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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acagcaaagaaactaggggtggactcatttccacatctgctatttatgcgttatgccatatgattgtttcaaatctaaacaacactttggttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAG

Basic information

species Zea mays
transcript GRMZM2G109429_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109429_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g66960.1 (Oryza sativa), 3'ss of exon 1
-----acagcaaagaaactaggggtggactcatttccacatctgctatttatgcgttatgccatatgattgtttcaaatctaaacaacactttggttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAG
      |||     |  |||  ||   |   | |||   || ||   |  |   ||| || ||      | ||||  ||  |  ||     ||| ||   ||||||  |||||||||| |||| ||||||||| || |||||||||||||||||||||||||||
aggattcagtcttcat-ctactggcaaagcaaattc---atgtggattcaactagttgtgtcaaccagct-tttctgattaattcatttgcttgtttggttgcagAATTGGTGGAGGACTGCCGTAAATGTTGTACAGAGGATTCAGATGATTCTATCAGCAAG
















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|211452461|gb|FL410333.1|FL410333
EST:     CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|211390309|gb|FL404115.1|FL404115
EST:     CGCCCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCGTAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|37382347|gb|CF628115.1|CF628115
EST:     CGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|78027093|gb|DV495480.1|DV495480
EST:     CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|211264276|gb|FL294960.1|FL294960
EST:     CGCCCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|13558509|gb|BG549865.1|BG549865
EST:     CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|211122267|gb|FL373642.1|FL373642
EST:     CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|211425792|gb|FL370218.1|FL370218
EST:     CGCCCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCGTAAATKTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|148934019|gb|EC878027.2|EC878027
EST:     CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|5058588|gb|AI737064.1|AI737064
EST:     GCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGAAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: GCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|211444189|gb|FL421109.1|FL421109
EST:     CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|60349419|gb|DN216392.1|DN216392
EST:     CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|211214746|gb|FL397473.1|FL397473
EST:     CGCCCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCGTAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|13558052|gb|BG549408.1|BG549408
EST:     CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|211264271|gb|FL294955.1|FL294955
EST:     CGCCCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|13558051|gb|BG549407.1|BG549407
EST:     CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|211173040|gb|FL404342.1|FL404342
EST:     CGCCCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCGTAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|13562227|gb|BG550447.1|BG550447
EST:     CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|211108328|gb|FL388568.1|FL388568
EST:     CGCCCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCGTAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|211003072|gb|FL395292.1|FL395292
EST:     CGCCCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCGTAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|148934022|gb|EC878030.2|EC878030
EST:     CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|211116346|gb|FL427489.1|FL427489
EST:     CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|78090328|gb|DV518702.1|DV518702
EST:     CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|148953620|gb|EC898976.2|EC898976
EST:     CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|211489672|gb|FL462920.1|FL462920
EST:     CGCCCTCTGCTCCGACTGCAACGCGCTMTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGANTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
EST: gi|78090327|gb|DV518701.1|DV518701
EST:     CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAG                         AGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA
genomic: CGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTA

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: 226

GGCGAGCGGCTCGGGGCGAGGGAGTGCGAGGACCTGGGGTTCACCGGCCTCGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 255

GGCGAGCGGCTCGGGGCGAGGGAGTGCGAGGACCTGGGGTTCACCGGCCTCGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 299

GGCGAGCGGCTCGGGGCGAGGGAGTGCGAGGACCTGGGGTTCACCGGCCTCGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 237

GGCGAGCGGCTCGGGGCGAGGGAGTGCGAGGACCTGGGGTTCACCGGCCTCGCTCTCTGCTCCGACTGCAACGCGCTCTCCGAGTTCGTCAAGGACCAAGgtacgcccgg ... ttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcgttatgccatatgattgtttcaaatctaaacaacactttggttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAG
                           atctaaa  putative branch site (score: 237)
                         aaatctaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acagcaaagaaactaggggtggactcatttccacatctgctatttatgcgttatgccatatgattgtttcaaatctaaacaacactttggttctgtgcagAGCTGGTGGAGGATTGCCATAAATGTTGCACCGAGGATTCAGATGATTCTATCAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - -aaagaaa
- - - - - - - - - - - - - - - - -catctgc
- - - - - - - - - - - - - - - - - - - - - - - - - -tatgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaaca