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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGCATTTGGACTCCTACTTTGAAAAACCAGATAATATACGACGACGGTTCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatctgaactggttgtcattattttctataaggcccagctactgtttgagcatctaaaaagcttatttacaattaccgcaccag

Basic information

species Zea mays
transcript GRMZM2G304362_T01
intron # 14
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|32932369|gb|CF037181.1|CF037181
EST:     TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACACGGCGGTCGACCG
genomic: TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
EST: gi|32934636|gb|CF039448.1|CF039448
EST:     TCTGTCCAGAGGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
genomic: TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
EST: gi|33093398|gb|CF053392.1|CF053392
EST:     CGGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
genomic: CGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
EST: gi|28931227|gb|CB334588.1|CB334588
EST:     TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
genomic: TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
EST: gi|13150171|gb|BG320493.1|BG320493
EST:     TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTTGACCG
genomic: TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
EST: gi|32907431|gb|CF012244.1|CF012244
EST:     TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
genomic: TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
EST: gi|32934774|gb|CF039586.1|CF039586
EST:     TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
genomic: TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
EST: gi|29577171|gb|CB617283.1|CB617283
EST:     TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
genomic: TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
EST: gi|32933139|gb|CF037951.1|CF037951
EST:     TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
genomic: TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
EST: gi|32945530|gb|CF050349.1|CF050349
EST:     TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATAGCGGTCGACCG
genomic: TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
EST: gi|32934883|gb|CF039695.1|CF039695
EST:     TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
genomic: TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
EST: gi|32933143|gb|CF037955.1|CF037955
EST:     TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
genomic: TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
EST: gi|31356810|gb|CD441167.1|CD441167
EST:     TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
genomic: TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
EST: gi|32931555|gb|CF036367.1|CF036367
EST:     TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
genomic: TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
EST: gi|91053675|gb|EB164093.1|EB164093
EST:     TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
genomic: TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
EST: gi|211165342|gb|FL103230.1|FL103230
EST:     TCTGTCCAGAAGATAGCAGAAATCCCAGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTTGACCG
genomic: TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
EST: gi|211165339|gb|FL103227.1|FL103227
EST:     TCTGTCCAGAAGATAGCAGAAATCCCAGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTTGACCG
genomic: TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
EST: gi|91879055|gb|EB409012.1|EB409012
EST:     CTGTCCAGAAGATAGCAGAGATCCCCGGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
genomic: CTGTCCAGAAGATAGCAGAAATCCC-GGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
EST: gi|33094392|gb|CF054386.1|CF054386
EST:     TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
genomic: TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
EST: gi|32935070|gb|CF039882.1|CF039882
EST:     TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
genomic: TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
EST: gi|31405947|gb|CD484679.1|CD484679
EST:     TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
genomic: TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
EST: gi|32932471|gb|CF037283.1|CF037283
EST:     TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
genomic: TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
EST: gi|211165344|gb|FL103232.1|FL103232
EST:     TCTGTCCAGAAGATAGCAGAAATCCCAGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTTGACCG
genomic: TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
EST: gi|32932118|gb|CF036930.1|CF036930
EST:     TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAA                         AACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG
genomic: TCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCG

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: 416

TGGGCATTTGGACTCCTACTTTGAAAAACCAGATAATATACGACGACGGTTCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCGCGGATGCTACATCGACCAAAGCCAGAGCCTCAATGTCCACATGGAGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

TGGGCATTTGGACTCCTACTTTGAAAAACCAGATAATATACGACGACGGTTCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCGCGGATGCTACATCGACCAAAGCCAGAGCCTCAATGTCCACATGGAGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 120

TGGGCATTTGGACTCCTACTTTGAAAAACCAGATAATATACGACGACGGTTCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCGCGGATGCTACATCGACCAAAGCCAGAGCCTCAATGTCCACATGGAGCAA


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 51

TGGGCATTTGGACTCCTACTTTGAAAAACCAGATAATATACGACGACGGTTCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatct ... accgcaccagAACTGTTTGGGAGATCAAGCAGAAAACTTTAGTTGACATGGCGGTCGACCGCGGATGCTACATCGACCAAAGCCAGAGCCTCAATGTCCACATGGAGCAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGCATTTGGACTCCTACTTTGAAAAACCAGATAATATACGACGACGGTTCTGTCCAGAAGATAGCAGAAATCCCGGACGATCTTAAAGCAATCTACAAgtatgtatctgaactggttgtcattattttctataaggcccagctactgtttgagcatctaaaaagcttatttacaattaccgcaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA