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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcagtagtttggagtacatttcgattcctctcagttatgcttaaccatagcatgacgattccgccttgtcgtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG

Basic information

species Zea mays
transcript GRMZM5G828229_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G828229_T02 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os08g05570.1 (Oryza sativa), 3'ss of exon 15
gtaatcagtagtttggagtacatttcgattcctctcagttatgcttaaccatagcatgacgattccgccttgtcgtaat-tgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
||||||||| || |      | |   |  || |   | |     ||   |||   || ||   |  ||||| | ||| | || |||||| || ||||||||||||||||| |||||||| | |||||||
gtaatcagttgtctttcactc-tagagtatctttgtactctcatttgcacatcttattac--ctttgccttcttgtactgtgcagATAGTCGACTGAAGGGTGTTTTCCTTGAGAGTGGTAGCTCAGAG
















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|113665703|gb|DW828711.1|DW828711
EST:     AACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: AACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|211009192|gb|FL302293.1|FL302293
EST:     CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|86466009|gb|DY232382.1|DY232382
EST:     CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|86471329|gb|DY237699.1|DY237699
EST:     CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|60340056|gb|DN207029.1|DN207029
EST:     CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|87152588|gb|DY397377.1|DY397377
EST:     CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|60342475|gb|DN209448.1|DN209448
EST:     CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|18655110|gb|BM499915.1|BM499915
EST:     CG-AGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|211009193|gb|FL302294.1|FL302294
EST:     CGAAGTAGGGAACTYTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|211410389|gb|FL480482.1|FL480482
EST:     CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|110943981|gb|EE164138.1|EE164138
EST:     CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTTTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|60355749|gb|DN222722.1|DN222722
EST:     CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|32848350|gb|CD988031.1|CD988031
EST:     CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|86467590|gb|DY233960.1|DY233960
EST:     CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTTTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|40303824|gb|CK348211.1|CK348211
EST:     CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|148929039|gb|EC874295.2|EC874295
EST:     CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|211520540|gb|FL475907.1|FL475907
EST:     CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTGGTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|71760295|gb|DR958232.1|DR958232
EST:     CGAAGTAGGGAACTCTGATCCAAAGGTTGGGACTTTCTGGATCGACTTTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|22490231|gb|BU050154.1|BU050154
EST:     CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|148990926|gb|EE032349.2|EE032349
EST:     CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|78103955|gb|DV522373.1|DV522373
EST:     CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|87153578|gb|DY398367.1|DY398367
EST:     CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|5510847|gb|AI857231.1|AI857231
EST:     CGAAGTAGGGAACTTTGATCC-AAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|4572936|gb|AI586585.1|AI586585
EST:     TTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: TTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|60341998|gb|DN208971.1|DN208971
EST:     CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|33101850|gb|CF061810.1|CF061810
EST:     CGAAGTAGGGAACTTTGATCTAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|148933345|gb|EC877007.2|EC877007
EST:     CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|33102180|gb|CF062140.1|CF062140
EST:     CGAAGTAGGGAACTTTGATCTAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|33090861|gb|CF050855.1|CF050855
EST:     CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|32831851|gb|CD971529.1|CD971529
EST:     GAAGTAGGGAACCTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: GAAGTAGGGAA-CTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
EST: gi|14190977|gb|BG833207.1|BG833207
EST:     CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTG                         ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
genomic: CGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG

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), 44 (downstream exon)
Score: 213

TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 154

TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 117

TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 126

TCGGCGAAGCAGTCGAAGTAGGGAACTTTGATCCAAAGGTTGCGACTTTCTGGATCGACTCTGgtaatcagta ... gtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctctcagttatgcttaaccatagcatgacgattccgccttgtcgtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG
             gcttaac  putative branch site (score: 126)
                                              taattgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcagtagtttggagtacatttcgattcctctcagttatgcttaaccatagcatgacgattccgccttgtcgtaattgtagATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA