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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGACGCCAAAGACGAAGAGGAGTTTTATGCTAAATCACCACCTCGAAATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatgaaattataatgttcttttgtactggcattatcttagctgagcttacatttttttcttttcttggcag

Basic information

species Zea mays
transcript GRMZM2G152319_T02
intron # 13
splice site 5'
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|6022224|gb|AW067152.1|AW067152
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
EST: gi|6952326|gb|AW424394.1|AW424394
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCTGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
EST: gi|6195038|gb|AW147142.1|AW147142
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCTGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
EST: gi|6827796|gb|AW331439.1|AW331439
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCTGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
EST: gi|6166619|gb|AW144883.1|AW144883
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCTGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
EST: gi|21987664|gb|BQ779192.1|BQ779192
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
EST: gi|6057103|gb|AW091508.1|AW091508
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
EST: gi|32945441|gb|CF050260.1|CF050260
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCTGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
EST: gi|71431160|gb|DR812210.1|DR812210
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
EST: gi|78025210|gb|DV493597.1|DV493597
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
EST: gi|6166618|gb|AW144882.1|AW144882
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCTGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
EST: gi|93281627|gb|EB673891.1|EB673891
EST:     ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGG                         CCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA
genomic: ATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAA

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: 79

TGATGACGCCAAAGACGAAGAGGAGTTTTATGCTAAATCACCACCTCGAAATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAAACCGATGACATACTGATAGGGGACAGTCAAAGTAGTTGGAATTGGAACC


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

TGATGACGCCAAAGACGAAGAGGAGTTTTATGCTAAATCACCACCTCGAAATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAAACCGATGACATACTGATAGGGGACAGTCAAAGTAGTTGGAATTGGAACC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 91

TGATGACGCCAAAGACGAAGAGGAGTTTTATGCTAAATCACCACCTCGAAATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAAACCGATGACATACTGATAGGGGACAGTCAAAGTAGTTGGAATTGGAACC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 55

TGATGACGCCAAAGACGAAGAGGAGTTTTATGCTAAATCACCACCTCGAAATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatg ... ttcttggcagCCTGATTCACTCGGACCACTGGACTTGGACATACCGGCCGTGAGATATCAAACCGATGACATACTGATAGGGGACAGTCAAAGTAGTTGGAATTGGAACC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGACGCCAAAGACGAAGAGGAGTTTTATGCTAAATCACCACCTCGAAATGACAAAACTAATGAGTTGAAGGATCAACCTTTAGCTGACATATATTGGgtacttgatgaaattataatgttcttttgtactggcattatcttagctgagcttacatttttttcttttcttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA