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

TTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATCCAATCACAGATAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctctctctgtatatgtatatacttaacccctggaaattgcatcccttgctcaaaatggacctccaacatgttcatttattatgatatcgcctag...

Basic information

species Zea mays
transcript GRMZM2G150616_T01
intron # 3
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|211412244|gb|FL229030.1|FL229030
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|78121836|gb|DV540220.1|DV540220
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|211412254|gb|FL229040.1|FL229040
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACGACAATTACTGTTGATGAGATTGCNACACCAGGGGCTGAAGAC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGG-CTGAAGAC
EST: gi|148936370|gb|EC880462.2|EC880462
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|211414795|gb|FL229043.1|FL229043
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|33104534|gb|CF064494.1|CF064494
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|211412252|gb|FL229038.1|FL229038
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACAACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|22715017|gb|BU197555.1|BU197555
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACAACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|149110762|gb|EE190597.2|EE190597
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|148973802|gb|EE024938.2|EE024938
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|149088362|gb|EE177462.2|EE177462
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|91050628|gb|EB161046.1|EB161046
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|116815705|gb|EC858392.1|EC858392
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGTCTGAAGAC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGG-CTGAAGAC
EST: gi|211412253|gb|FL229039.1|FL229039
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|31348886|gb|CD433243.1|CD433243
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACAACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|14204290|gb|BG837967.1|BG837967
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|32838380|gb|CD978058.1|CD978058
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|211412247|gb|FL229033.1|FL229033
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACAACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|211412248|gb|FL229034.1|FL229034
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|211412256|gb|FL229042.1|FL229042
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACAACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|211412243|gb|FL229029.1|FL229029
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACAACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|22542179|gb|BU092617.1|BU092617
EST:     AAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACAACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: AAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|33104065|gb|CF064025.1|CF064025
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|211412250|gb|FL229036.1|FL229036
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACAACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|32855345|gb|CD995026.1|CD995026
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|93013107|gb|EB638627.1|EB638627
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|94473288|gb|EB702246.1|EB702246
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|211412249|gb|FL229035.1|FL229035
EST:     AAAGAACAAGAACATGGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACNACAATTACTGNTTGATGAGATTGCAACACCAGGGCTGAAGAC
genomic: AAAGAACAAGAACATG-ACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTG-TTGATGAGATTGCAACACCAGGGCTGAAGAC
EST: gi|32934430|gb|CF039242.1|CF039242
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|211412245|gb|FL229031.1|FL229031
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACAACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|211412255|gb|FL229041.1|FL229041
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|211412242|gb|FL229028.1|FL229028
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACAACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
EST: gi|211061032|gb|FL204119.1|FL204119
EST:     TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAAT                         ATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC
genomic: TAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACC

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: 628

TTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATCCAATCACAGATAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACCATCTTAAGCTTTGCTGTTCCTGATCAGAGATCTGGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 688

TTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATCCAATCACAGATAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACCATCTTAAGCTTTGCTGTTCCTGATCAGAGATCTGGAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 509

TTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATCCAATCACAGATAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACCATCTTAAGCTTTGCTGTTCCTGATCAGAGATCTGGAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 634

TTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATCCAATCACAGATAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctct ... tgatgttcagATCATTACGACAATTACTGTTGATGAGATTGCAACACCAGGGCTGAAGACCATCTTAAGCTTTGCTGTTCCTGATCAGAGATCTGGAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTAGCACAAAGAAAGCTGACCTGATCCTTGGCGAGATCCAATCACAGATAAAGAACAAGAACATGACCATAGATGTGAAAGCAAACTCGGAGTCAAATgtaaatctctctctgtatatgtatatacttaacccctggaaattgcatcccttgctcaaaatggacctccaacatgttcatttattatgatatcgcctag

- - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctccaac