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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCATGCCGGGTGGGGCCCACGCCGCCGGCGCCGCGGACCAGATGCAGGTGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCCAAGgtgagcgggtttctcccccttttccgccgctggcgtgtggctccggcgtcccggagcggtcgcgcaggcctaccggatctctccgctccggccccggcgt...

Basic information

species Zea mays
transcript GRMZM2G151916_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|50339419|gb|CO534545.1|CO534545
EST:     ACACGGCCCCGCGGACGCCAAG                         CATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
genomic: ACACGGCCCCGCGGACGCCAAGgtgagcgggt ... tctgtaacagCATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
EST: gi|211449760|gb|FL269008.1|FL269008
EST:     TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCCGTCGCCAAG                         CATGCTGGTTCTATGATTGAAGGGAGTGATCCAGTCACGGGTCATATAATC
genomic: TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCCAAGgtgagcgggt ... tctgtaacagCATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
EST: gi|211451889|gb|FL269015.1|FL269015
EST:     TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCCAAG                         CATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
genomic: TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCCAAGgtgagcgggt ... tctgtaacagCATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
EST: gi|211451885|gb|FL269011.1|FL269011
EST:     TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCCGTCGCCAAG                         CATGCTGGTTCTATGATTGAAGGGAGTGATCCAGTCACGGGTCATATAATC
genomic: TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCCAAGgtgagcgggt ... tctgtaacagCATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
EST: gi|211451891|gb|FL269017.1|FL269017
EST:     TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCCAAG                         CATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
genomic: TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCCAAGgtgagcgggt ... tctgtaacagCATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
EST: gi|211449756|gb|FL269004.1|FL269004
EST:     TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGG-CCCGCGGACGCCAAG                         CATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
genomic: TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCCAAGgtgagcgggt ... tctgtaacagCATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
EST: gi|31363742|gb|CD448099.1|CD448099
EST:     TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCCAACGCCAAG                         CATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
genomic: TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCCAAGgtgagcgggt ... tctgtaacagCATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
EST: gi|211451886|gb|FL269012.1|FL269012
EST:     TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCCGTCGCCAAG                         CATGCTGGTTCTATGATTGAAGGGAGTGATCCAGTCACGGGTCATATAATC
genomic: TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCCAAGgtgagcgggt ... tctgtaacagCATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
EST: gi|29577163|gb|CB617275.1|CB617275
EST:     TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCCAAG                         CATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
genomic: TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCCAAGgtgagcgggt ... tctgtaacagCATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
EST: gi|86470098|gb|DY236468.1|DY236468
EST:     ACACGGCCCCGCGGACGCCAAG                         CATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
genomic: ACACGGCCCCGCGGACGCCAAGgtgagcgggt ... tctgtaacagCATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
EST: gi|211449759|gb|FL269007.1|FL269007
EST:     TGGACCAGCCGCTCCCCGCTGCGGCCGCACTCGGCCCCGCGGACGCCAAG                         CATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
genomic: TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCCAAGgtgagcgggt ... tctgtaacagCATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
EST: gi|50339420|gb|CO534546.1|CO534546
EST:     ACACGGCCCCGCGGACGCCAAG                         CATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
genomic: ACACGGCCCCGCGGACGCCAAGgtgagcgggt ... tctgtaacagCATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
EST: gi|6865198|gb|AW360548.1|AW360548
EST:     TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCCGTCGCCAAG                         CATGCTGGTTCTATGATTGAAGGGAGTGATCCAGTCACGGGTCATATAATC
genomic: TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCCAAGgtgagcgggt ... tctgtaacagCATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
EST: gi|19822262|gb|BQ048286.1|BQ048286
EST:     ACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCCAACGCCAAGCAG                         CATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAAT
genomic: ACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCC-A--AGgtgagcgggt ... tctgtaacagCATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAAT
EST: gi|211449757|gb|FL269005.1|FL269005
EST:     TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGG-CCCGCGGACGCCAAG                         CATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
genomic: TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCCAAGgtgagcgggt ... tctgtaacagCATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
EST: gi|211451888|gb|FL269014.1|FL269014
EST:     TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCCAAG                         CATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
genomic: TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCCAAGgtgagcgggt ... tctgtaacagCATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC
EST: gi|211449762|gb|FL269010.1|FL269010
EST:     TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCCGTCGCCAAG                         CATGCTGGTTCTATGATTGAAGGGAGTGATCCAGTCACGGGTCATATAATC
genomic: TGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCCAAGgtgagcgggt ... tctgtaacagCATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATC

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: 49 (upstream exon), 48 (downstream exon)
Score: 211

AGCCATGCCGGGTGGGGCCCACGCCGCCGGCGCCGCGGACCAGATGCAGGTGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCCAAGgtgagcgggt ... tctgtaacagCATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATCTCAACAACCATTGGAGGGAAGAATGGAGAGCCTAAAAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 168

AGCCATGCCGGGTGGGGCCCACGCCGCCGGCGCCGCGGACCAGATGCAGGTGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCCAAGgtgagcgggt ... tctgtaacagCATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATCTCAACAACCATTGGAGGGAAGAATGGAGAGCCTAAAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 149

AGCCATGCCGGGTGGGGCCCACGCCGCCGGCGCCGCGGACCAGATGCAGGTGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCCAAGgtgagcgggt ... tctgtaacagCATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATCTCAACAACCATTGGAGGGAAGAATGGAGAGCCTAAAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 144

AGCCATGCCGGGTGGGGCCCACGCCGCCGGCGCCGCGGACCAGATGCAGGTGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCCAAGgtgagcgggt ... tctgtaacagCATGCTGGTTCTATGATTGAAGGGAATGATCCAGTCACGGGTCATATAATCTCAACAACCATTGGAGGGAAGAATGGAGAGCCTAAAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCCATGCCGGGTGGGGCCCACGCCGCCGGCGCCGCGGACCAGATGCAGGTGGACCAGCCGCTCCCCGCTGCGGCCGCACACGGCCCCGCGGACGCCAAGgtgagcgggtttctcccccttttccgccgctggcgtgtggctccggcgtcccggagcggtcgcgcaggcctaccggatctctccgctccggccccggcgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccgccgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccggc