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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctttcggcctatctgcctttaattctctatgcaaacacaggcacatgcacccatcttttcgtttaagaaagcatacacattgcttggtgactgacgatggcaaacgggaattttatccgatagGTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACGCCGGACCGGGCGAAGGCGGCCAAGCGGCTGGTGGAGTGCGCCGTTCGCG

Basic information

species Zea mays
transcript GRMZM2G069713_T02
intron # 3
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|76012866|gb|DT940036.1|DT940036
EST:     AGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGG                         GTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
genomic: AGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGGgtagctttcg ... tatccgatagGTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
EST: gi|149087973|gb|EE287216.2|EE287216
EST:     AGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGG                         GTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
genomic: AGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGGgtagctttcg ... tatccgatagGTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
EST: gi|78110759|gb|DV529157.1|DV529157
EST:     AGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGG                         GTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
genomic: AGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGGgtagctttcg ... tatccgatagGTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
EST: gi|148976022|gb|EE025881.2|EE025881
EST:     AGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGG                         GTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
genomic: AGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGGgtagctttcg ... tatccgatagGTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
EST: gi|86474250|gb|DY240620.1|DY240620
EST:     AGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGG                         GTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
genomic: AGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGGgtagctttcg ... tatccgatagGTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
EST: gi|50325661|gb|CO520787.1|CO520787
EST:     AGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGG                         GTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
genomic: AGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGGgtagctttcg ... tatccgatagGTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
EST: gi|148935756|gb|EC879800.2|EC879800
EST:     GATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGG                         GTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
genomic: GATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGGgtagctttcg ... tatccgatagGTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
EST: gi|149104582|gb|EE290033.2|EE290033
EST:     AAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTCCCGACGGG                         GTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
genomic: AAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGGgtagctttcg ... tatccgatagGTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
EST: gi|148945978|gb|EC891272.2|EC891272
EST:     AGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGG                         GTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
genomic: AGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGGgtagctttcg ... tatccgatagGTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
EST: gi|78087334|gb|DV515727.1|DV515727
EST:     AGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGG                         GTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
genomic: AGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGGgtagctttcg ... tatccgatagGTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
EST: gi|74246502|gb|DT654416.1|DT654416
EST:     AGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGG                         GTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
genomic: AGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGGgtagctttcg ... tatccgatagGTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
EST: gi|91878208|gb|EB408165.1|EB408165
EST:     AGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGG                         GTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
genomic: AGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGGgtagctttcg ... tatccgatagGTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
EST: gi|50329314|gb|CO524440.1|CO524440
EST:     AGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGG                         GTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG
genomic: AGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGGgtagctttcg ... tatccgatagGTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACG

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: 40 (upstream exon), 48 (downstream exon)
Score: 13

CGACTACTGCGTCAAGGACTGCGGTGTCATCTCTACGCCGGAGGTGACGCAGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGGgtagctttcg ... tatccgatagGTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACGCCGGACCGGGCGAAGGCGGCCAAGCGGCTGGTGGAGTGCGCCGTTCGCG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 51

CGACTACTGCGTCAAGGACTGCGGTGTCATCTCTACGCCGGAGGTGACGCAGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGGgtagctttcg ... tatccgatagGTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACGCCGGACCGGGCGAAGGCGGCCAAGCGGCTGGTGGAGTGCGCCGTTCGCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 111

CGACTACTGCGTCAAGGACTGCGGTGTCATCTCTACGCCGGAGGTGACGCAGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGGgtagctttcg ... tatccgatagGTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACGCCGGACCGGGCGAAGGCGGCCAAGCGGCTGGTGGAGTGCGCCGTTCGCG


Block sizes: 43 (upstream exon), 43 (downstream exon)
Score: 13

CGACTACTGCGTCAAGGACTGCGGTGTCATCTCTACGCCGGAGGTGACGCAGAAGAGGATCAGCAGCAGTGACCAATTTATCATCCTCGCTACCGACGGGgtagctttcg ... tatccgatagGTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACGCCGGACCGGGCGAAGGCGGCCAAGCGGCTGGTGGAGTGCGCCGTTCGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagcatacacattgcttggtgactgacgatggcaaacgggaattttatccgatagGTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACGCCGGACCGGGCGAAGGCGGCCAAGCGGCTGGTGGAGTGCGCCGTTCGCG
                    gactgac  putative branch site (score: 13)
 ttttatcc  putative PPT
 aattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagctttcggcctatctgcctttaattctctatgcaaacacaggcacatgcacccatcttttcgtttaagaaagcatacacattgcttggtgactgacgatggcaaacgggaattttatccgatagGTATGGGACGTGCTCTCCAACGACGAGGCGGTACATATCGTGGCGGGGACGCCGGACCGGGCGAAGGCGGCCAAGCGGCTGGTGGAGTGCGCCGTTCGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG