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

GGAGCAGCTAAACATAACCCGTAAAAAATATAGACAGTCCAGATTAGAACAGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctcttactctttttgtaagttaagctttgtaaattttctatccacatgttgttgacaattgtcttggaatag

Basic information

species Zea mays
transcript GRMZM2G048045_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G048045_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g48964.1 (Oryza sativa), 5'ss of exon 3
GGAGCAGCTAAACATAACCCGTAAAAAATATAGACAGTCCAGATTAGAACAGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttg-cctcttactctttttgtaagttaagctttgtaaattttctatccacatgttgttgacaattgtcttggaatag
|||| |||||   || || ||| | ||||| |||||| |||||||||| |||||||| |||||||||||  | ||||| |||||||||| |||    |||||  | ||| ||      |   |  ||  | || | |   |||    |  |||    ||||||| |||| |        
GGAGAAGCTAGCGATCACACGTGATAAATACAGACAGACCAGATTAGATCAGTACAAGAATTATGAGAACATGCCTAATTCTGGAGAAGCAGCCGCAAAGgtgcgtccttttgaaagctcactgtgtagaactgtctgtgtttgtgcttgaca----gttgacacttgtgtacag----

upper sequence: GRMZM2G048045_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT3G13340.2 (Arabidopsis thaliana), 5'ss of exon 3
GGAGCAGCTAAACATAACCCGTAAAAAATATAGACAGTCCAGATTAGAACAGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAA------GAAGCTATGAAGgtt-tgcctcttactctttttgtaagttaagctttgtaaattttctatccacatgttgttgacaattgtcttggaatag
|||    || || ||  |  |  | ||||| |||||  | |||||||||||||| || |||||||| ||||| ||||| |||||||||      |||    | | |||| |  |   |  || | |  |    | ||  ||     |     |  ||| |  |        |||| | |    ||
GGACAGACTTAATATTTCTAGAGAGAAATACAGACAAACTAGATTAGAACAGTATAAGAATTATGAAAATGTCCCTAATTCTGGAGAATCATCAGAAAAGgtaagggttatatcctctgatcctctatttgtattagtgttcaggttagctcagtcacctaatacatcattttgtatggattcag

upper sequence: GRMZM2G048045_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT1G55680.1 (Arabidopsis thaliana), 5'ss of exon 3
GGAGCAGCTAAACATAACCCGTAAAAAATATAGACAGTCCAGATTAGAACAGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctcttactctttttgtaagttaagctttgtaaattttctatccacatgttgttgacaattgtcttggaatag---------------------------
|||   ||| |  || ||  |  | | ||| |||||  | ||| |||||||||| ||||||||||| ||||| ||||||||||| |||    |   ||| ||  | ||   | ||| | |||    || | ||| |   | ||||||  |  | |   | | | | |  ||  | |                             
GGACAGGCTTAGTATTACGAGAGAGACATACAGACAAACTAGACTAGAACAGTATAAAAATTATGAAAATGTCCCTAACTCTGGGGAATCTTCAGGGAAAgtaagtcttccattctctatgtctcgtaggttttctttttcttctat--atgtttcactaatattgggtttcaactgatacttatcatttgcttaatgaattcag

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|21432290|gb|BQ547780.1|BQ547780
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
EST: gi|211511963|gb|FL422086.1|FL422086
EST:     AGTACMAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAGCCAACAGAGAAA
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAA
EST: gi|88756008|gb|DY540149.1|DY540149
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAGCCAACAGA-AAAGGTGGAATGTACTATGAGTTCAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
EST: gi|211068069|gb|FL377958.1|FL377958
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGT-CAGACG
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACG
EST: gi|211451825|gb|FL381435.1|FL381435
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
EST: gi|78103766|gb|DV522194.1|DV522194
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
EST: gi|211456722|gb|FL410364.1|FL410364
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
EST: gi|211214580|gb|FL385221.1|FL385221
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
EST: gi|211509379|gb|FL412049.1|FL412049
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
EST: gi|33101585|gb|CF061545.1|CF061545
EST:     GTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
genomic: GTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
EST: gi|148942098|gb|EC887100.2|EC887100
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
EST: gi|211109347|gb|FL402577.1|FL402577
EST:     GAGAAGAAGCTATGAAG                         GATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
genomic: GAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
EST: gi|211447310|gb|FL370711.1|FL370711
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
EST: gi|71332422|gb|DR803167.1|DR803167
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
EST: gi|211493638|gb|FL397225.1|FL397225
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCA
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCA
EST: gi|211169918|gb|FL423118.1|FL423118
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
EST: gi|13126325|gb|BG316895.1|BG316895
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
EST: gi|32802872|gb|CD955108.1|CD955108
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
EST: gi|211536231|gb|FL396284.1|FL396284
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAA-CCAACAGAGAAAAGTGGA-TGGGTACTATGAGTTCAGACGAA
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATG--TACTATGAGTTCAGACGAA
EST: gi|211538762|gb|FL372743.1|FL372743
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
EST: gi|9952999|gb|BE639582.1|BE639582
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
EST: gi|71320210|gb|DR796860.1|DR796860
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAAT

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: 269

GGAGCAGCTAAACATAACCCGTAAAAAATATAGACAGTCCAGATTAGAACAGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 284

GGAGCAGCTAAACATAACCCGTAAAAAATATAGACAGTCCAGATTAGAACAGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 269

GGAGCAGCTAAACATAACCCGTAAAAAATATAGACAGTCCAGATTAGAACAGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 378

GGAGCAGCTAAACATAACCCGTAAAAAATATAGACAGTCCAGATTAGAACAGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAGCCAACAGAGAAAGGTGGAATGTACTATGAGTTCAGACGAAATACTCGATCGATTAAGTCAACTATTCTACATTTTCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGCAGCTAAACATAACCCGTAAAAAATATAGACAGTCCAGATTAGAACAGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctcttactctttttgtaagttaagctttgtaaattttctatccacatgttgttgacaattgtcttggaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC