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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgttgggagtggctatagtaacaatcggacttatgtttcctgtggatgaattttggtcgtggagtagatctgtgcactgatgtgtggttctgttgcagGCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGAAGTCACTAGCGAGGTGGATCAAGTTCGTGCTCTTCAGGAAGAAGTCGTC

Basic information

species Zea mays
transcript GRMZM5G897073_T04
intron # 4
splice site 3'
intron type U2

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|88752874|gb|DY537015.1|DY537015
EST:     ATGCCCTTGCTGGTGCAGGGGGGAACACATTTTAGTTTCACAACCTTCAT                         GCCTCTTAACCCCTCTGATCCTGGGGGGTGGCAGATTAGACTCCGAAGGGG
genomic: ATGCCCTTGCTGGTGCAGGGGGGAACACATTT-AGTTTCACAACCTTCATgtgagccctt ... tctgttgcagGC-TCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGG
EST: gi|32837950|gb|CD977628.1|CD977628
EST:     ATGCCCTTGCTGGTGCAGGGGGGAACCACATTTAGTTTCACAACCTTCAT                         GCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGA
genomic: ATGCCCTTGCTGGTGCAGGGGGGAA-CACATTTAGTTTCACAACCTTCATgtgagccctt ... tctgttgcagGCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGA
EST: gi|60345564|gb|DN212537.1|DN212537
EST:     GATGCCCTTGCTGGTGCAGGGGGGAACACATTTAGTTTCACAACCTTCAT                         GCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGA
genomic: GATGCCCTTGCTGGTGCAGGGGGGAACACATTTAGTTTCACAACCTTCATgtgagccctt ... tctgttgcagGCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGA
EST: gi|91050400|gb|EB160818.1|EB160818
EST:     GATGCCCTTGCTGGTGCAGGGGGGAACACATTTAGTTTCACAACCTTCAT                         GCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGA
genomic: GATGCCCTTGCTGGTGCAGGGGGGAACACATTTAGTTTCACAACCTTCATgtgagccctt ... tctgttgcagGCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGA
EST: gi|32838909|gb|CD978590.1|CD978590
EST:     ATGCCCTTGCTGGTGCAGGGGGGAACCACATTTAGTTTCACAACCTTCAT                         GCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGA
genomic: ATGCCCTTGCTGGTGCAGGGGGGAA-CACATTTAGTTTCACAACCTTCATgtgagccctt ... tctgttgcagGCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGA

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: 102

CAAAGATGACTAAAGAAGAGGAAGATGAAGAATACCTCGAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGGAACACATTTAGTTTCACAACCTTCATgtgagccctt ... tctgttgcagGCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGAAGTCACTAGCGAGGTGGATCAAGTTCGTGCTCTTCAGGAAGAAGTCGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 17

CAAAGATGACTAAAGAAGAGGAAGATGAAGAATACCTCGAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGGAACACATTTAGTTTCACAACCTTCATgtgagccctt ... tctgttgcagGCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGAAGTCACTAGCGAGGTGGATCAAGTTCGTGCTCTTCAGGAAGAAGTCGTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 9

CAAAGATGACTAAAGAAGAGGAAGATGAAGAATACCTCGAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGGAACACATTTAGTTTCACAACCTTCATgtgagccctt ... tctgttgcagGCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGAAGTCACTAGCGAGGTGGATCAAGTTCGTGCTCTTCAGGAAGAAGTCGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 32

CAAAGATGACTAAAGAAGAGGAAGATGAAGAATACCTCGAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGGAACACATTTAGTTTCACAACCTTCATgtgagccctt ... tctgttgcagGCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGAAGTCACTAGCGAGGTGGATCAAGTTCGTGCTCTTCAGGAAGAAGTCGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatgaattttggtcgtggagtagatctgtgcactgatgtgtggttctgttgcagGCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGAAGTCACTAGCGAGGTGGATCAAGTTCGTGCTCTTCAGGAAGAAGTCGTC
                               cactgat  putative branch site (score: 32)
                                            ttctgtt  putative PPT
     aatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgttgggagtggctatagtaacaatcggacttatgtttcctgtggatgaattttggtcgtggagtagatctgtgcactgatgtgtggttctgttgcagGCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGAAGTCACTAGCGAGGTGGATCAAGTTCGTGCTCTTCAGGAAGAAGTCGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT