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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggtattctttgtttgtttgctagtgagcgtttgttcccagatcccaattgttcatttatttggagctttgctctgatggacttttgatcaagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCGCAGGCGCAACTGCCTTCTGGCTGCTGTTTGAGGTCATGGATTACCACCT

Basic information

species Zea mays
transcript GRMZM2G004349_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004349_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g45050.2 (Oryza sativa), 3'ss of exon 1
--aggtattctttgtttgtttgctagtgagcgtttgttcccagatcccaattgttcatttatttgga---gctttgctctgatggacttttgatcaagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCGCAGGCGCAACTGCCTTCTGGCTGCTGTTTGAGGTCATGGATTACCACCT
      |  ||  | || |||| | |  || ||     |   |   |  |||||| ||  ||  |||   ||| | ||||||||  ||| || |   | ||||||| || ||||| |||||||||||||||||||  ||||| | |||||| ||||| ||||| || ||| |||||||||||||||| ||||||||||| || ||
gcttaaaccctgagattctttgtttggtagtgtag---ctgggtatcttattgtttat--atggggatttgctctcctctgatgtgcttatgtttgtggttgcagCTGCTGATCTCTTTCTATGGAGGAACAAGAAAATCTCCGTTGGGGTACTCGCTGGCGCCACGGCCATCTGGCTGCTGTTTGAAGTCATGGATTATCATCT
















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|67018312|gb|CO447061.1|CO447061
EST:     CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGC                         CGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
genomic: CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
EST: gi|211535247|gb|FL240263.1|FL240263
EST:     CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGC                         CGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
genomic: CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
EST: gi|211538250|gb|FL240276.1|FL240276
EST:     CATCTTCGGGCGCGAKAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGC                         -G-CCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
genomic: CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
EST: gi|24462568|gb|BM660099.1|BM660099
EST:     CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGC                         CGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTTGCTC
genomic: CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGT-GCTC
EST: gi|211538248|gb|FL240274.1|FL240274
EST:     CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGC                         CGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
genomic: CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
EST: gi|211538246|gb|FL240272.1|FL240272
EST:     CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGC                         CGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
genomic: CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
EST: gi|211134636|gb|FL257232.1|FL257232
EST:     CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGC                         CGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
genomic: CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
EST: gi|211135570|gb|FL257238.1|FL257238
EST:     CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGC                         -GKCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
genomic: CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
EST: gi|211538255|gb|FL240281.1|FL240281
EST:     CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGC                         -GGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
genomic: CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
EST: gi|211134630|gb|FL257226.1|FL257226
EST:     CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGC                         CGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
genomic: CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
EST: gi|211535252|gb|FL240268.1|FL240268
EST:     CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGC                         CGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
genomic: CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
EST: gi|211134635|gb|FL257231.1|FL257231
EST:     CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGC                         CGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
genomic: CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
EST: gi|211532247|gb|FL240249.1|FL240249
EST:     CATCTTCGGGCGCGAGAWGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGC                         -GGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
genomic: CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
EST: gi|211134632|gb|FL257228.1|FL257228
EST:     CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGC                         SGNCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
genomic: CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
EST: gi|211535244|gb|FL240260.1|FL240260
EST:     CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGC                         SGCCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
genomic: CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
EST: gi|211134640|gb|FL257236.1|FL257236
EST:     CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGC                         -GGNCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTC
genomic: CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGG-CCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTC
EST: gi|211134639|gb|FL257235.1|FL257235
EST:     CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGC                         CGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
genomic: CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
EST: gi|211535243|gb|FL240259.1|FL240259
EST:     CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGC                         CGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
genomic: CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
EST: gi|211137033|gb|FK978933.1|FK978933
EST:     CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGC                         CGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
genomic: CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
EST: gi|211137965|gb|FK978943.1|FK978943
EST:     CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGC                         CGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
genomic: CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
EST: gi|211538253|gb|FL240279.1|FL240279
EST:     CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGC                         CGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
genomic: CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
EST: gi|211538249|gb|FL240275.1|FL240275
EST:     CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGC                         SG-CCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG
genomic: CATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCG

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: 667

GACGACGAGCGCTCGTCGGCGACGGCCGCCGTGAAGGCCAAGATCTACCGCATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCGCAGGCGCAACTGCCTTCTGGCTGCTGTTTGAGGTCATGGATTACCACCT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 60

GACGACGAGCGCTCGTCGGCGACGGCCGCCGTGAAGGCCAAGATCTACCGCATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCGCAGGCGCAACTGCCTTCTGGCTGCTGTTTGAGGTCATGGATTACCACCT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 65

GACGACGAGCGCTCGTCGGCGACGGCCGCCGTGAAGGCCAAGATCTACCGCATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCGCAGGCGCAACTGCCTTCTGGCTGCTGTTTGAGGTCATGGATTACCACCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 240

GACGACGAGCGCTCGTCGGCGACGGCCGCCGTGAAGGCCAAGATCTACCGCATCTTCGGGCGCGAGAAGCCCGTGCACTCCGTCCTCGGCGGCGGCAAGCgtaagcccgg ... aagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCGCAGGCGCAACTGCCTTCTGGCTGCTGTTTGAGGTCATGGATTACCACCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattgttcatttatttggagctttgctctgatggacttttgatcaagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCGCAGGCGCAACTGCCTTCTGGCTGCTGTTTGAGGTCATGGATTACCACCT
                                     ttttgat  putative branch site (score: 240)
      ttcatttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggtattctttgtttgtttgctagtgagcgtttgttcccagatcccaattgttcatttatttggagctttgctctgatggacttttgatcaagcttgcagCGGCCGATCTGTTTCTATGGAGGAACAAGAGGATCTCTGGTGGGGTGCTCGCAGGCGCAACTGCCTTCTGGCTGCTGTTTGAGGTCATGGATTACCACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - -ttcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatggac