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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcccttattagtcttttctgttttgttgtcaaacttaagttatcaacacagtattgtcttgtcagttgttctcattaactttctttcctccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG

Basic information

species Zea mays
transcript GRMZM2G100620_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100620_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g15700.1 (Oryza sativa), 3'ss of exon 2
-tgcccttattagtcttttctgttttgttgtcaaacttaagttatcaacacagtattgtcttgtcagttgttctcattaactttctttcctccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG
      ||||      |||  ||   | | ||        ||          | |      |  ||     | |  |||| | |||||||| ||||| ||||||||||||| ||||| |||||| | || || || || ||||||||||| | |||||||||||| ||||| ||||||
ggatagttatgctatctttaagtccagctatctggacatggtcgaatctgttggaagaatctaacacaaaatatt-ttaattatctttccttccttttcagTTAAGATTGGAAGACCTGGGTATCAGGTGACTAAGCAGTATGATCCTGACATGAAGCAACACTCATTTCTTTTTGAG
















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|211400055|gb|FL136245.1|FL136245
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|78111551|gb|DV529948.1|DV529948
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|211397253|gb|FL247604.1|FL247604
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|211460799|gb|FL247625.1|FL247625
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|19351244|gb|BM895776.1|BM895776
EST:     GCCCGCGCAGCCCCAGCCCAACATGCGCAAGCTTGCCCCCCGCATGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|149014483|gb|EE044106.2|EE044106
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|19272503|gb|BM888759.1|BM888759
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|211397250|gb|FL247601.1|FL247601
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|211458287|gb|FL247622.1|FL247622
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|91056062|gb|EB166480.1|EB166480
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|18648819|gb|BM497638.1|BM497638
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|211402590|gb|FL136247.1|FL136247
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|148944813|gb|EC889958.2|EC889958
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|78092801|gb|DV521175.1|DV521175
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|211460800|gb|FL247626.1|FL247626
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|78077143|gb|DV505577.1|DV505577
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|148937013|gb|EC881184.2|EC881184
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|211402592|gb|FL136249.1|FL136249
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|149111002|gb|EE294501.2|EE294501
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|37417746|gb|CF646533.1|CF646533
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|50330974|gb|CO526100.1|CO526100
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|78113433|gb|DV531825.1|DV531825
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|32863198|gb|CF002880.1|CF002880
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|6564142|gb|AW231764.1|AW231764
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|149081122|gb|EE170228.2|EE170228
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|211458278|gb|FL247613.1|FL247613
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|211402594|gb|FL136251.1|FL136251
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|211400054|gb|FL136244.1|FL136244
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCCGGGTATAAAGTAACCAAACAATATGATCCTGAG
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCC-GGGTATAAAGTAACCAAACAATATGATCCTGAG
EST: gi|211402593|gb|FL136250.1|FL136250
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|211460801|gb|FL247627.1|FL247627
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|211402591|gb|FL136248.1|FL136248
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
EST: gi|18648881|gb|BM497700.1|BM497700
EST:     GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTG                         TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA
genomic: GCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGA

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: 507

AGGCACCAGACCAACCTCGCCAAGCGCGCCGCCCGAGAGGCCAAGGATGCGCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 326

AGGCACCAGACCAACCTCGCCAAGCGCGCCGCCCGAGAGGCCAAGGATGCGCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 299

AGGCACCAGACCAACCTCGCCAAGCGCGCCGCCCGAGAGGCCAAGGATGCGCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 280

AGGCACCAGACCAACCTCGCCAAGCGCGCCGCCCGAGAGGCCAAGGATGCGCCCGCGCAGCCCCAGCCCAACAAGCGCAAGCTTGCCCCCCGCAAGTCTGgtgcgtgaaa ... ccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacacagtattgtcttgtcagttgttctcattaactttctttcctccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG
                            cattaac  putative branch site (score: 280)
                     ttgttctcattaactt  CT-rich tract
                             attaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcccttattagtcttttctgttttgttgtcaaacttaagttatcaacacagtattgtcttgtcagttgttctcattaactttctttcctccctttgcagTTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA