:     CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATTGTAACAAAAAGCGG                         CTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
genomic: CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGGgtacagattt ... atgtttccagCTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
EST: gi|16379404|gb|BI992921.1|BI992921
EST:     CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG                         CTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
genomic: CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGGgtacagattt ... atgtttccagCTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
EST: gi|101388001|gb|EB816015.1|EB816015
EST:     CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG                         CTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
genomic: CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGGgtacagattt ... atgtttccagCTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
EST: gi|10697624|gb|BE997348.1|BE997348
EST:     CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG                         CTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
genomic: CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGGgtacagattt ... atgtttccagCTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
EST: gi|93011639|gb|EB637159.1|EB637159
EST:     CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG                         CTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
genomic: CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGGgtacagattt ... atgtttccagCTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
EST: gi|71300514|gb|DR786312.1|DR786312
EST:     CTCGCAGCGGCAAAAGCTGGTGGCATGAAGTGTATCGTAACAAAAAGCGG                         CTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTT
genomic: CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGGgtacagattt ... atgtttccagCTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTT
EST: gi|60352425|gb|DN219398.1|DN219398
EST:     CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG                         CTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
genomic: CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGGgtacagattt ... atgtttccagCTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
EST: gi|78075281|gb|DV503715.1|DV503715
EST:     CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG                         CTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
genomic: CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGGgtacagattt ... atgtttccagCTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
EST: gi|71766391|gb|DR964328.1|DR964328
EST:     CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG                         CTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
genomic: CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGGgtacagattt ... atgtttccagCTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
EST: gi|60357150|gb|DN224123.1|DN224123
EST:     CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGG                         CTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
genomic: CTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGGgtacagattt ... atgtttccagCTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
EST: gi|94478039|gb|EB706997.1|EB706997
EST:     CAAAAGCTGCCGGCATGAAGTGTATTTTTACAAAAAGCGG                         CTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCAT
genomic: CAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGGgtacagattt ... atgtttccagCTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCA-

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 3 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 25

CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGGgtacagattt ... atgtttccagCTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCATTGGTGACCCGCCAGAAGTGCGCTTCGATTTGGATTTCTGCGCCAAGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGGgtacagattt ... atgtttccagCTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCATTGGTGACCCGCCAGAAGTGCGCTTCGATTTGGATTTCTGCGCCAAGTTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 66

CTGTGTTGTTATTGAAGACAGTACTATAGGGCTCGCAGCGGCAAAAGCTGCCGGCATGAAGTGTATCGTAACAAAAAGCGGgtacagattt ... atgtttccagCTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCATTGGTGACCCGCCAGAAGTGCGCTTCGATTTGGATTTCTGCGCCAAGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattatagttttggtgctcattttataaccagatctaccgtaaatatgtttccagCTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCATTGGTGACCCGCCAGAAGTGCGCTTCGATTTGGATTTCTGCGCCAAGTTG
                      ttataac  putative branch site (score: 66)
                                              tgtttcc  putative PPT
                 tcattttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttctgtgttacgatatttttatgaccgatgttgctgattgtccggattatagttttggtgctcattttataaccagatctaccgtaaatatgtttccagCTACACTGCAGAAGAGGACTTCGAGACAGCAGATGCAGTGTTCGATTGCATTGGTGACCCGCCAGAAGTGCGCTTCGATTTGGATTTCTGCGCCAAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
-ttctgtg
- - - - - - - - - - - - - - - gttgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - -ttttggt