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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttacttgataaagtatttttagaactagtctggaattattctgtctcagatgaaaccaacaattttggttgtttgctcactgcttcttttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT

Basic information

species Zea mays
transcript GRMZM2G395842_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G395842_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g21390.1 (Oryza sativa), 3'ss of exon 1
gtttacttgataaagtatttttagaactagtctggaattattctgtctcagatgaaaccaacaattttggttgtttgctcactgcttcttttgt------------tatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT
      ||| ||   |||  |  ||   ||        |   ||  ||  |||  |||  | | || |||| ||||||| || | |  ||| ||            |||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| || |||| ||||||| |||| |||
------ttgttatgttatcct--gattcagatca----ttcccttcctgggattgaacggaaagttctggtagtttgcttacagttcttttggttatgttttgatctatcagGGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAGTTCTCCCATGATTGGAATGATCAACCAAACAAT
















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|211441986|gb|FL189209.1|FL189209
EST:     ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAA                         AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAAgtaatttttc ... ttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|211441984|gb|FL189207.1|FL189207
EST:     ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAA                         AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAAgtaatttttc ... ttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|211441982|gb|FL189205.1|FL189205
EST:     ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAA                         AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAAgtaatttttc ... ttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|44682125|gb|CK787173.1|CK787173
EST:     ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAA                         AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAAgtaatttttc ... ttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|211441987|gb|FL189210.1|FL189210
EST:     ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAA                         AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAAgtaatttttc ... ttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|211441980|gb|FL189203.1|FL189203
EST:     ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAA                         AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAAgtaatttttc ... ttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|88753027|gb|DY537168.1|DY537168
EST:     ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAA                         AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAAgtaatttttc ... ttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|211441979|gb|FL189202.1|FL189202
EST:     ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAA                         AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAAgtaatttttc ... ttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|71435076|gb|DR816126.1|DR816126
EST:     ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAA                         AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAAgtaatttttc ... ttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|211441978|gb|FL189201.1|FL189201
EST:     ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAA                         AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAAgtaatttttc ... ttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|50333765|gb|CO528891.1|CO528891
EST:     ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAA                         AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAAgtaatttttc ... ttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|89754462|gb|DY685237.1|DY685237
EST:     ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAA                         AGTTCTTTGCAAGTTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACT
genomic: ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAAgtaatttttc ... ttgttatcagAGTTCTTTGCAAGTT-CTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACT
EST: gi|211441988|gb|FL189211.1|FL189211
EST:     ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAANAA                         AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAAgtaatttttc ... ttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|78119832|gb|DV538216.1|DV538216
EST:     ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAA                         AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAAgtaatttttc ... ttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|13557990|gb|BG549346.1|BG549346
EST:     ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGTCATGTCGACTAAGAA                         AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAAgtaatttttc ... ttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|74240963|gb|DT648877.1|DT648877
EST:     ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAA                         AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAAgtaatttttc ... ttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|101389164|gb|EB816537.1|EB816537
EST:     ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAA                         AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAAgtaatttttc ... ttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
EST: gi|89757793|gb|DY687242.1|DY687242
EST:     ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAA                         AGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG
genomic: ACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAAgtaatttttc ... ttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTG

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), 47 (downstream exon)
Score: 135

GGGGCGAAGCCTAGGTGACGGCGCTGTTAGTCGCCTCTAGTAGCTGCGCGACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAAgtaatttttc ... ttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 136

GGGGCGAAGCCTAGGTGACGGCGCTGTTAGTCGCCTCTAGTAGCTGCGCGACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAAgtaatttttc ... ttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

GGGGCGAAGCCTAGGTGACGGCGCTGTTAGTCGCCTCTAGTAGCTGCGCGACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAAgtaatttttc ... ttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

GGGGCGAAGCCTAGGTGACGGCGCTGTTAGTCGCCTCTAGTAGCTGCGCGACGCGGGCTGGCTTGTCCGATCGGTTTGCCTCGGCCATGTCGACTAAGAAgtaatttttc ... ttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcagatgaaaccaacaattttggttgtttgctcactgcttcttttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT
                              tgctcac  putative branch site (score: 141)
                                ctcactgcttctttt  CT-rich tract
              aacaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttacttgataaagtatttttagaactagtctggaattattctgtctcagatgaaaccaacaattttggttgtttgctcactgcttcttttgttatcagAGTTCTTTGCAAGTTCTTCATGCATGGAGCTTGCTTGAAAGGAGAGTACTGTGAATTCTCCCACGACTGGAGTGATCAAGCAAATAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- ttacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - caacaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcttc