Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggcttaagactcttctcttcgactgctgcttgtagcttactttatttgttgaacactgagcatcaccatcctgatgcctctggatgcgcag

Basic information

species Zea mays
transcript GRMZM2G022019_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|18169348|gb|BM339188.1|BM339188
EST:     AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT                         GACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
EST: gi|87157574|gb|DY402363.1|DY402363
EST:     AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT                         GACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
EST: gi|31250200|gb|CD219224.1|CD219224
EST:     AGTAGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT                         GACGACTCTAAGAGAGACAAGCCCAGCAGGGGTGGGCGGTACACCGTGTAA
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
EST: gi|17931403|gb|BM268363.1|BM268363
EST:     AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT                         GACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
EST: gi|17931601|gb|BM268561.1|BM268561
EST:     AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT                         GACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
EST: gi|21987193|gb|BQ778721.1|BQ778721
EST:     AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT                         GACGACTCTAAG
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAG
EST: gi|211062307|gb|FL474478.1|FL474478
EST:     AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT                         GACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
EST: gi|18163629|gb|BM333468.1|BM333468
EST:     AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT                         GACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
EST: gi|4887347|gb|AI677446.1|AI677446
EST:     AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT                         GACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
EST: gi|32851639|gb|CD991320.1|CD991320
EST:     AGGGGAAGGATGTCATCGACTACAACGACAAGATCACGGACACTTTCCAT                         GACGACTCTAAGAGAGACAAGCCCAGCAGA
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGA
EST: gi|50322671|gb|CO517797.1|CO517797
EST:     AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT                         GACGACTTTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACCCCGTGTAA
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
EST: gi|76010904|gb|DT938074.1|DT938074
EST:     AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT                         GACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
EST: gi|78026174|gb|DV494561.1|DV494561
EST:     AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT                         GACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
EST: gi|16918090|gb|BM073572.1|BM073572
EST:     AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT                         GACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
EST: gi|71437159|gb|DR818209.1|DR818209
EST:     AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT                         GACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
EST: gi|76010903|gb|DT938073.1|DT938073
EST:     AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT                         GACGACTTTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
EST: gi|50322672|gb|CO517798.1|CO517798
EST:     AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT                         GACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
EST: gi|32164823|gb|CD670141.1|CD670141
EST:     AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT                         GACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
EST: gi|71758459|gb|DR956396.1|DR956396
EST:     AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT                         GACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
EST: gi|18168337|gb|BM338177.1|BM338177
EST:     AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT                         GACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
EST: gi|31558353|gb|CD527565.1|CD527565
EST:     AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT                         GACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
EST: gi|31250144|gb|CD219168.1|CD219168
EST:     AGTAGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT                         GACGACTCTAAGAGAGACAAGCCCAGCAGGGGTGGGCGGTACACCGTGTAA
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
EST: gi|16925812|gb|BM078880.1|BM078880
EST:     AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT                         GACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
EST: gi|91049925|gb|EB160343.1|EB160343
EST:     AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCAT                         GACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA
genomic: AGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAA

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), 49 (downstream exon)
Score: 157

GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAAGCTGGACGTCAAGAAGGCCGTTGCTTTGGATTGGAAGTGGAGAGCGGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 275

GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAAGCTGGACGTCAAGAAGGCCGTTGCTTTGGATTGGAAGTGGAGAGCGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 176

GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAAGCTGGACGTCAAGAAGGCCGTTGCTTTGGATTGGAAGTGGAGAGCGGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 157

GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggctta ... ggatgcgcagGACGACTCTAAGAGAGACAAGCCCAGCAGAGGTGGGCGGTACACCGTGTAAGCTGGACGTCAAGAAGGCCGTTGCTTTGGATTGGAAGTGGAGAGCGGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAACATTGGCAAGAAGTGGAAGGATGTCATCGACTACAACGACAAGATCACGTACACTTTCCATgtatggcttaagactcttctcttcgactgctgcttgtagcttactttatttgttgaacactgagcatcaccatcctgatgcctctggatgcgcag

- - - - - - - - AGTGGA
- - - - - - - - - TGGAAG
- - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - AGATCA