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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACCTCCTACTCAGACAGTGCCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcgtatttatttgtatgtaaaggcttgatttgtgttaggattggtagtatggatccttttcagctggttctagtgcaggcaacatttgcaatc...

Basic information

species Zea mays
transcript GRMZM2G105772_T01
intron # 4
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|109179157|gb|EC379841.1|EC379841
EST:     CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTAT                         TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|211414766|gb|FL112972.1|FL112972
EST:     CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTS-ACCAGCACCTAT                         TGTACCTGTCAGTGCACTGGCTGC
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGC
EST: gi|148969759|gb|EE020640.2|EE020640
EST:     CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTAT                         TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|149051783|gb|EE155908.2|EE155908
EST:     CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTAT                         TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|60396086|gb|DN228955.1|DN228955
EST:     CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTAT                         TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|148943103|gb|EC888159.2|EC888159
EST:     CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTAT                         TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|9732269|gb|BE511021.1|BE511021
EST:     CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTAT                         TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|78118533|gb|DV536917.1|DV536917
EST:     CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTAT                         TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|148991633|gb|EE033168.2|EE033168
EST:     CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTAT                         TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|91054260|gb|EB164678.1|EB164678
EST:     CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTAT                         TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|211414779|gb|FL112985.1|FL112985
EST:     CTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTS-AGCCAGCACCTAT                         TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCA-CCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|21843204|gb|BQ703785.1|BQ703785
EST:     CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTAT                         TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|91876143|gb|EB406100.1|EB406100
EST:     CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTAT                         TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|211414778|gb|FL112984.1|FL112984
EST:     CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTAT                         TGTACCTGTCAGTGC
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGC
EST: gi|211414770|gb|FL112976.1|FL112976
EST:     CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTS-ACCAGCACCTAT                         TGTACCTGTCAGTGCACTGGCTGC
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGC
EST: gi|32910960|gb|CF015772.1|CF015772
EST:     CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTAT                         TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|74240960|gb|DT648874.1|DT648874
EST:     CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTAT                         TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|32861117|gb|CF000799.1|CF000799
EST:     CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTAT                         TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|76011555|gb|DT938725.1|DT938725
EST:     CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTAT                         TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|148956696|gb|EC902566.2|EC902566
EST:     CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTAT                         TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|211412220|gb|FL112964.1|FL112964
EST:     CTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCATCCAGCACCTAT                         TGTACCTGTCAGTGCACTG
genomic: CTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCA-CCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTG
EST: gi|149001065|gb|EE038319.2|EE038319
EST:     CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTAT                         TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|91057192|gb|EB167610.1|EB167610
EST:     CCTGTTGTTCCACCTCAAACGTGAGCAGCCCCAGCTGCACCAGCACCTAT                         TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|91878897|gb|EB408854.1|EB408854
EST:     CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCACCACCTAT                         TGTACCTGTCAGTGCACTGGCTGCAACTGCTACCGCCTCAGCAGCTCCTGC
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|149096952|gb|EE182751.2|EE182751
EST:     CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTAT                         TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|211412226|gb|FL112970.1|FL112970
EST:     CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTS-ACCAGCACCTAT                         TGTACCTGTCAGTGCACTGGCTGCAACTGCTACAG
genomic: CCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAG

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), 41 (downstream exon)
Score: 74

GCACCTCCTACTCAGACAGTGCCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATC


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 43

GCACCTCCTACTCAGACAGTGCCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATC


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 53

GCACCTCCTACTCAGACAGTGCCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATC


Block sizes: 44 (upstream exon), 45 (downstream exon)
Score: 31

GCACCTCCTACTCAGACAGTGCCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcg ... tctgaattagTGTACCTGTCAGTGCACTGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTATC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACCTCCTACTCAGACAGTGCCTGTTGTTCCACCTCAAACGTCAGCAGCCCCAGCTGCACCAGCACCTATgtgagcttcgtatttatttgtatgtaaaggcttgatttgtgttaggattggtagtatggatccttttcagctggttctagtgcaggcaacatttgcaatc

- - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC