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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttccagcctgctaatcacacatctgtgttattaggcgcttttgtccacttacaattcacattactgtttccttagatatcctccatctgggaaa...

Basic information

species Zea mays
transcript GRMZM2G143462_T06
intron # 5
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|211394218|gb|FL229512.1|FL229512
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|74242202|gb|DT650116.1|DT650116
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|148995692|gb|EE034914.2|EE034914
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|89759371|gb|DY688230.1|DY688230
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|71764241|gb|DR962178.1|DR962178
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|30306905|gb|CD001578.1|CD001578
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAA
EST: gi|32936801|gb|CF041620.1|CF041620
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|211488314|gb|FK957004.1|FK957004
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|148947026|gb|EC892323.2|EC892323
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|89758471|gb|DY687642.1|DY687642
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|89761592|gb|DY689541.1|DY689541
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|9731840|gb|BE510592.1|BE510592
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|211394219|gb|FL229513.1|FL229513
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|211394220|gb|FL229514.1|FL229514
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|78111156|gb|DV529553.1|DV529553
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|148999208|gb|EE036127.2|EE036127
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|211491194|gb|FK957015.1|FK957015
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGT
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGT
EST: gi|93280956|gb|EB673220.1|EB673220
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|149095756|gb|EE181396.2|EE181396
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|71771539|gb|DR969476.1|DR969476
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|32805412|gb|CD957648.1|CD957648
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
EST: gi|76912415|gb|DV164721.1|DV164721
EST:     GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACA                         GGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA
genomic: GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAA

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: 45 (upstream exon), 49 (downstream exon)
Score: 404

GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAATGTTGACACAATAATTAACCAGCTAATGGAGATGGGTGGGGGCAGTTGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 150

GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAATGTTGACACAATAATTAACCAGCTAATGGAGATGGGTGGGGGCAGTTGG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 154

GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAATGTTGACACAATAATTAACCAGCTAATGGAGATGGGTGGGGGCAGTTGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 265

GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttcc ... tttttgctagGGCACCTAACACACATGACAATGCGGCATCAAATCTTCTGTCTGGAAGGAATGTTGACACAATAATTAACCAGCTAATGGAGATGGGTGGGGGCAGTTGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGGCACCAATTACAACTTCTCAGCCTGAAGGACTTCCTGCACAgtatatttccagcctgctaatcacacatctgtgttattaggcgcttttgtccacttacaattcacattactgtttccttagatatcctccatctgggaaa

- - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctccatc