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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatctttattggtccctaattcatatctacttggcgttgggttgacttatgtttcctaattctgcttatcaaactaatattttttttttggcattgttccaaagTGCAAATGCTGGCGCTGCAACAGCCCAAGCAGACAAAAAAAAATCTTCAAAAGCAAGAAATAAACATACAGTAGAAGCTTCTGCTGATGACACCGAAGGA

Basic information

species Zea mays
transcript GRMZM2G015875_T01
intron # 7
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|211344865|gb|FL106766.1|FL106766
EST:     GTGACAGATGCCCCAGGAGAAAGACGTTACAATTTGAAACACAGTAGAGC                         TGCAAATGCTGGCGCTGCAACAGCCCAAGCAGACNNNNNNNNNTCTTCAAA
genomic: GTGACAGATGCCCCAGGAGAAAGACGTTACAATTTGAGACACAGTAGAGCgtaagtatct ... tgttccaaagTGCAAATGCTGGCGCTGCAACAGCCCAAGCAGACAAAAAAAAATCTTCAAA
EST: gi|60336733|gb|DN203706.1|DN203706
EST:     GTGACAGATGCCCCAGGAGAAAGACGTTACAATTTGAGACACAGTAGAGC                         TGCAAATGCTGGCGCTGCAACAGCCCAAGCAGACNNNNNNNNNTCTTCAAA
genomic: GTGACAGATGCCCCAGGAGAAAGACGTTACAATTTGAGACACAGTAGAGCgtaagtatct ... tgttccaaagTGCAAATGCTGGCGCTGCAACAGCCCAAGCAGACAAAAAAAAATCTTCAAA
EST: gi|32849045|gb|CD988726.1|CD988726
EST:     GTGACAGATGCCCCAGGAGAAAGACGTTACAATTTGAGACACAGTAGAGC                         TGCAAATGCTGGCGCTGCAACAGCCCAAGCAGAGAAAAA
genomic: GTGACAGATGCCCCAGGAGAAAGACGTTACAATTTGAGACACAGTAGAGCgtaagtatct ... tgttccaaagTGCAAATGCTGGCGCTGCAACAGCCCAAGCAGACAAAAA
EST: gi|60399051|gb|DN231867.1|DN231867
EST:     GTGACAGATGCCCCAGGAGAAAGACGTTACAATTTGAGACACAGTAGAGC                         TGCAAATGCTGGCGCTGCAACAGCCCAAGCAGACNNNNNNNNNTCTTCAAA
genomic: GTGACAGATGCCCCAGGAGAAAGACGTTACAATTTGAGACACAGTAGAGCgtaagtatct ... tgttccaaagTGCAAATGCTGGCGCTGCAACAGCCCAAGCAGACAAAAAAAAATCTTCAAA
EST: gi|211516762|gb|FL084664.1|FL084664
EST:     TGACAGATGCCCCAGGAGAAAGACGTTTACA-TTTGAGACACAGTAGAGC                         TGCAAATGCTGGCGCTGCAACAGCCCAAGCA
genomic: TGACAGATGCCCCAGGAGAAAGACGTT-ACAATTTGAGACACAGTAGAGCgtaagtatct ... tgttccaaagTGCAAATGCTGGCGCTGCAACAGCCCAAGCA
EST: gi|20512915|gb|BQ280101.1|BQ280101
EST:     GTGACAGATGCCCCAGGAGAAAGACGTTACAATTTGAGACACAGAAGAGC                         TGCAAATGCTGGCGCTGCAACAG
genomic: GTGACAGATGCCCCAGGAGAAAGACGTTACAATTTGAGACACAGTAGAGCgtaagtatct ... tgttccaaagTGCAAATGCTGGCGCTGCAACAG
EST: gi|31349416|gb|CD433773.1|CD433773
EST:     GTGACAGATGCCCCAGGAGAAAGACGTTACAATTTGAGACACAGTAGAGC                         TGCAAATGCTGGCGCTGCAACAGCCCAAGCAGACNNNNNNNNNTCTTCAAA
genomic: GTGACAGATGCCCCAGGAGAAAGACGTTACAATTTGAGACACAGTAGAGCgtaagtatct ... tgttccaaagTGCAAATGCTGGCGCTGCAACAGCCCAAGCAGACAAAAAAAAATCTTCAAA
EST: gi|32838004|gb|CD977682.1|CD977682
EST:     GTGACAGATGCCCCAGGAGAAAGACGTTACAATTTGAGACACAGTAGAGC                         TGCAAATGCTGGCGCTGCAACAGCCCAAGCAGAGAAAAAGAAATCTTCAAA
genomic: GTGACAGATGCCCCAGGAGAAAGACGTTACAATTTGAGACACAGTAGAGCgtaagtatct ... tgttccaaagTGCAAATGCTGGCGCTGCAACAGCCCAAGCAGACAAAAAAAAATCTTCAAA
EST: gi|67014458|gb|CO443207.1|CO443207
EST:     GTGACAGATGCCCCAGGAGAAAGACGTTACAATTTGAGACACAGTAGAGC                         TGCAAATGCTGGCGCTGCAACAGCCCAAGCAGACAAAAAGAAATCTTCAAA
genomic: GTGACAGATGCCCCAGGAGAAAGACGTTACAATTTGAGACACAGTAGAGCgtaagtatct ... tgttccaaagTGCAAATGCTGGCGCTGCAACAGCCCAAGCAGACAAAAAAAAATCTTCAAA

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), 48 (downstream exon)
Score: 332

GTGTTTCACTTGGAGGGCAGCGCCGTAAGAGGCGGCAAACTGCTGGGGCAGTGACAGATGCCCCAGGAGAAAGACGTTACAATTTGAGACACAGTAGAGCgtaagtatct ... tgttccaaagTGCAAATGCTGGCGCTGCAACAGCCCAAGCAGACAAAAAAAAATCTTCAAAAGCAAGAAATAAACATACAGTAGAAGCTTCTGCTGATGACACCGAAGGA


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 121

GTGTTTCACTTGGAGGGCAGCGCCGTAAGAGGCGGCAAACTGCTGGGGCAGTGACAGATGCCCCAGGAGAAAGACGTTACAATTTGAGACACAGTAGAGCgtaagtatct ... tgttccaaagTGCAAATGCTGGCGCTGCAACAGCCCAAGCAGACAAAAAAAAATCTTCAAAAGCAAGAAATAAACATACAGTAGAAGCTTCTGCTGATGACACCGAAGGA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 106

GTGTTTCACTTGGAGGGCAGCGCCGTAAGAGGCGGCAAACTGCTGGGGCAGTGACAGATGCCCCAGGAGAAAGACGTTACAATTTGAGACACAGTAGAGCgtaagtatct ... tgttccaaagTGCAAATGCTGGCGCTGCAACAGCCCAAGCAGACAAAAAAAAATCTTCAAAAGCAAGAAATAAACATACAGTAGAAGCTTCTGCTGATGACACCGAAGGA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 142

GTGTTTCACTTGGAGGGCAGCGCCGTAAGAGGCGGCAAACTGCTGGGGCAGTGACAGATGCCCCAGGAGAAAGACGTTACAATTTGAGACACAGTAGAGCgtaagtatct ... tgttccaaagTGCAAATGCTGGCGCTGCAACAGCCCAAGCAGACAAAAAAAAATCTTCAAAAGCAAGAAATAAACATACAGTAGAAGCTTCTGCTGATGACACCGAAGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttcctaattctgcttatcaaactaatattttttttttggcattgttccaaagTGCAAATGCTGGCGCTGCAACAGCCCAAGCAGACAAAAAAAAATCTTCAAAAGCAAGAAATAAACATACAGTAGAAGCTTCTGCTGATGACACCGAAGGA
                      aactaat  putative branch site (score: 142)
                                            ttgttcc  putative PPT
             tgcttatcaaactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatctttattggtccctaattcatatctacttggcgttgggttgacttatgtttcctaattctgcttatcaaactaatattttttttttggcattgttccaaagTGCAAATGCTGGCGCTGCAACAGCCCAAGCAGACAAAAAAAAATCTTCAAAAGCAAGAAATAAACATACAGTAGAAGCTTCTGCTGATGACACCGAAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT