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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAGgtttgcactttttaggctttcagttatgttttgttcctagttaggcgtttttatcctcccatttccccatcataactcatgtgaaaaatagttagttacc...

Basic information

species Zea mays
transcript GRMZM2G021864_T01
intron # 16
splice site 5'
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|33091337|gb|CF051331.1|CF051331
EST:     CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG                         GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
genomic: CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
EST: gi|78022987|gb|DV491374.1|DV491374
EST:     CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG                         GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
genomic: CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
EST: gi|32931903|gb|CF036715.1|CF036715
EST:     CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG                         GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
genomic: CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
EST: gi|211458170|gb|FL127582.1|FL127582
EST:     CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG                         GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
genomic: CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
EST: gi|89248917|gb|DY620703.1|DY620703
EST:     CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG                         GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
genomic: CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
EST: gi|89758497|gb|DY687658.1|DY687658
EST:     CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG                         GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
genomic: CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
EST: gi|211460681|gb|FL127583.1|FL127583
EST:     CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG                         GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
genomic: CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
EST: gi|32934210|gb|CF039022.1|CF039022
EST:     CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG                         GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
genomic: CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
EST: gi|78106767|gb|DV525185.1|DV525185
EST:     CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG                         GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
genomic: CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
EST: gi|32912991|gb|CF017803.1|CF017803
EST:     GGCTGATCAAGCACAAGAGAACAATTATGGACTCAGAAGTTTTGGATGAG                         GATCTGGTGGAGATTGGCTCCTCTGGGGTCCTAGATCCT
genomic: T-CTGATCAAGCACAAGAGAACAAT-ATGGACTCAGAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCT
EST: gi|116827696|gb|EC871624.1|EC871624
EST:     GAAG-TTTGGATGAG                         GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTANATCCTAGTTTTATTGAG
genomic: GAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
EST: gi|32930527|gb|CF035339.1|CF035339
EST:     CGTCTGATCAAGCGCAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG                         GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
genomic: CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
EST: gi|5915604|gb|AW053245.1|AW053245
EST:     CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG                         GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
genomic: CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
EST: gi|32932800|gb|CF037612.1|CF037612
EST:     CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG                         GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
genomic: CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
EST: gi|5713643|gb|AI943635.1|AI943635
EST:     ATATGGACTCAGAAGTTTTGGATGAG                         GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
genomic: ATATGGACTCAGAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
EST: gi|5361116|gb|AI795731.1|AI795731
EST:     CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG                         GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
genomic: CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
EST: gi|32932808|gb|CF037620.1|CF037620
EST:     CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG                         GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
genomic: CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
EST: gi|91054831|gb|EB165249.1|EB165249
EST:     CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG                         GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
genomic: CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
EST: gi|13381810|gb|BG458485.1|BG458485
EST:     CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG                         GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
genomic: CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
EST: gi|12968788|gb|BG265825.1|BG265825
EST:     CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAG                         GATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG
genomic: CGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAG

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: 48 (upstream exon), 49 (downstream exon)
Score: 81

GTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 38

GTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 72

GTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 63

GTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAGgtttgcactt ... cctcgttcagGATCTGGTGGAGATTGGCTCCTCTGGTGTCCTAGATCCTAGTTTTATTGAGAAGCTGAGTGAAGAAAACATCGCTCTGTTTTCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCTCATTTGCAATCGTCTGATCAAGCACAAGAGAACAATATGGACTCAGAAGTTTTGGATGAGgtttgcactttttaggctttcagttatgttttgttcctagttaggcgtttttatcctcccatttccccatcataactcatgtgaaaaatagttagttacc

- - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaaata