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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGCGCCTGCTGCGAGGCCAGCCTGCGCCGCCTCGACGCCGGCTACATCGACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccacttggccaccttgccgcattctcattctgcttgcagtgcagctgttgctattatgaattattgtgccgaaatcgctgcag

Basic information

species Zea mays
transcript GRMZM2G176903_T01
intron # 2
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|148939129|gb|EC883560.2|EC883560
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
EST: gi|211147832|gb|FL424917.1|FL424917
EST:     ACCTCTACTACCAGCACCGSGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
EST: gi|211225824|gb|FL402232.1|FL402232
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAA
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAA
EST: gi|71305516|gb|DR788901.1|DR788901
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
EST: gi|67012842|gb|CO441591.1|CO441591
EST:     ATCGAGGATACG                         ATTGGTGAGCTCAAGAA-TTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
genomic: ATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
EST: gi|50335316|gb|CO530442.1|CO530442
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGG
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGG
EST: gi|149075226|gb|EE163727.2|EE163727
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
EST: gi|91873626|gb|EB403583.1|EB403583
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
EST: gi|76291653|gb|DV031221.1|DV031221
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
EST: gi|26457624|gb|CA829207.1|CA829207
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCG
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCG
EST: gi|60355739|gb|DN222712.1|DN222712
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
EST: gi|71441912|gb|DR822962.1|DR822962
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
EST: gi|148968047|gb|EE019380.2|EE019380
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
EST: gi|71449217|gb|DR830267.1|DR830267
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
EST: gi|76283461|gb|DV023029.1|DV023029
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
EST: gi|149084348|gb|EE173792.2|EE173792
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
EST: gi|91878987|gb|EB408944.1|EB408944
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGA
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGA
EST: gi|71769570|gb|DR967507.1|DR967507
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
EST: gi|211403228|gb|FL400071.1|FL400071
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
EST: gi|71313078|gb|DR793066.1|DR793066
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGG--AGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
EST: gi|76932705|gb|DV173124.1|DV173124
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
EST: gi|148990970|gb|EE032401.2|EE032401
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
EST: gi|93016813|gb|EB642333.1|EB642333
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
EST: gi|50324103|gb|CO519229.1|CO519229
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
EST: gi|91877439|gb|EB407396.1|EB407396
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGA-GGTCAAGTACATCGGC
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
EST: gi|60401458|gb|DN234265.1|DN234265
EST:     ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACG                         ATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC
genomic: ACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGC

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: 47 (upstream exon), 49 (downstream exon)
Score: 137

ACGCGCCTGCTGCGAGGCCAGCCTGCGCCGCCTCGACGCCGGCTACATCGACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGCTTGTCAGAGGCCAGCCCAGACACAATCCGCCGTGCGCACGCCGTGCATC


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 66

ACGCGCCTGCTGCGAGGCCAGCCTGCGCCGCCTCGACGCCGGCTACATCGACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGCTTGTCAGAGGCCAGCCCAGACACAATCCGCCGTGCGCACGCCGTGCATC


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 60

ACGCGCCTGCTGCGAGGCCAGCCTGCGCCGCCTCGACGCCGGCTACATCGACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGCTTGTCAGAGGCCAGCCCAGACACAATCCGCCGTGCGCACGCCGTGCATC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 91

ACGCGCCTGCTGCGAGGCCAGCCTGCGCCGCCTCGACGCCGGCTACATCGACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccact ... atcgctgcagATTGGTGAGCTCAAGAAGTTGGTGGAGGAGGGGAAGGTCAAGTACATCGGCTTGTCAGAGGCCAGCCCAGACACAATCCGCCGTGCGCACGCCGTGCATC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGCGCCTGCTGCGAGGCCAGCCTGCGCCGCCTCGACGCCGGCTACATCGACCTCTACTACCAGCACCGCGTCGACACCACCGTCCCCATCGAGGATACGgtctgccacttggccaccttgccgcattctcattctgcttgcagtgcagctgttgctattatgaattattgtgccgaaatcgctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT