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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgggtaattatcttgttgtcggcgctcgctgtacctccatgtttgtgcaatgactgacgcagagttgcatccgttcttatcagGAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGACCACTTAGCAGTGGTTCGGAGACTACCAAAGAGGCAAGTCCATCAACCT

Basic information

species Zea mays
transcript GRMZM2G156956_T01
intron # 13
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|71332238|gb|DR803044.1|DR803044
EST:     GGTGCCGCCCTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAG                         GAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGA
genomic: GGTGCCGCCCTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAGgtacgggtaa ... ttcttatcagGAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGA
EST: gi|4966476|gb|AI691332.1|AI691332
EST:     GGTGCCGCCCTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAG                         GAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGA
genomic: GGTGCCGCCCTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAGgtacgggtaa ... ttcttatcagGAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGA
EST: gi|60394908|gb|DN227777.1|DN227777
EST:     GGTGCCGCCCTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAG                         GAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACA
genomic: GGTGCCGCCCTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAGgtacgggtaa ... ttcttatcagGAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACA
EST: gi|5915119|gb|AW052760.1|AW052760
EST:     GTGCCGTCCTTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAG                         GAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGA
genomic: GTGCCG-CCCTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAGgtacgggtaa ... ttcttatcagGAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGA
EST: gi|67012060|gb|CO440809.1|CO440809
EST:     GGTGCCGCCCTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAG                         GAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGA
genomic: GGTGCCGCCCTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAGgtacgggtaa ... ttcttatcagGAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGA
EST: gi|78024790|gb|DV493177.1|DV493177
EST:     GGTGCCGCCCTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAG                         GAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGA
genomic: GGTGCCGCCCTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAGgtacgggtaa ... ttcttatcagGAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGA
EST: gi|71332239|gb|DR803045.1|DR803045
EST:     GGTGCCGCCCTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAG                         GAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGA
genomic: GGTGCCGCCCTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAGgtacgggtaa ... ttcttatcagGAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGA
EST: gi|37377624|gb|CF625431.1|CF625431
EST:     TGGCCCGAACGCAGGAGACCAG                         GTACCATTCCCTGTGGGTAACAATGTTTGTTCTCGGTCCGGGAGGAACAGA
genomic: TGGCCCGAACGCAGGAGACCAGgtacgggtaa ... ttcttatcagGAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGA
EST: gi|32851005|gb|CD990686.1|CD990686
EST:     GGTGCCGTCCTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAG                         GAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGA
genomic: GGTGCCGCCCTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAGgtacgggtaa ... ttcttatcagGAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGA
EST: gi|78076812|gb|DV505246.1|DV505246
EST:     GGTGCCGCCCTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAG                         GAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGA
genomic: GGTGCCGCCCTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAGgtacgggtaa ... ttcttatcagGAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGA

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: 103

CGCTTTGATTGCTCATTTCCAGAATTCTAGCCTGATGAATGAAGAGAAATGGTGCCGCCCTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAGgtacgggtaa ... ttcttatcagGAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGACCACTTAGCAGTGGTTCGGAGACTACCAAAGAGGCAAGTCCATCAACCT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 70

CGCTTTGATTGCTCATTTCCAGAATTCTAGCCTGATGAATGAAGAGAAATGGTGCCGCCCTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAGgtacgggtaa ... ttcttatcagGAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGACCACTTAGCAGTGGTTCGGAGACTACCAAAGAGGCAAGTCCATCAACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 97

CGCTTTGATTGCTCATTTCCAGAATTCTAGCCTGATGAATGAAGAGAAATGGTGCCGCCCTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAGgtacgggtaa ... ttcttatcagGAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGACCACTTAGCAGTGGTTCGGAGACTACCAAAGAGGCAAGTCCATCAACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 260

CGCTTTGATTGCTCATTTCCAGAATTCTAGCCTGATGAATGAAGAGAAATGGTGCCGCCCTATGCTTTTCCACAAAGATGGCCCGAACGCAGGAGACCAGgtacgggtaa ... ttcttatcagGAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGACCACTTAGCAGTGGTTCGGAGACTACCAAAGAGGCAAGTCCATCAACCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtacctccatgtttgtgcaatgactgacgcagagttgcatccgttcttatcagGAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGACCACTTAGCAGTGGTTCGGAGACTACCAAAGAGGCAAGTCCATCAACCT
                       gactgac  putative branch site (score: 260)
                                         tccgttctt  putative PPT
                                             ttcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgggtaattatcttgttgtcggcgctcgctgtacctccatgtttgtgcaatgactgacgcagagttgcatccgttcttatcagGAACCATTCCCTGTGGGTAACAATGTTCGTTCTCGGTCCGGGAGGAACAGACCACTTAGCAGTGGTTCGGAGACTACCAAAGAGGCAAGTCCATCAACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG