Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGGAAGAGGTAAATATAGTGAGGTCTTTGAAGGCATCAATGTTAACAATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaaggaatatgctgccttttctttgcaacattttcccttgcacattctgttttcaagtgaatttacagttttgatgatagaagttggtgccaaagagttactgtcatgaacgtagtcatcttcatggtgggtcttttaacatacccttcatatgtcttggcag

Basic information

species Zea mays
transcript GRMZM2G047855_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047855_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g55389.1 (Oryza sativa), 5'ss of exon 2
AGTTGGAAGAGGTAAATATAGTGAGGTCTTTGAAGGCATCAATGTTAACAATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaaggaatatgctgccttttctttgcaacattttcccttgcacattctgttttcaagtgaatttacagttttgatgatagaagttggtgccaaagagttactgtcatgaacgtagtcatcttcatggtgggtcttttaacatacccttcatatgtcttggcag
|||||||||||||||||||||||| ||||||||||||||||||||||||||  |||||||||||||||| ||||| || |||||||| ||||||||||||||| || |  ||   |  || || || |||  ||    |    ||| |      ||| | ||   |  || ||  | |    | ||                                                                                   
AGTTGGAAGAGGTAAATATAGTGAAGTCTTTGAAGGCATCAATGTTAACAACAATGAGAAATGCATCATCAAGATACTCAAGCCTGTGAAGAAAAAGAAGgtatttaattgatcttattgactgttttttttaattgctagtgttgaa------gttcttaacctacctttcatatgtttgaacag-----------------------------------------------------------------------------------
















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|67025945|gb|CO454694.1|CO454694
EST:     ATAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|67040594|gb|CO466849.1|CO466849
EST:     ATAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|60357494|gb|DN224467.1|DN224467
EST:     ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|149072965|gb|EE161226.2|EE161226
EST:     ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGGTCCAA-CAT
genomic: ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGG-TCCAAACAT
EST: gi|32870874|gb|CF010556.1|CF010556
EST:     ATAATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGGGGAGGTCCAAACATT
genomic: ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|148932884|gb|EE285654.2|EE285654
EST:     ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|149039473|gb|EE046613.2|EE046613
EST:     ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|149109955|gb|EE293764.2|EE293764
EST:     TTATGAGAAATGCATCATTAAGATCCCTTAAGCCCGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: TTATGAGAAATGCATCATTAAGATCC-TTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|87156044|gb|DY400833.1|DY400833
EST:     ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|31911129|gb|CD651772.1|CD651772
EST:     ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|149104221|gb|EE289654.2|EE289654
EST:     ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|149072883|gb|EE161139.2|EE161139
EST:     ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|60353455|gb|DN220428.1|DN220428
EST:     ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|149097607|gb|EE183500.2|EE183500
EST:     ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|211275425|gb|FK954598.1|FK954598
EST:     ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCT
genomic: ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCT
EST: gi|211273622|gb|FK954596.1|FK954596
EST:     ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACT-CAGAATCTCTGTGGAGGTCC
genomic: ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCC
EST: gi|30031785|gb|CB833636.1|CB833636
EST:     ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|148971083|gb|EE021924.2|EE021924
EST:     ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|31997699|gb|CD661721.1|CD661721
EST:     ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|30705447|gb|CD058786.1|CD058786
EST:     ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|71446427|gb|DR827477.1|DR827477
EST:     ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAG                         ATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
genomic: ATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATT
EST: gi|71441899|gb|DR822949.1|DR822949
EST:     TTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAAGAAC                         ATCAAAAGGAAGATCAAAATACTTCAAAATCTCTGTGGAGGTCCAAACAT
genomic: TTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAA-GAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACAT

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), 46 (downstream exon)
Score: 301

AGTTGGAAGAGGTAAATATAGTGAGGTCTTTGAAGGCATCAATGTTAACAATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATTGTGAAGTTGCTTGATATTGTCAGAGATCAGCATTCAAAGACTCCCAGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 400

AGTTGGAAGAGGTAAATATAGTGAGGTCTTTGAAGGCATCAATGTTAACAATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATTGTGAAGTTGCTTGATATTGTCAGAGATCAGCATTCAAAGACTCCCAGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 503

AGTTGGAAGAGGTAAATATAGTGAGGTCTTTGAAGGCATCAATGTTAACAATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATTGTGAAGTTGCTTGATATTGTCAGAGATCAGCATTCAAAGACTCCCAGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 201

AGTTGGAAGAGGTAAATATAGTGAGGTCTTTGAAGGCATCAATGTTAACAATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaag ... gtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATTGTGAAGTTGCTTGATATTGTCAGAGATCAGCATTCAAAGACTCCCAGTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGGAAGAGGTAAATATAGTGAGGTCTTTGAAGGCATCAATGTTAACAATTATGAGAAATGCATCATTAAGATCCTTAAGCCTGTCAAGAAAAAGAAGgtacttgaaggaatatgctgccttttctttgcaacattttcccttgcacattctgttttcaagtgaatttacagttttgatgatagaagttggtgccaaagagttactgtcatgaacgtagtcatcttcatggtgggtcttttaacatacccttcatatgtcttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG