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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agactgtaccgctgacattttcagttccatctagtcgtgccgtggatgccacaacttggtctaacgactctgatcgggttttttttttttttggtttcagATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTTGATCTTGGATACCTGATCCGCAATTTGGGGCTGATTGAGTCACTTGACC

Basic information

species Zea mays
transcript GRMZM2G375904_T02
intron # 1
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|149049840|gb|EE048527.2|EE048527
EST:     TCGGTGCCGCCTCGGGCGAGATCCGCTCCGCGTGCCCCGCCGCTGCCGAG                         ATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTT
genomic: TCGGTGCCGCCTCGGGCGAGATCCGCTCCGCGTGCCCCGCCGCTGCCGAGgtgagctccg ... ttggtttcagATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTT
EST: gi|211195286|gb|FK977677.1|FK977677
EST:     TCGGTGCCGCCTCGGGCGAGATCCGCTCCGCGTGCCCCGCCGCTGCCGAG                         ATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTT
genomic: TCGGTGCCGCCTCGGGCGAGATCCGCTCCGCGTGCCCCGCCGCTGCCGAGgtgagctccg ... ttggtttcagATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTT
EST: gi|28873651|gb|CB329610.1|CB329610
EST:     TCGGTGCCGCCTCGGGCGAGATCCGCTCCGCGTGCCCCGCCGCTGCCGAG                         ATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTT
genomic: TCGGTGCCGCCTCGGGCGAGATCCGCTCCGCGTGCCCCGCCGCTGCCGAGgtgagctccg ... ttggtttcagATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTT
EST: gi|149070121|gb|EE158521.2|EE158521
EST:     TCGGTGCCGCCTCGGGCGAGATCCGCTCCGCGTGCCCCGCCGCTGCCGAG                         ATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTT
genomic: TCGGTGCCGCCTCGGGCGAGATCCGCTCCGCGTGCCCCGCCGCTGCCGAGgtgagctccg ... ttggtttcagATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTT
EST: gi|211195291|gb|FK977682.1|FK977682
EST:     TCGGTGCCGCCTCGGGCGAGATCCGCTCCGCGTGCCCCGCCGCTGCCGAG                         ATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTT
genomic: TCGGTGCCGCCTCGGGCGAGATCCGCTCCGCGTGCCCCGCCGCTGCCGAGgtgagctccg ... ttggtttcagATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTT
EST: gi|89250841|gb|DY622627.1|DY622627
EST:     TCGGTGCCGCCTCGGGCGAGATCCGCTCCGCGTGCCCCGCCGCTGCCGAG                         ATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTT
genomic: TCGGTGCCGCCTCGGGCGAGATCCGCTCCGCGTGCCCCGCCGCTGCCGAGgtgagctccg ... ttggtttcagATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTT
EST: gi|71765287|gb|DR963224.1|DR963224
EST:     GCCTCGGGCCGTCGGGCGAGATCCGCTCCGCGTGCCCCGCCGCTGCCGAG                         ATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTT
genomic: G-C-C--GCC-TCGGGCGAGATCCGCTCCGCGTGCCCCGCCGCTGCCGAGgtgagctccg ... ttggtttcagATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTT
EST: gi|211097010|gb|FL478910.1|FL478910
EST:     TCGGTGCCGCCTCGGGCGAGATCCGCTCCGCGTGCCCCACCGCTGCCGAG                         ATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTT
genomic: TCGGTGCCGCCTCGGGCGAGATCCGCTCCGCGTGCCCCGCCGCTGCCGAGgtgagctccg ... ttggtttcagATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTT
EST: gi|213183785|gb|FM191845.1|FM191845
EST:     CCGCGTGCCCCGCCGCTGCCGAG                         ATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTT
genomic: CCGCGTGCCCCGCCGCTGCCGAGgtgagctccg ... ttggtttcagATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTT
EST: gi|211195284|gb|FK977675.1|FK977675
EST:     TCGGTGCCGCCTCGGGCGAGATCCGCTCCGCGTGCCCCGCCGCTGCCGAG                         ATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTT
genomic: TCGGTGCCGCCTCGGGCGAGATCCGCTCCGCGTGCCCCGCCGCTGCCGAGgtgagctccg ... ttggtttcagATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTT
EST: gi|211195287|gb|FK977678.1|FK977678
EST:     TCGGTGCCGCCTCGGGCGAGATCCGCTCCGCGTGCCCCGCCGCTGCCGAG                         ATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTT
genomic: TCGGTGCCGCCTCGGGCGAGATCCGCTCCGCGTGCCCCGCCGCTGCCGAGgtgagctccg ... ttggtttcagATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTT

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: 48 (upstream exon), 49 (downstream exon)
Score: 101

AGCGGGTCGCGAGTCGCGACTCGCGAGTGCCCGCTTTTGCTCCAATCCAATCGGTGCCGCCTCGGGCGAGATCCGCTCCGCGTGCCCCGCCGCTGCCGAGgtgagctccg ... ttggtttcagATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTTGATCTTGGATACCTGATCCGCAATTTGGGGCTGATTGAGTCACTTGACC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 132

AGCGGGTCGCGAGTCGCGACTCGCGAGTGCCCGCTTTTGCTCCAATCCAATCGGTGCCGCCTCGGGCGAGATCCGCTCCGCGTGCCCCGCCGCTGCCGAGgtgagctccg ... ttggtttcagATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTTGATCTTGGATACCTGATCCGCAATTTGGGGCTGATTGAGTCACTTGACC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 107

AGCGGGTCGCGAGTCGCGACTCGCGAGTGCCCGCTTTTGCTCCAATCCAATCGGTGCCGCCTCGGGCGAGATCCGCTCCGCGTGCCCCGCCGCTGCCGAGgtgagctccg ... ttggtttcagATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTTGATCTTGGATACCTGATCCGCAATTTGGGGCTGATTGAGTCACTTGACC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 98

AGCGGGTCGCGAGTCGCGACTCGCGAGTGCCCGCTTTTGCTCCAATCCAATCGGTGCCGCCTCGGGCGAGATCCGCTCCGCGTGCCCCGCCGCTGCCGAGgtgagctccg ... ttggtttcagATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTTGATCTTGGATACCTGATCCGCAATTTGGGGCTGATTGAGTCACTTGACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgccacaacttggtctaacgactctgatcgggttttttttttttttggtttcagATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTTGATCTTGGATACCTGATCCGCAATTTGGGGCTGATTGAGTCACTTGACC
                                 ttttttttttttttgg  CT-rich tract
                                 ttttttttttttttgg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agactgtaccgctgacattttcagttccatctagtcgtgccgtggatgccacaacttggtctaacgactctgatcgggttttttttttttttggtttcagATAGAGGGTGTCGTCCCCACTCCCCAGCATCTGGTTCCACGGAGAGTTGTTGATCTTGGATACCTGATCCGCAATTTGGGGCTGATTGAGTCACTTGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- -ctgtacc
- - - - - gctgaca
- - - - - - - - - - - - - - - - - -cgtgccg
- - - - - - - - - - - - - - - - - - - - - tggatgc