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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaattcacttattaacccattccatttaccgtcgttcacggtatacctatcgattgccaactgtttcgctaagctttttttttccgtccatgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACTCTAAAGCTGTCTTGCTATTCAAGTCTGGGTGATTGTCGCAGCCAATACA

Basic information

species Zea mays
transcript GRMZM2G472231_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G472231_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g15260.1 (Oryza sativa), 3'ss of exon 2
-----ttgaattcacttattaacccattccatttaccgtcgttcacggtatacctatcg--attgccaactgtttcgctaagctttttttttccgtccatgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACTCTAAAGCTGTCTTGCTATTCAAGTCTGGGTGATTGTCGCAGCCAATACA
        | || | | || ||   || ||  ||     | ||    |  ||   |  |  ||  ||  |  |||| |  |    |||||  |      || |||||| || ||||| || |||||||| ||||||||||| ||||| |||||||| |||||||| |||||||||||||| |||||||||||| || ||| ||||  
acttcacaactttagtaatgaatttatgcc-cttgtttccatttgatgcgtattgaatgttatgccctgcaatttcacccaagcctttttgcc------tggtgcagGGTCCTACGTAACACACGAGACGAACTACTTTGTGTATTTTTACATCGATTCTAAAGCCGTCTTGCTATTCAAATCTGGGTGATTGGCGTAGCTAATATC
















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|211202480|gb|FL075815.1|FL075815
EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCCTACGTGACGCACGAGACAAACTACTTTATATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|29130865|gb|CB381569.1|CB381569
EST:     CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|32939186|gb|CF044005.1|CF044005
EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCCTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|18164831|gb|BM334670.1|BM334670
EST:     CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|32849974|gb|CD989655.1|CD989655
EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCCTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|211199915|gb|FL075798.1|FL075798
EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|76281556|gb|DV021124.1|DV021124
EST:     CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|211202481|gb|FL075816.1|FL075816
EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCCTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|211199921|gb|FL075804.1|FL075804
EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCCTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|211199918|gb|FL075801.1|FL075801
EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATTGTCGGCCGCAACTTCG                         GTTCCTACGTGACGCACGAGACAAACTACTTTAWATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|211199917|gb|FL075800.1|FL075800
EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCCTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|78021298|gb|DV489685.1|DV489685
EST:     CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|30306731|gb|CD001404.1|CD001404
EST:     CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|60399080|gb|DN231894.1|DN231894
EST:     CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|211199919|gb|FL075802.1|FL075802
EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCCTACGTGACGCACGAGACAAACTACTTTATATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|211202478|gb|FL075813.1|FL075813
EST:     CGACAAGAACCACGGCCA-ACCTGGCACTGCATCGTCGGGCGSAACTTCG                         GTTCTTACGTGACGCACGAGACA
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACA
EST: gi|29946095|gb|CB815976.1|CB815976
EST:     CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|211202479|gb|FL075814.1|FL075814
EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCTTACGTGACGCAC
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCAC
EST: gi|18181427|gb|BM382637.1|BM382637
EST:     GCATCGTCGGCCGCAACTTCG                         GTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: GCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|29130306|gb|CB381010.1|CB381010
EST:     CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|30704768|gb|CD058596.1|CD058596
EST:     CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|18165144|gb|BM334983.1|BM334983
EST:     CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|18171185|gb|BM341025.1|BM341025
EST:     CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|31612227|gb|CD568849.1|CD568849
EST:     CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|67013294|gb|CO442043.1|CO442043
EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCCTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|60356545|gb|DN223518.1|DN223518
EST:     CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|211202477|gb|FL075812.1|FL075812
EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|211540674|gb|FL444170.1|FL444170
EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCCTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|18170938|gb|BM340778.1|BM340778
EST:     CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|5740448|gb|AI948138.1|AI948138
EST:     CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|29946093|gb|CB815975.1|CB815975
EST:     CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|211199924|gb|FL075807.1|FL075807
EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|76281555|gb|DV021123.1|DV021123
EST:     CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTTTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
EST: gi|211199922|gb|FL075805.1|FL075805
EST:     CGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCAACTTCG                         GTTCCTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT
genomic: CGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACT

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), 48 (downstream exon)
Score: 219

GAGAAGCACAGTATGGAGAAGGACATCGCGGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACTCTAAAGCTGTCTTGCTATTCAAGTCTGGGTGATTGTCGCAGCCAATACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 135

GAGAAGCACAGTATGGAGAAGGACATCGCGGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACTCTAAAGCTGTCTTGCTATTCAAGTCTGGGTGATTGTCGCAGCCAATACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

GAGAAGCACAGTATGGAGAAGGACATCGCGGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACTCTAAAGCTGTCTTGCTATTCAAGTCTGGGTGATTGTCGCAGCCAATACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 72

GAGAAGCACAGTATGGAGAAGGACATCGCGGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCAACTTCGgtaatgctct ... catgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACTCTAAAGCTGTCTTGCTATTCAAGTCTGGGTGATTGTCGCAGCCAATACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacctatcgattgccaactgtttcgctaagctttttttttccgtccatgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACTCTAAAGCTGTCTTGCTATTCAAGTCTGGGTGATTGTCGCAGCCAATACA
                              ctttttttttccgtcc  CT-rich tract
                          taagcttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaattcacttattaacccattccatttaccgtcgttcacggtatacctatcgattgccaactgtttcgctaagctttttttttccgtccatgatgcagGTTCTTACGTGACGCACGAGACAAACTACTTTGTATATTTCTACATCGACTCTAAAGCTGTCTTGCTATTCAAGTCTGGGTGATTGTCGCAGCCAATACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - ccattcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtttc