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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcctagattgctcagtattctcttggtgttcccgttgtatgtttaaaccaatagatctacttgttttatccgctaacaaactgttatacgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG

Basic information

species Zea mays
transcript GRMZM2G021742_T02
intron # 5
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|148969289|gb|EE020059.2|EE020059
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|50326107|gb|CO521233.1|CO521233
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|78117951|gb|DV536338.1|DV536338
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|71446950|gb|DR828000.1|DR828000
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|71317917|gb|DR795718.1|DR795718
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|60356065|gb|DN223038.1|DN223038
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|78118268|gb|DV536655.1|DV536655
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|60353183|gb|DN220156.1|DN220156
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACT
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACT
EST: gi|211124519|gb|FL463077.1|FL463077
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|31364112|gb|CD448467.1|CD448467
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTTGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|91053554|gb|EB163972.1|EB163972
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|211242314|gb|FL469535.1|FL469535
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|60356070|gb|DN223043.1|DN223043
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
EST: gi|5650116|gb|AI920476.1|AI920476
EST:     AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAG                         GCTGCTATTGCAAATGCCCACACTCTTGAGGAAGCTGCAAGGCTAGAACAG
genomic: AAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG

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: 321

AACGTTTACTCCTGGTCTGCCTGATGCTCAGGACATCACAATGGAGCCACAAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

AACGTTTACTCCTGGTCTGCCTGATGCTCAGGACATCACAATGGAGCCACAAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

AACGTTTACTCCTGGTCTGCCTGATGCTCAGGACATCACAATGGAGCCACAAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 167

AACGTTTACTCCTGGTCTGCCTGATGCTCAGGACATCACAATGGAGCCACAAGGTCCTAAAGTAGTTGCTCCAACTCCTGAACAAATCACAGCTATCAAGgtacatgcat ... acgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaaccaatagatctacttgttttatccgctaacaaactgttatacgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG
                            cgctaac  putative branch site (score: 167)
                  ttgttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcctagattgctcagtattctcttggtgttcccgttgtatgtttaaaccaatagatctacttgttttatccgctaacaaactgttatacgtttgtagGCTGCTATTGCAAATGCCCACACTCTCGAGGAAGCTGCAAGGCTAGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - tggtgtt
- - - - - - - - - - - - - - - - - - -ttgtatg
- - - - - - - - - - - - - - - - - - - - - - - -aaaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taacaaa