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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCACTGGCATCGTCGGCGGCGCCTTGTCGCAGGCGGTGCACGCCGAGACCGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCCgtgagtgcctgcccgcccgcgcctcacatagctttttttttttctttggaactacagtattcatctgatgcgcctacttttaatttgctatggcacag

Basic information

species Zea mays
transcript GRMZM5G804323_T01
intron # 1
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|149008839|gb|EE041046.2|EE041046
EST:     CGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCC                         CCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
genomic: CGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCCgtgagtgcct ... tatggcacagCCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
EST: gi|15632642|gb|BI679735.1|BI679735
EST:     CGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCC                         CCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
genomic: CGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCCgtgagtgcct ... tatggcacagCCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
EST: gi|15499400|gb|BI595913.1|BI595913
EST:     CGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCC                         CCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
genomic: CGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCCgtgagtgcct ... tatggcacagCCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
EST: gi|149034772|gb|EE155072.2|EE155072
EST:     GGAGCCCCGCCCCCGCCCTCCGGTGGACTCC                         CCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
genomic: GGAGCCCCGCCGCCGCCCTCCGGTGGACTCCgtgagtgcct ... tatggcacagCCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
EST: gi|211516905|gb|FL431699.1|FL431699
EST:     CGTCAAGACCATCAAGATTGGAGCCCCGCCGCCGCCCTCCGGTGGACTCC                         CCGGGACTCTTAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
genomic: CGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCCgtgagtgcct ... tatggcacagCCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
EST: gi|16925715|gb|BM078783.1|BM078783
EST:     CGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCC                         CCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
genomic: CGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCCgtgagtgcct ... tatggcacagCCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
EST: gi|15590205|gb|BI674821.1|BI674821
EST:     CGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCC                         CCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
genomic: CGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCCgtgagtgcct ... tatggcacagCCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
EST: gi|15499623|gb|BI596136.1|BI596136
EST:     CGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCC                         CCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
genomic: CGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCCgtgagtgcct ... tatggcacagCCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
EST: gi|28984872|gb|BQ539237.2|BQ539237
EST:     CCCTCCGGTGGACTCC                         CCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
genomic: CCCTCCGGTGGACTCCgtgagtgcct ... tatggcacagCCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
EST: gi|211025253|gb|FL073322.1|FL073322
EST:     CGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCC                         CCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
genomic: CGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCCgtgagtgcct ... tatggcacagCCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
EST: gi|14364915|gb|BG946726.1|BG946726
EST:     CGCCCTCCGGTGGACTCC                         CCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
genomic: CGCCCTCCGGTGGACTCCgtgagtgcct ... tatggcacagCCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
EST: gi|71321912|gb|DR797644.1|DR797644
EST:     CGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCC                         CCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
genomic: CGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCCgtgagtgcct ... tatggcacagCCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
EST: gi|18171152|gb|BM340992.1|BM340992
EST:     CGTCAAGACCATCAAGATCGGATCCCCGCCGCCGCCCTCCGGTGGACTCC                         CCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
genomic: CGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCCgtgagtgcct ... tatggcacagCCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
EST: gi|4730591|gb|AI649757.1|AI649757
EST:     CGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCC                         CCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
genomic: CGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCCgtgagtgcct ... tatggcacagCCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
EST: gi|211022802|gb|FL073307.1|FL073307
EST:     ATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCC                         CCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
genomic: ATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCCgtgagtgcct ... tatggcacagCCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
EST: gi|211516907|gb|FL431701.1|FL431701
EST:     CGGTGGACTCC                         CCGGGACTCTTAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
genomic: CGGTGGACTCCgtgagtgcct ... tatggcacagCCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
EST: gi|76017001|gb|DT944171.1|DT944171
EST:     CGTCAAGACCATCAAGATGGGAGCCCCGCCGCCGCCCTCCGGTGGACTCC                         CCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
genomic: CGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCCgtgagtgcct ... tatggcacagCCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
EST: gi|15208975|gb|BI430859.1|BI430859
EST:     CGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCC                         CCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG
genomic: CGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCCgtgagtgcct ... tatggcacagCCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGG

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), 24 (downstream exon)
Score: 6

GCCACTGGCATCGTCGGCGGCGCCTTGTCGCAGGCGGTGCACGCCGAGACCGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCCgtgagtgcct ... tatggcacagCCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGGAGCGGTTCTACCTGCAGCCGCTGCCGCCGGCGGAGGCGGTGGCGAGGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1065

GCCACTGGCATCGTCGGCGGCGCCTTGTCGCAGGCGGTGCACGCCGAGACCGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCCgtgagtgcct ... tatggcacagCCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGGAGCGGTTCTACCTGCAGCCGCTGCCGCCGGCGGAGGCGGTGGCGAGGGT


Block sizes: 38 (upstream exon), 43 (downstream exon)
Score: 2

GCCACTGGCATCGTCGGCGGCGCCTTGTCGCAGGCGGTGCACGCCGAGACCGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCCgtgagtgcct ... tatggcacagCCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGGAGCGGTTCTACCTGCAGCCGCTGCCGCCGGCGGAGGCGGTGGCGAGGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 448

GCCACTGGCATCGTCGGCGGCGCCTTGTCGCAGGCGGTGCACGCCGAGACCGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCCgtgagtgcct ... tatggcacagCCGGGACTCTGAACTCTGACCAGGCGAGGGACTTCGACCTCCCCTTGAAGGAGCGGTTCTACCTGCAGCCGCTGCCGCCGGCGGAGGCGGTGGCGAGGGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCACTGGCATCGTCGGCGGCGCCTTGTCGCAGGCGGTGCACGCCGAGACCGTCAAGACCATCAAGATCGGAGCCCCGCCGCCGCCCTCCGGTGGACTCCgtgagtgcctgcccgcccgcgcctcacatagctttttttttttctttggaactacagtattcatctgatgcgcctacttttaatttgctatggcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA