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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcacaaaatattaagtgttattatatcttacgtggtccagtacaacatttgagttgcattttgtgaataaggtaccttatccctattgttctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG

Basic information

species Zea mays
transcript GRMZM2G155543_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155543_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g45190.1 (Oryza sativa), 3'ss of exon 7
tcacaaaatattaagtgttattatatcttacgtggtccagtaca--acatttgagttgcattt-tgtgaataaggtacc--ttatccctattgttctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG
      | | || | |  |     || ||     |   ||||     |  |||  ||| | |     |||||| |   |  | ||  || || | || ||||||||||||||||||||||||||  ||||||||||| ||||||||||| ||||||||||||||||||||||  |||||  ||
-----cactgttcactcctcagccatattggccagcaaagtatctttcgcttgccttgtactgacacgaataatgcctcattaatttcttttatcctatgtgtagACATCTGCTTTGATTTCAAGATTGACAGAAGAAAGAAACTCTGCTATTCAGCAGAACAATAAGCTTCTCGAGGAGATG
















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|71772475|gb|DR970407.1|DR970407
EST:     GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
genomic: GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
EST: gi|7227720|gb|AW566361.1|AW566361
EST:     GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
genomic: GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
EST: gi|29946302|gb|CB816081.1|CB816081
EST:     GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
genomic: GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
EST: gi|76935911|gb|DV174526.1|DV174526
EST:     CTCGGCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
genomic: CTCGGCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
EST: gi|76929778|gb|DV172159.1|DV172159
EST:     GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
genomic: GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
EST: gi|91049216|gb|EB159634.1|EB159634
EST:     GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
genomic: GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
EST: gi|211349055|gb|FL306904.1|FL306904
EST:     ACACCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
genomic: ACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
EST: gi|7216902|gb|AW563024.1|AW563024
EST:     GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
genomic: GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
EST: gi|60347102|gb|DN214075.1|DN214075
EST:     GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
genomic: GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
EST: gi|71303117|gb|DR787664.1|DR787664
EST:     GCTGTAAAAACTCATATAGATCAAAAGGGCTACACCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
genomic: GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
EST: gi|71432736|gb|DR813786.1|DR813786
EST:     CTCGGCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAATTTTGCCATTCAG
genomic: CTCGGCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
EST: gi|83278536|gb|DV942544.1|DV942544
EST:     GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
genomic: GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
EST: gi|74242014|gb|DT649928.1|DT649928
EST:     GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
genomic: GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
EST: gi|149109098|gb|EE293135.2|EE293135
EST:     GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTTTGCCATTCAG
genomic: GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
EST: gi|211179444|gb|FL364372.1|FL364372
EST:     ACACCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
genomic: ACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
EST: gi|101381660|gb|EB812887.1|EB812887
EST:     GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
genomic: GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
EST: gi|211127671|gb|FL432566.1|FL432566
EST:     GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
genomic: GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
EST: gi|60396382|gb|DN229251.1|DN229251
EST:     GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
genomic: GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
EST: gi|78073696|gb|DV502130.1|DV502130
EST:     GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
genomic: GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
EST: gi|4647574|gb|AI622649.1|AI622649
EST:     CGGCTGTAAAAACTCATATAGATCAAAAGGACTACCCCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
genomic: CGGCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
EST: gi|76011373|gb|DT938543.1|DT938543
EST:     GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
genomic: GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
EST: gi|74240612|gb|DT648526.1|DT648526
EST:     GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
genomic: GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
EST: gi|71431011|gb|DR812061.1|DR812061
EST:     GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAATTCTGCCATTCAG
genomic: GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
EST: gi|78545068|gb|DV622566.1|DV622566
EST:     GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAG                         ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG
genomic: GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAG

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: 480

GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG


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

GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 81

GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 286

GCTGTAAAAACTCATATAGATCAAAAGGACTACACCTCCGAGgtgagctcca ... ctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttgagttgcattttgtgaataaggtaccttatccctattgttctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG
                                  tccctattgttctct  CT-rich tract
            attttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcacaaaatattaagtgttattatatcttacgtggtccagtacaacatttgagttgcattttgtgaataaggtaccttatccctattgttctctgtgtagACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA