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'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaattgttggcataacttcaatgtactccaagtagttctggattctccattttctactgctatattatgtcctgaagcgtattcaaaattttctgacagGTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTTGCAGATTATGTCTCTATATGGCCTACCAAATTCCAAAACAAAACTAATG

Basic information

species Zea mays
transcript GRMZM2G085577_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 9
gaaattgttggcataacttcaatgtactccaagtagttctggattctccattttctactgctatatta------tgtcctgaagcgtattcaaaattttctgacagGTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTTGCAGATTATGTCTCTATATGGCCTACCAAATTCCAAAACAAAACTAATG
       |  | ||  |  | || |  |  |||||  ||   ||| |    |||||  |   |  | |       || |||||| ||  | ||   | ||  |||||||||||||||||||||||| || ||||||||||||||| |||| || |||||||| ||| ||||||||||||| | |||||| || |||||||| ||||
----caatatggatccccactattt-ttttaagtatgtcaacattatttgctttctcatataagttgaggaggtcgtactgaagtgtgctgaattctctcc-acagGTGAATGGAGTGGCTGAGTTACACAGCAACATTTTGAAGGAAGAGCTTTTTGCAGACTATCTCTCTATATGGCCCAACAAATTTCAGAACAAAACAAATG

upper sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT3G46970.1 (Arabidopsis thaliana), 3'ss of exon 10
gaaattgttggcataacttcaatgtactccaagtagttctggattctccattttctactgctatattatgtcctgaagcgtattc--aaaattttctgacagGTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTTGCAGATTATGTCTCTATATGGCCTACCAAATTCCAAAACAAAACTAATG
      ||  |  |     || |||   | ||||  |  |  ||| |   | |||   ||   | ||   | |     |  |||   |     || |  ||||||||||| || ||| |||| || ||  | || ||||||   ||  |||| ||||| ||||||||||||||||| | ||| || |||||||| |||||||
------gtaag--tggtcccactgt---caaagttatgttatattgtt--tcttcccatgtagtcttggtttcaagtactcattatgagggcctttttgcagGTGAATGGCGTTGCTCAGTTACACAGTGATATCTTGAAGGCTGAGTTATTCGCAGACTATGTCTCTATATGGCCAAACAAGTTTCAAAACAAGACTAATG

upper sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv06s0004g06020.t01 (Vitis vinifera), 3'ss of exon 9
gaaattgttggcataacttcaatgtactccaagtagttctggattctccattttctactgctatattatgtcctgaagcgtattc----aaaattttctgacagGTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTTGCAGATTATGTCTCTATATGGCCTACCAAATTCCAAAACAAAACTAATG
    || ||    ||| |||  | | |  |   |   |||   | ||||||||| |       ||  |  |    ||||   ||     |  |   |    ||||| ||||| || ||| |||| || ||  | ||||| ||    ||  |||||||||| ||||||||||||||||| ||||| ||||| || ||||| ||||
---tttcttcctttaatttctctcttcctctcttctctctctgt-ctccattttttttgcacgtacaaatttgaaaagcaactttctcgaccacccttgtgcagGTAAATGGTGTTGCTCAGTTACACAGTGATATTTTAAAAGCCGAGTTATTTGCAGACTATGTCTCTATATGGCCCACCAAGTTCCAGAATAAAACCAATG

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|116826388|gb|EC870170.1|EC870170
EST:     AGAAGCCGGTAGTGCGCATGGCAAATTTGTGTGTGGTGTCTTCTCATACG                         GTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTT
genomic: AGAAGCCGGTAGTGCGCATGGCAAATTTGTGTGTGGTGTCTTCTCATACGgtaaatacag ... tttctgacagGTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTT
EST: gi|211057776|gb|FL419530.1|FL419530
EST:     AGAAGCCGGTAGTGCGCATGGCAAATTTGTGTGTGGTGTCTTCTCATACG                         GTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTT
genomic: AGAAGCCGGTAGTGCGCATGGCAAATTTGTGTGTGGTGTCTTCTCATACGgtaaatacag ... tttctgacagGTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTT
EST: gi|211327557|gb|FL371056.1|FL371056
EST:     AGAAGCCGGTAGTGCGCATGGCAAATTTGTGTGTGGTGTCTTCTCATACG                         GTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTT
genomic: AGAAGCCGGTAGTGCGCATGGCAAATTTGTGTGTGGTGTCTTCTCATACGgtaaatacag ... tttctgacagGTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTT
EST: gi|211056531|gb|FL371323.1|FL371323
EST:     AGAAGCCGGTAGTGCGCATGGCAAATTTGTGTGTGGTGTCTTCTCATACG                         GTGAATGGAGTGGCTGAGTTGCGTAGCAACATTTTGAAGCAAGAACTATTT
genomic: AGAAGCCGGTAGTGCGCATGGCAAATTTGTGTGTGGTGTCTTCTCATACGgtaaatacag ... tttctgacagGTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTT
EST: gi|94480423|gb|EB709381.1|EB709381
EST:     AGAAGCCGGTAGTGCGCATGGCAAATTTGTGTGTGGTGTCTTCTCATACG                         GTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTT
genomic: AGAAGCCGGTAGTGCGCATGGCAAATTTGTGTGTGGTGTCTTCTCATACGgtaaatacag ... tttctgacagGTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTT
EST: gi|76924590|gb|DV170029.1|DV170029
EST:     AGAAGCCGGTAGTGCGCATGGCAAATTTGTGTGTGGTGTCTTCTCATACG                         GTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTT
genomic: AGAAGCCGGTAGTGCGCATGGCAAATTTGTGTGTGGTGTCTTCTCATACGgtaaatacag ... tttctgacagGTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTT
EST: gi|91877192|gb|EB407149.1|EB407149
EST:     ACAAGCCGGTAGTGCGCATGGCAAATTTGTGTGTGGTGTCTTCTCATACG                         GTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTT
genomic: AGAAGCCGGTAGTGCGCATGGCAAATTTGTGTGTGGTGTCTTCTCATACGgtaaatacag ... tttctgacagGTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTT

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: 413

AATGGAGGGAAAAATCGATTCAATGAAAGTTTTAGATAATTCGAACCCCCAGAAGCCGGTAGTGCGCATGGCAAATTTGTGTGTGGTGTCTTCTCATACGgtaaatacag ... tttctgacagGTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTTGCAGATTATGTCTCTATATGGCCTACCAAATTCCAAAACAAAACTAATG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 361

AATGGAGGGAAAAATCGATTCAATGAAAGTTTTAGATAATTCGAACCCCCAGAAGCCGGTAGTGCGCATGGCAAATTTGTGTGTGGTGTCTTCTCATACGgtaaatacag ... tttctgacagGTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTTGCAGATTATGTCTCTATATGGCCTACCAAATTCCAAAACAAAACTAATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 104

AATGGAGGGAAAAATCGATTCAATGAAAGTTTTAGATAATTCGAACCCCCAGAAGCCGGTAGTGCGCATGGCAAATTTGTGTGTGGTGTCTTCTCATACGgtaaatacag ... tttctgacagGTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTTGCAGATTATGTCTCTATATGGCCTACCAAATTCCAAAACAAAACTAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 496

AATGGAGGGAAAAATCGATTCAATGAAAGTTTTAGATAATTCGAACCCCCAGAAGCCGGTAGTGCGCATGGCAAATTTGTGTGTGGTGTCTTCTCATACGgtaaatacag ... tttctgacagGTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTTGCAGATTATGTCTCTATATGGCCTACCAAATTCCAAAACAAAACTAATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccattttctactgctatattatgtcctgaagcgtattcaaaattttctgacagGTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTTGCAGATTATGTCTCTATATGGCCTACCAAATTCCAAAACAAAACTAATG
                                            ttttct  CT-rich tract
                                   tattcaaaattttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaattgttggcataacttcaatgtactccaagtagttctggattctccattttctactgctatattatgtcctgaagcgtattcaaaattttctgacagGTGAATGGAGTGGCTGAGTTGCATAGCAACATTTTGAAGCAAGAACTATTTGCAGATTATGTCTCTATATGGCCTACCAAATTCCAAAACAAAACTAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - -tgttggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaagc