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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcgtgttaagtgaatttctgctcgctccatgtacactatggttatgtgaaataaagctttgataggttgtgactttgatgtgtgtttctgtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT

Basic information

species Zea mays
transcript GRMZM2G010754_T01
intron # 2
splice site 3'
intron type U2

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|8665254|gb|BE186070.1|BE186070
EST:     TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAG                         AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
genomic: TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
EST: gi|60352925|gb|DN219898.1|DN219898
EST:     TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAG                         AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
genomic: TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
EST: gi|211198262|gb|FL232390.1|FL232390
EST:     TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAG                         AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
genomic: TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
EST: gi|60344656|gb|DN211629.1|DN211629
EST:     TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAG                         AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
genomic: TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
EST: gi|8665559|gb|BE186375.1|BE186375
EST:     TGACAGACCCAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAG                         AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
genomic: TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
EST: gi|5018459|gb|AI714652.1|AI714652
EST:     CAAAGGAAAAG                         AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGNCGAGCAAGAGAAAAG
genomic: CAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
EST: gi|211200810|gb|FL232404.1|FL232404
EST:     TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAG                         AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
genomic: TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
EST: gi|60343805|gb|DN210778.1|DN210778
EST:     TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAG                         AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
genomic: TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
EST: gi|60339898|gb|DN206871.1|DN206871
EST:     TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAG                         AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
genomic: TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
EST: gi|78024507|gb|DV492894.1|DV492894
EST:     TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAG                         AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
genomic: TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
EST: gi|5456187|gb|AI833877.1|AI833877
EST:     TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAG                         AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
genomic: TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
EST: gi|26456161|gb|CA827744.1|CA827744
EST:     CGACAGGAACAAAGGAAAAG                         AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
genomic: CGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
EST: gi|149076085|gb|EE164662.2|EE164662
EST:     TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAG                         AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
genomic: TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
EST: gi|213172009|gb|FM190576.1|FM190576
EST:     TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAG                         AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
genomic: TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
EST: gi|211198269|gb|FL232397.1|FL232397
EST:     TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAG                         AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
genomic: TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
EST: gi|211103961|gb|FL232383.1|FL232383
EST:     TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAG                         AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
genomic: TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
EST: gi|149076084|gb|EE164661.2|EE164661
EST:     TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAG                         AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
genomic: TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
EST: gi|211101495|gb|FL232372.1|FL232372
EST:     TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAG                         AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
genomic: TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
EST: gi|211101493|gb|FL232370.1|FL232370
EST:     TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAG                         AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
genomic: TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
EST: gi|211386269|gb|FL454547.1|FL454547
EST:     TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAG                         AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
genomic: TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
EST: gi|211103965|gb|FL232387.1|FL232387
EST:     TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAG                         AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
genomic: TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
EST: gi|67011144|gb|CO439893.1|CO439893
EST:     TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAG                         AGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG
genomic: TGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAG

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: 282

GACAAGAAGGAGAGCAAGAGGAGGAGCCGAGACGACAGGGAGGATGACGATGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 200

GACAAGAAGGAGAGCAAGAGGAGGAGCCGAGACGACAGGGAGGATGACGATGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 202

GACAAGAAGGAGAGCAAGAGGAGGAGCCGAGACGACAGGGAGGATGACGATGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT


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

GACAAGAAGGAGAGCAAGAGGAGGAGCCGAGACGACAGGGAGGATGACGATGACAGACACAAGAAGAAGGGGAAACACATCGACAGGAACAAAGGAAAAGgttgggttcc ... gtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgaaataaagctttgataggttgtgactttgatgtgtgtttctgtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT
                            ctttgat  putative branch site (score: 212)
                                        tttctgt  putative PPT
     aataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcgtgttaagtgaatttctgctcgctccatgtacactatggttatgtgaaataaagctttgataggttgtgactttgatgtgtgtttctgtgttgatagAGAGAGATTCGAAGGATAGGCATTCCAAGGAGAAGACGAGCAAGAGAAAAGACAAGGACGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA