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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtgaaaaaaattcaattatacattgccttcgggccatctatacagtatacattataatgaaccatcacgtgacagCTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAG

Basic information

species Zea mays
transcript GRMZM2G066440_T01
intron # 10
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|211094279|gb|FL470654.1|FL470654
EST:     AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAG                         CTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
genomic: AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAGgtatggtgaa ... cacgtgacagCTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
EST: gi|111991228|gb|EE332430.1|EE332430
EST:     AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAG                         CTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
genomic: AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAGgtatggtgaa ... cacgtgacagCTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
EST: gi|16919952|gb|BM074437.1|BM074437
EST:     AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAG                         CTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
genomic: AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAGgtatggtgaa ... cacgtgacagCTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
EST: gi|24764480|gb|CA399644.1|CA399644
EST:     AACAGCTCCAGTGGCAATCAGTTCGGTGGTACTACCAGCTTTCATGGCAG                         CTATGGTAACAGCAGCCAGAACAATCAGACAGGTGACAATCCGAGCTTTCC
genomic: AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAGgtatggtgaa ... cacgtgacagCTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
EST: gi|32907008|gb|CF011821.1|CF011821
EST:     AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAG                         CTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
genomic: AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAGgtatggtgaa ... cacgtgacagCTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
EST: gi|60396317|gb|DN229186.1|DN229186
EST:     AAGCTTTCATGCCAG                         CTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
genomic: AAGCTTTCATGCCAGgtatggtgaa ... cacgtgacagCTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
EST: gi|32919364|gb|CF024176.1|CF024176
EST:     AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAG                         CTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
genomic: AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAGgtatggtgaa ... cacgtgacagCTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
EST: gi|37401565|gb|CF638149.1|CF638149
EST:     AACAGCTCCAGTGGCAATCAGTTCGGTGGTACTACCAGCTTTCATGGCAG                         CTATGGTAACAGCAGCCAGAACAATCAGACAGGTGACAATCCGAGCTTTCC
genomic: AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAGgtatggtgaa ... cacgtgacagCTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
EST: gi|60341740|gb|DN208713.1|DN208713
EST:     AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAG                         CTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
genomic: AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAGgtatggtgaa ... cacgtgacagCTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
EST: gi|116823588|gb|EC867128.1|EC867128
EST:     AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAG                         CTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
genomic: AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAGgtatggtgaa ... cacgtgacagCTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
EST: gi|33095213|gb|CF055207.1|CF055207
EST:     AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAG                         CTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
genomic: AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAGgtatggtgaa ... cacgtgacagCTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
EST: gi|149072974|gb|EE161235.2|EE161235
EST:     AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAG                         CTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
genomic: AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAGgtatggtgaa ... cacgtgacagCTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
EST: gi|50336101|gb|CO531227.1|CO531227
EST:     AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAG                         CTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
genomic: AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAGgtatggtgaa ... cacgtgacagCTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
EST: gi|32921823|gb|CF026635.1|CF026635
EST:     AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAG                         CTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
genomic: AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAGgtatggtgaa ... cacgtgacagCTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
EST: gi|78120607|gb|DV538991.1|DV538991
EST:     AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAG                         CTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC
genomic: AACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAGgtatggtgaa ... cacgtgacagCTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCC

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), 47 (downstream exon)
Score: 195

CTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAGgtatggtgaa ... cacgtgacagCTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 61

CTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAGgtatggtgaa ... cacgtgacagCTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 113

CTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAGgtatggtgaa ... cacgtgacagCTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAG


Block sizes: 43 (upstream exon), 45 (downstream exon)
Score: 60

CTTCCATAACAGCTCTAGTGGCAATCAGTTCGGTGATACTACAAGCTTTCATGCCAGgtatggtgaa ... cacgtgacagCTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgccttcgggccatctatacagtatacattataatgaaccatcacgtgacagCTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAG
                         tatacattataatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtgaaaaaaattcaattatacattgccttcgggccatctatacagtatacattataatgaaccatcacgtgacagCTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT