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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgttgaactgccctaaattgcttttatgctgtaagatgtacagttttacgccttgcatcgatagttcctgctgttctgactctgttgtgctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGAAAAGCTTCTTTCTCATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGG

Basic information

species Zea mays
transcript GRMZM2G037743_T02
intron # 1
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|4834957|gb|AI670183.1|AI670183
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAG                         GTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|60399258|gb|DN232072.1|DN232072
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAG                         GTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|71307535|gb|DR789986.1|DR789986
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAG                         GTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|211032355|gb|FL404689.1|FL404689
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAG                         GTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|211496712|gb|FL402047.1|FL402047
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAG                         -TATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|211034438|gb|FL381557.1|FL381557
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAG                         GTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|211303219|gb|FL395619.1|FL395619
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAG                         -TATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|60339444|gb|DN206417.1|DN206417
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAG                         GTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|78026862|gb|DV495249.1|DV495249
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAG                         GTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|211277143|gb|FL403154.1|FL403154
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAG                         GTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|211401579|gb|FL440168.1|FL440168
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAG                         GTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|211212627|gb|FL412323.1|FL412323
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAG                         GTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|211264292|gb|FL408789.1|FL408789
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAG                         GTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|50330964|gb|CO526090.1|CO526090
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAG                         GTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|211463969|gb|FL402454.1|FL402454
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCA-                         GTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|211224183|gb|FL422640.1|FL422640
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAG                         GTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|211363155|gb|FL382231.1|FL382231
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCA-                         GTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|211518774|gb|FL409538.1|FL409538
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAG                         -TATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|211334965|gb|FL423295.1|FL423295
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAG                         GTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|60344084|gb|DN211057.1|DN211057
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAG                         GTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|211207325|gb|FL408317.1|FL408317
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAG                         GTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|211374539|gb|FL412450.1|FL412450
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAG                         GTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|211063342|gb|FL405199.1|FL405199
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAG                         GTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|211332698|gb|FL418372.1|FL418372
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAG                         GTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|211288084|gb|FL387842.1|FL387842
EST:     GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCA-                         GTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: GACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
EST: gi|60357036|gb|DN224009.1|DN224009
EST:     CAAGGACATCATCCACTCCCGCAG                         GTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA
genomic: CAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGA

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), 48 (downstream exon)
Score: 112

ATTCCTCCGCCGCAGGACCGTGGGACGAGGCCGAGACGGAGATCCTCCGCGACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGAAAAGCTTCTTTCTCATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 146

ATTCCTCCGCCGCAGGACCGTGGGACGAGGCCGAGACGGAGATCCTCCGCGACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGAAAAGCTTCTTTCTCATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 88

ATTCCTCCGCCGCAGGACCGTGGGACGAGGCCGAGACGGAGATCCTCCGCGACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGAAAAGCTTCTTTCTCATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 86

ATTCCTCCGCCGCAGGACCGTGGGACGAGGCCGAGACGGAGATCCTCCGCGACGTCGAGCCCATCGTGAATATCGTCAAGGACATCATCCACTCCCGCAGgtcagcttcg ... gctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGAAAAGCTTCTTTCTCATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttacgccttgcatcgatagttcctgctgttctgactctgttgtgctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGAAAAGCTTCTTTCTCATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGG
                              ttctgac  putative branch site (score: 86)
                                               tataaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgttgaactgccctaaattgcttttatgctgtaagatgtacagttttacgccttgcatcgatagttcctgctgttctgactctgttgtgctataacagGTATAAAAATGGTGAATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGAAAAGCTTCTTTCTCATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- tgttgaa
- - - - - tgcccta
- - - - - - - - - -ttgcttt
- - - - - - - - - - - - - tatgctg
- - - - - - - - - - - - - - - - - - gatgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - ccttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgttgt