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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttcttttttccgtttcggttcatcttctatcaaagtacatgcccatgctatgccattttcatcttcgtttcccttaaactgcaaacacacatt...

Basic information

species Zea mays
transcript GRMZM2G118316_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118316_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os12g07060.1 (Oryza sativa), 5'ss of exon 14
GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttcttttttccgtttcggttcatcttctatcaaagtacatgcccatg-ctatgccattttcatcttcgtttcccttaaactgcaaacacacatt--------------------------------------------------------------------------------------------------
 |||||||||| |||   || || |||||||||| |||||||||||||||  || || |||||||||| |||||||    ||||| |      |       | |  |       |   |    ||| ||  |   ||| ||| | | |||    |||||| ||  |     ||                                                                                                  
ATCAGAGAGGATCCTGTCTTCCGTAGAGAAGGCAACCATGTGCATGTTGACGCTATTATAAGCATTGCCCAGgtcaccactctttctgtttggtttccctgtttgatgctgttatgattatatatgacttaggtctttacatatacattttatgtaaactaca--cctcttttaggaaaaaggaaaatcatgtagcgcatgatgaccaattctgctgtctatgcagatattccttttatgattaatagttctaaaactgcttgattttcag
















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|148947432|gb|EC892855.2|EC892855
EST:     GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG                         GCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
genomic: GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttc ... tcgtttacagGCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
EST: gi|149101261|gb|EE187373.2|EE187373
EST:     GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG                         GCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
genomic: GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttc ... tcgtttacagGCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
EST: gi|60397506|gb|DN230322.1|DN230322
EST:     GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG                         GCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
genomic: GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttc ... tcgtttacagGCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
EST: gi|93017255|gb|EB642775.1|EB642775
EST:     GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG                         GCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
genomic: GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttc ... tcgtttacagGCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
EST: gi|71757144|gb|DR955081.1|DR955081
EST:     GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG                         GCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
genomic: GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttc ... tcgtttacagGCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
EST: gi|211267316|gb|FL091730.1|FL091730
EST:     GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG                         GCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
genomic: GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttc ... tcgtttacagGCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
EST: gi|76922540|gb|DV169051.1|DV169051
EST:     GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG                         GCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
genomic: GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttc ... tcgtttacagGCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
EST: gi|17929416|gb|BM266376.1|BM266376
EST:     GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG                         GCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
genomic: GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttc ... tcgtttacagGCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
EST: gi|86469547|gb|DY235917.1|DY235917
EST:     GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG                         GCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
genomic: GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttc ... tcgtttacagGCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
EST: gi|60398827|gb|DN231643.1|DN231643
EST:     GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG                         GCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
genomic: GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttc ... tcgtttacagGCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
EST: gi|211267317|gb|FL091731.1|FL091731
EST:     GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG                         GCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
genomic: GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttc ... tcgtttacagGCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
EST: gi|71769071|gb|DR967008.1|DR967008
EST:     GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG                         GCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
genomic: GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttc ... tcgtttacagGCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
EST: gi|71427930|gb|DR808980.1|DR808980
EST:     GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG                         GCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
genomic: GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttc ... tcgtttacagGCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
EST: gi|211435107|gb|FL442358.1|FL442358
EST:     CCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG                         GCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
genomic: CCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttc ... tcgtttacagGCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
EST: gi|6022509|gb|AW067542.1|AW067542
EST:     GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG                         GCTGTCCTAGGTGGAACTGTCACTGTACCAACCCTCACTGGAAATGTTACA
genomic: GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttc ... tcgtttacagGCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
EST: gi|37397730|gb|CF636173.1|CF636173
EST:     GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG                         GCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
genomic: GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttc ... tcgtttacagGCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
EST: gi|32847340|gb|CD987021.1|CD987021
EST:     GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG                         GCTGTCCTAGGTGGAACTGTCACGGT
genomic: GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttc ... tcgtttacagGCTGTCCTAGGTGGAACTGTCACGGT
EST: gi|67040336|gb|CO466591.1|CO466591
EST:     GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG                         GCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
genomic: GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttc ... tcgtttacagGCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
EST: gi|40337178|gb|CK371248.1|CK371248
EST:     GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAG                         GCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA
genomic: GAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttc ... tcgtttacagGCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACA

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: 75

GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttc ... tcgtttacagGCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112

GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttc ... tcgtttacagGCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 106

GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttc ... tcgtttacagGCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 87

GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttc ... tcgtttacagGCTGTCCTAGGTGGAACTGTCACGGTACCAACCCTCACTGGAAATGTTACAGTCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttcttttttccgtttcggttcatcttctatcaaagtacatgcccatgctatgccattttcatcttcgtttcccttaaactgcaaacacacatt

- - - - - - - - - - -  AAGAGA