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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcatttcagcatagtttttttttctttcctgggtgaggaaaacatcacatttactcctaatctggtcttaagatgataacttgcttattttgttggcagGCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAG

Basic information

species Zea mays
transcript GRMZM2G104769_T02
intron # 3
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|76913822|gb|DV165266.1|DV165266
EST:     TTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAG                         GCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAA
genomic: TTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAGgtgagtgggt ... ttgttggcagGCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAA
EST: gi|211321471|gb|FL171489.1|FL171489
EST:     TTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAG                         GCACATTACATGCTCGGGTTATCTCTTG
genomic: TTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAGgtgagtgggt ... ttgttggcagGCACATTACATGCTCGGGTTATCTCTTG
EST: gi|211321469|gb|FL171487.1|FL171487
EST:     TTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAG                         GCACATTACATGCTCGGGTTATCTCTTGTCAACGGCCAAAGATTATCAGAA
genomic: TTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAGgtgagtgggt ... ttgttggcagGCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAA
EST: gi|211321468|gb|FL171486.1|FL171486
EST:     TTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAG                         GCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAA
genomic: TTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAGgtgagtgggt ... ttgttggcagGCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAA
EST: gi|94476727|gb|EB705685.1|EB705685
EST:     TTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAG                         GCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAA
genomic: TTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAGgtgagtgggt ... ttgttggcagGCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAA
EST: gi|211196887|gb|FL171483.1|FL171483
EST:     TTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAG                         GCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAA
genomic: TTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAGgtgagtgggt ... ttgttggcagGCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAA
EST: gi|61119637|gb|DN560598.1|DN560598
EST:     TTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAG                         GCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAA
genomic: TTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAGgtgagtgggt ... ttgttggcagGCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAA
EST: gi|211321467|gb|FL171485.1|FL171485
EST:     TTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAG                         GCACATTACATGCTCGGGTTATCTCTTGTNCA-CAGCCAAAGATTATCAGA
genomic: TTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAGgtgagtgggt ... ttgttggcagGCACATTACATGCTCGGGTTATCTCTTGT-CAACAGCCAAAGATTATCAGA
EST: gi|211321466|gb|FL171484.1|FL171484
EST:     TTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAG                         GCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAA
genomic: TTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAGgtgagtgggt ... ttgttggcagGCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAA
EST: gi|149106376|gb|EE292096.2|EE292096
EST:     TTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAG                         GCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAA
genomic: TTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAGgtgagtgggt ... ttgttggcagGCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAA
EST: gi|91054321|gb|EB164739.1|EB164739
EST:     TTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAG                         GCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAA
genomic: TTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAGgtgagtgggt ... ttgttggcagGCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAA

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), 44 (downstream exon)
Score: 23

TGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAGgtgagtgggt ... ttgttggcagGCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 77

TGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAGgtgagtgggt ... ttgttggcagGCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 59

TGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAGgtgagtgggt ... ttgttggcagGCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 40

TGAGTGGACTAGAGTTGAGGAAGATTGCAGAACAGCTATCCAGCTTGACAGCCAGTCTGTTAAGgtgagtgggt ... ttgttggcagGCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacatttactcctaatctggtcttaagatgataacttgcttattttgttggcagGCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAG
                             tgataac  putative branch site (score: 40)
                                       cttatttt  putative PPT
                                        ttattttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcatttcagcatagtttttttttctttcctgggtgaggaaaacatcacatttactcctaatctggtcttaagatgataacttgcttattttgttggcagGCACATTACATGCTCGGGTTATCTCTTGTCAACAGCCAAAGATTATCAGAAGGAATAAAATCACTGGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - -ttcagca
- - - - - - - - - - - - - ttcctgg
- - - - - - - - - - - - - - - - - - - - -aacatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttat