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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatcatcatctttgaatccctatgttatgccgctcaaagtggatttttttttctttgctgactagcagaattgtatgtagGATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTTATGGCTGCATTCCCTTCAGCTAAGCCACCACTGGGAGTGTTTTTCGCAG

Basic information

species Zea mays
transcript GRMZM2G104294_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104294_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g55960.1 (Oryza sativa), 3'ss of exon 11
---gttatcatcatctttgaatccctatgttatgccgctcaaagtggatttttttttctttgctgactagcagaattgtatgta----gGATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTTATGGCTGCATTCCCTTCAGCTAAGCCACCACTGGGAGTGTTTTTCGCAG
   ||     ||   || |||   | ||  || |    |  ||||||  | | | |||| |||||||    ||| ||| |||||    |||||| |||||||||||| ||   ||||| || || || |||||||||||||||||||||||||||||||||||||| ||||||||||| || || ||||
gtagtgcctttctagttagaacttccattctaggatcttttaagtggtatatatattctctgctgaccgctagacttgcatgtatacagGATGAATATTCTCAATGGGTAGTAGCTAGCCAAAGAAGCCTTCTTGAAGTTATGGCTGCATTCCCTTCAGCTAAGCCCCCACTGGGAGTATTCTTTGCAG
















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|20506752|gb|BQ279326.1|BQ279326
EST:     ATCCAGCTGAAGCTGAACGACTTAGGTTCTTGGCCTCTCCTGCTGGAAAG                         GATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTT
genomic: ATCCAGCTGAAGCTGAACGACTTAGGTTCTTGGCCTCTCCTGCTGGAAAGgttatcatca ... ttgtatgtagGATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTT
EST: gi|194716812|gb|FK933971.1|FK933971
EST:     ATCCAGCTGAAGCTGAACGACTTAGGTTCTTGGCCTCTCCTGCTGGAAAG                         GATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTT
genomic: ATCCAGCTGAAGCTGAACGACTTAGGTTCTTGGCCTCTCCTGCTGGAAAGgttatcatca ... ttgtatgtagGATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTT
EST: gi|32921358|gb|CF026170.1|CF026170
EST:     ATCCAGCTGAAGCTGAACGACTTAAGTTCTTGGCCTCTCCTGCTGGAAAG                         GATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTT
genomic: ATCCAGCTGAAGCTGAACGACTTAGGTTCTTGGCCTCTCCTGCTGGAAAGgttatcatca ... ttgtatgtagGATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTT
EST: gi|32832538|gb|CD972216.1|CD972216
EST:     ATCCAGCTGAAGCTGAACGACTTAGGTTCTTGGCCTCTCCTGCTGGAAAG                         GATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTT
genomic: ATCCAGCTGAAGCTGAACGACTTAGGTTCTTGGCCTCTCCTGCTGGAAAGgttatcatca ... ttgtatgtagGATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTT
EST: gi|32929828|gb|CF034640.1|CF034640
EST:     ATCCAGCTGAAGCTGAACGACTTAGGTTCTTGGCCTCTCCTGCTGGAAAG                         GATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTT
genomic: ATCCAGCTGAAGCTGAACGACTTAGGTTCTTGGCCTCTCCTGCTGGAAAGgttatcatca ... ttgtatgtagGATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTT
EST: gi|67024128|gb|CO452877.1|CO452877
EST:     ATCCAGCTGAAGCTGAACGACTTAGGTTCTTGGCCTCTCCTGCTGGAAAG                         GATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTT
genomic: ATCCAGCTGAAGCTGAACGACTTAGGTTCTTGGCCTCTCCTGCTGGAAAGgttatcatca ... ttgtatgtagGATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTT
EST: gi|22819046|gb|BU499136.1|BU499136
EST:     ATCCAGCTGAAGCTGAACGACTTAGGTTCTTGGCCTCTCCTGCTGGAAAG                         GATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTT
genomic: ATCCAGCTGAAGCTGAACGACTTAGGTTCTTGGCCTCTCCTGCTGGAAAGgttatcatca ... ttgtatgtagGATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTT
EST: gi|32921381|gb|CF026193.1|CF026193
EST:     ATCCAGCTGAAGCTGAACGACTTAGGTTCTTGGCCTCTCCTGCTGGAAAG                         GATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTT
genomic: ATCCAGCTGAAGCTGAACGACTTAGGTTCTTGGCCTCTCCTGCTGGAAAGgttatcatca ... ttgtatgtagGATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTT
EST: gi|211465905|gb|FL134197.1|FL134197
EST:     ATCCAGCTGAAGCTGAACGACTTAGGTTCTTGGCCTCTCCTGCTGGAAAG                         GATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTT
genomic: ATCCAGCTGAAGCTGAACGACTTAGGTTCTTGGCCTCTCCTGCTGGAAAGgttatcatca ... ttgtatgtagGATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTT
EST: gi|32928791|gb|CF033603.1|CF033603
EST:     ATCCAGCTGAAGCTGAACGACTTAGGTTCTTGGCCTCTCCTGCTGGAAAG                         GATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTT
genomic: ATCCAGCTGAAGCTGAACGACTTAGGTTCTTGGCCTCTCCTGCTGGAAAGgttatcatca ... ttgtatgtagGATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTT

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: 47 (upstream exon), 49 (downstream exon)
Score: 121

GCTGCTTTGCTTGCTTTAGCTTCTCATGCATCTGATCCAGCTGAAGCTGAACGACTTAGGTTCTTGGCCTCTCCTGCTGGAAAGgttatcatca ... ttgtatgtagGATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTTATGGCTGCATTCCCTTCAGCTAAGCCACCACTGGGAGTGTTTTTCGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 237

GCTGCTTTGCTTGCTTTAGCTTCTCATGCATCTGATCCAGCTGAAGCTGAACGACTTAGGTTCTTGGCCTCTCCTGCTGGAAAGgttatcatca ... ttgtatgtagGATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTTATGGCTGCATTCCCTTCAGCTAAGCCACCACTGGGAGTGTTTTTCGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

GCTGCTTTGCTTGCTTTAGCTTCTCATGCATCTGATCCAGCTGAAGCTGAACGACTTAGGTTCTTGGCCTCTCCTGCTGGAAAGgttatcatca ... ttgtatgtagGATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTTATGGCTGCATTCCCTTCAGCTAAGCCACCACTGGGAGTGTTTTTCGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 208

GCTGCTTTGCTTGCTTTAGCTTCTCATGCATCTGATCCAGCTGAAGCTGAACGACTTAGGTTCTTGGCCTCTCCTGCTGGAAAGgttatcatca ... ttgtatgtagGATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTTATGGCTGCATTCCCTTCAGCTAAGCCACCACTGGGAGTGTTTTTCGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgccgctcaaagtggatttttttttctttgctgactagcagaattgtatgtagGATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTTATGGCTGCATTCCCTTCAGCTAAGCCACCACTGGGAGTGTTTTTCGCAG
                              tgctgac  putative branch site (score: 208)
                 atttttttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatcatcatctttgaatccctatgttatgccgctcaaagtggatttttttttctttgctgactagcagaattgtatgtagGATGAGTATTCTCAATGGATAACTGCTAGTCAGAGGAGTCTTCTTGAAGTTATGGCTGCATTCCCTTCAGCTAAGCCACCACTGGGAGTGTTTTTCGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT