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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgtctcatctaggatgtttttaatgttcaaatgccttcaatgttgaaggagggaattgcgaagttgttttgtgatgatatatataatatattgggcagAAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTCCGGTGCCTTATTTCACAAG

Basic information

species Zea mays
transcript GRMZM2G113619_T02
intron # 1
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|78086642|gb|DV515035.1|DV515035
EST:     CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAG                         AAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
genomic: CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAGgtatgcccgc ... tattgggcagAAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
EST: gi|78089708|gb|DV518082.1|DV518082
EST:     CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAG                         AAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
genomic: CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAGgtatgcccgc ... tattgggcagAAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
EST: gi|76280760|gb|DV020328.1|DV020328
EST:     CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAG                         AAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
genomic: CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAGgtatgcccgc ... tattgggcagAAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
EST: gi|91053257|gb|EB163675.1|EB163675
EST:     CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAG                         AAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
genomic: CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAGgtatgcccgc ... tattgggcagAAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
EST: gi|71424785|gb|DR806435.1|DR806435
EST:     CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAG                         AAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
genomic: CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAGgtatgcccgc ... tattgggcagAAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
EST: gi|50325343|gb|CO520469.1|CO520469
EST:     CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAG                         AAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
genomic: CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAGgtatgcccgc ... tattgggcagAAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
EST: gi|91877839|gb|EB407796.1|EB407796
EST:     CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAG                         AAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
genomic: CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAGgtatgcccgc ... tattgggcagAAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
EST: gi|93283253|gb|EB675517.1|EB675517
EST:     CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAG                         AAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
genomic: CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAGgtatgcccgc ... tattgggcagAAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
EST: gi|78080128|gb|DV508540.1|DV508540
EST:     CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAG                         AAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
genomic: CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAGgtatgcccgc ... tattgggcagAAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
EST: gi|6827481|gb|AW331124.1|AW331124
EST:     CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAG                         AAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
genomic: CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAGgtatgcccgc ... tattgggcagAAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
EST: gi|37419826|gb|CF647598.1|CF647598
EST:     CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAG                         AAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
genomic: CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAGgtatgcccgc ... tattgggcagAAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
EST: gi|32919341|gb|CF024153.1|CF024153
EST:     CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAG                         AAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
genomic: CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAGgtatgcccgc ... tattgggcagAAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
EST: gi|91057080|gb|EB167498.1|EB167498
EST:     CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAG                         AAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
genomic: CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAGgtatgcccgc ... tattgggcagAAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
EST: gi|71766653|gb|DR964590.1|DR964590
EST:     CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAG                         AAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
genomic: CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAGgtatgcccgc ... tattgggcagAAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
EST: gi|71311806|gb|DR792364.1|DR792364
EST:     CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAG                         AAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
genomic: CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAGgtatgcccgc ... tattgggcagAAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
EST: gi|91049342|gb|EB159760.1|EB159760
EST:     CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAG                         AAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
genomic: CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAGgtatgcccgc ... tattgggcagAAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
EST: gi|76291932|gb|DV031500.1|DV031500
EST:     CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAG                         AAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC
genomic: CCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAGgtatgcccgc ... tattgggcagAAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTC

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 3 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 11

CTTTCGTGGCCTTCCTTTTCCGGCGGCCACAAGTGGGCGAGCGGCGGCGCCCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAGgtatgcccgc ... tattgggcagAAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTCCGGTGCCTTATTTCACAAG


Block sizes: 49 (upstream exon), 25 (downstream exon)
Score: 13

CTTTCGTGGCCTTCCTTTTCCGGCGGCCACAAGTGGGCGAGCGGCGGCGCCCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAGgtatgcccgc ... tattgggcagAAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTCCGGTGCCTTATTTCACAAG


Block sizes: 48 (upstream exon), 32 (downstream exon)
Score: 11

CTTTCGTGGCCTTCCTTTTCCGGCGGCCACAAGTGGGCGAGCGGCGGCGCCCTTCACCAGGTCTTCGTCGGGCCCTTCACCGGCGACGAGCATCCACCAGgtatgcccgc ... tattgggcagAAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTCCGGTGCCTTATTTCACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaggagggaattgcgaagttgttttgtgatgatatatataatatattgggcagAAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTCCGGTGCCTTATTTCACAAG
                    ttgttttgtgatgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgtctcatctaggatgtttttaatgttcaaatgccttcaatgttgaaggagggaattgcgaagttgttttgtgatgatatatataatatattgggcagAAACGTGGAGCTCAGAGCATTGGTGCCTCTTTCCTCTTTCACCAAGGATTCCGGTGCCTTATTTCACAAG

- - - - - - - - tgttttt
- - - - - - - - - - - - - - - - - gccttca
- - - - - - - - - - - - - - - - - - - - - tgttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgat