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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccaaaaatactttaaaaccacaagtcactgaatggcatcagaattcagaacagcctgcaagctgttgctaaacttaacctagtagaattaccactttagttcagttcttctggactgagatatgtgctctgcaagagtgttagtaactagaagttactcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCTTTTCCAG

Basic information

species Zea mays
transcript GRMZM2G022866_T01
intron # 9
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|211302326|gb|FL459923.1|FL459923
EST:     TTAGTACGAGAGACACTTGTCGAGTTGGAATTGCCACATCTGCTACACAG                         CTGCGCACGAGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
genomic: TTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
EST: gi|45847020|gb|CN070963.1|CN070963
EST:     TTAGTACGAGAGACGCTTGTCGAGTTGGAATTGCCACATCTGCTACACAG                         CTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
genomic: TTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
EST: gi|18167421|gb|BM337260.1|BM337260
EST:     TTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAG                         CTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
genomic: TTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
EST: gi|78076799|gb|DV505233.1|DV505233
EST:     TTAGTACGAGAGACACTTGTCGAGTTGGAATTGCCACATCTGCTACACAG                         CTGCGCACGAGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
genomic: TTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
EST: gi|149086438|gb|EE175981.2|EE175981
EST:     TTAGTACGAGAGACACTTGTCGAGTTGGAATTGCCACATCTGCTACACAG                         CTGCGCACGAGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
genomic: TTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
EST: gi|12969746|gb|BG266636.1|BG266636
EST:     TTAGTACGAGAGACGCTTGTCGAGTTGGAATTGTCACATCTGCTACACAG                         CTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
genomic: TTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
EST: gi|71774726|gb|DR972604.1|DR972604
EST:     TTAGTACGAGAGACACTTGTCGAGTTGGAATTGCCACATCTGCTACACAG                         CTGCGCACGAGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
genomic: TTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
EST: gi|5706290|gb|AI942066.1|AI942066
EST:     TTAGTACGAGAGACGCTTGTCGAGTTGGAATTGCCACATCTGCTACNCAG                         CTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT
genomic: TTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCT

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), 29 (downstream exon)
Score: 21

GGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCTTTTCCAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 79

GGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCTTTTCCAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 21

GGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCTTTTCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 46

GGATCTCCCTTCTGTAAATTAGTACGAGAGACGCTTGTCGAGTTGGAATTACCACATCTGCTACACAGgtatccaaaa ... actcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCTTTTCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggactgagatatgtgctctgcaagagtgttagtaactagaagttactcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCTTTTCCAG
                              tagtaac  putative branch site (score: 46)
                                           ttactcct  putative PPT
                             ttagtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccaaaaatactttaaaaccacaagtcactgaatggcatcagaattcagaacagcctgcaagctgttgctaaacttaacctagtagaattaccactttagttcagttcttctggactgagatatgtgctctgcaagagtgttagtaactagaagttactcctgcagCTGCGCACGTGGCAGCCCCAAACGACAAGAATTTTTCAAGAAAAAGGGGCTTTTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA