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 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAACACATCTCGCGGCGGCGGCGGCGGCAGAGACAGGCGGCGGCCGCCGAGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacccgctggctccctattggttgttccccccgtttgatcttattccgtaatggcggtaggatctaatgttgaggaccagctgaaaatatcgca...

Basic information

species Zea mays
transcript GRMZM5G832108_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|71325732|gb|DR799552.1|DR799552
EST:     TGCACGTGAACTTCTATCGCAACT                         ATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
genomic: TGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
EST: gi|30031836|gb|CB833687.1|CB833687
EST:     AGCGGCGTGGGCAGCGTCATCCATGG-GCACGTGAACTTCTATCGCAACT                         ATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
genomic: AGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
EST: gi|15499453|gb|BI595966.1|BI595966
EST:     AGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACT                         ATGGT-AGAACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTT
genomic: AGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAG-ACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTT
EST: gi|15208760|gb|BI430644.1|BI430644
EST:     AGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACT                         ATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
genomic: AGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
EST: gi|31910679|gb|CD651545.1|CD651545
EST:     TCATCCATGGTGCACGTGAACTTCTATCGCAACT                         ATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
genomic: TCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
EST: gi|28361732|gb|CB240088.1|CB240088
EST:     AGCGG-G-GGGCAGCGTCATCCATGG-GCACGTGAACTTCTATCGCAACT                         ATGGTAAGACTTTC-AGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
genomic: AGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
EST: gi|22714268|gb|BU197466.1|BU197466
EST:     AGCGGCGTGGGCAGCGTCATCCATGG-GCACGTGAACTTCTATCGCAACT                         ATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
genomic: AGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
EST: gi|15426765|gb|BI542587.1|BI542587
EST:     AGCGGCGTGGGCAGCGTCATCCATGG-GCACGTGAACTTCTATCGCAACT                         ATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
genomic: AGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
EST: gi|120480881|gb|EH211075.1|EH211075
EST:     AGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACT                         ATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAKAAGGAGCGCCTTG
genomic: AGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
EST: gi|24767175|gb|CA402319.1|CA402319
EST:     AGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACT                         ATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
genomic: AGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
EST: gi|31359739|gb|CD444096.1|CD444096
EST:     AGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACT                         ATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
genomic: AGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
EST: gi|22715359|gb|BU197721.1|BU197721
EST:     AGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACT                         ATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
genomic: AGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
EST: gi|60399534|gb|DN232345.1|DN232345
EST:     TCATCCATGGTGCACGTGAACTTCTATCGCAACT                         ATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
genomic: TCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
EST: gi|30031591|gb|CB833442.1|CB833442
EST:     AGCGGCG-GGGCAGCGTCATCCATGG-GCACGTGAACTTCTATCGCAACT                         ATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
genomic: AGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
EST: gi|29167836|gb|CB411096.1|CB411096
EST:     AGCGG-GTGGGCAGCGTCATCCATGG-GCACGTGAACTTCTATCGCAACT                         ATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
genomic: AGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
EST: gi|31358049|gb|CD442406.1|CD442406
EST:     AGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACT                         ATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
genomic: AGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
EST: gi|28361535|gb|CB239891.1|CB239891
EST:     TCATCCATGG-GCACGTGAACTTCTATCGCAACT                         ATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
genomic: TCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
EST: gi|211245311|gb|FL400477.1|FL400477
EST:     AGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACT                         ATGGTAAGAC-TTYAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
genomic: AGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
EST: gi|20803373|gb|BQ294423.1|BQ294423
EST:     AGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACT                         ATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
genomic: AGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
EST: gi|28873527|gb|CB329505.1|CB329505
EST:     TGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACT                         ATGGT-AGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG
genomic: TGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTG

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: 298

CAAACACATCTCGCGGCGGCGGCGGCGGCAGAGACAGGCGGCGGCCGCCGAGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTGATGCTGAGTTGAAATTAGTGGGTGAATATGGCCTGAGGTGCAAGCGTGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 365

CAAACACATCTCGCGGCGGCGGCGGCGGCAGAGACAGGCGGCGGCCGCCGAGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTGATGCTGAGTTGAAATTAGTGGGTGAATATGGCCTGAGGTGCAAGCGTGA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 207

CAAACACATCTCGCGGCGGCGGCGGCGGCAGAGACAGGCGGCGGCCGCCGAGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTGATGCTGAGTTGAAATTAGTGGGTGAATATGGCCTGAGGTGCAAGCGTGA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 277

CAAACACATCTCGCGGCGGCGGCGGCGGCAGAGACAGGCGGCGGCCGCCGAGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacc ... tgtgacacagATGGTAAGACTTTCAAGAAGCCAAGGCGGCCTTATGAGAAGGAGCGCCTTGATGCTGAGTTGAAATTAGTGGGTGAATATGGCCTGAGGTGCAAGCGTGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAACACATCTCGCGGCGGCGGCGGCGGCAGAGACAGGCGGCGGCCGCCGAGCGGCGTGGGCAGCGTCATCCATGGTGCACGTGAACTTCTATCGCAACTgtaagctacccgctggctccctattggttgttccccccgtttgatcttattccgtaatggcggtaggatctaatgttgaggaccagctgaaaatatcgca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctcccta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcccccc