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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacctcatttatagcactccaattctacctttcagattcaagcaatatttttatgaatcttcctttttcatctag

Basic information

species Zea mays
transcript GRMZM2G075485_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075485_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g10220.1 (Oryza sativa), 5'ss of exon 3
AGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacctcatttatagcactccaatt-ctacctttcagattcaagcaatatttttatgaatcttcctttttcatctag
|||||| ||||| ||||||||||| |||||||| ||||| |||||||| ||||  |||||||| || ||||||||||||||||| ||  |||||||||||||| |||||| |||   || | |   ||| | | | ||    | | || |  |||||    | | ||   ||||| | |||
AGCCAAGGAGAAATTTCAGCAGCTTCAGAAGGTGATATCTATTCTTGGGGATGAGGAGAAAAGGGCATTATATGATGAGACTGGAATTGCTGATGATGATgtgagcacctgattccaagtagtgtgatttccaacctttcactcccagtag-attttctgaagttttgtcttttcctgtag

upper sequence: GRMZM2G075485_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT3G12170.1 (Arabidopsis thaliana), 5'ss of exon 3
AGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacctcatttatagcactccaattctacctttcagattcaagcaatatttttatgaatc--ttcctttttcatctag----
 || |||||||| ||||||||| |||| |||||||| || ||||| || |||| ||||||||||||  | |||||| | ||||||     |||||||| |||  |    | |   | ||   | ||| |  |        | |  ||  || || |||  ||    ||  ||    ||||      
TGCTAAAGAGAAATTTCAGCAGTTGCAAAAGGTTATTTCGATTCTCGGTGATGAAGAGAAAAGAGCAGTCTATGATCAAACTGGCTCAGTTGATGATGCTgtaagt---tgaaagaaagt-tttcaacttaagtaaaggtactggag-gattttcttacaaactggttatttccctatctcattag

upper sequence: GRMZM2G075485_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT5G06910.1 (Arabidopsis thaliana), 5'ss of exon 3
AGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct-catttatagcactc---caattctacc---tttcagattcaagcaatatttttatgaatcttcctttttcatctag-----------------------------
||| ||||| ||||| ||||||||||| || || ||||| |||||||| |||| ||||||||| ||  | |||||| | ||||||   | |||||||| |||| |   ||   ||| | |   |    || ||  | |   |     |  ||   ||  |  | || | | ||      |  |||                               
AGCTAAAGACAAGTTCCAGCAGCTGCAAAAAGTGATATCAATTCTTGGTGATGAAGAGAAAAGGGCAGTCTATGATCAAACTGGCTCAATTGATGATGCTgtgagtctctgtttttgttgtgtttgttcagtttgatcgagtgaagaaagcacttaacttcctcattagtattatgagattttcttaaacctgaggtgtttttccatgctcgttag

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|71757753|gb|DR955690.1|DR955690
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|91870824|gb|EB401103.1|EB401103
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|211337601|gb|FL103353.1|FL103353
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|78116316|gb|DV534703.1|DV534703
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|211337600|gb|FL103352.1|FL103352
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|211339984|gb|FL103354.1|FL103354
EST:     ATGTAGAGAAWAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|211342376|gb|FL103369.1|FL103369
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|211339995|gb|FL103365.1|FL103365
EST:     ATGCAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTAGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|211337599|gb|FL103351.1|FL103351
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|211339988|gb|FL103358.1|FL103358
EST:     ATGCAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTAGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|60341956|gb|DN208929.1|DN208929
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|211339990|gb|FL103360.1|FL103360
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|211342377|gb|FL103370.1|FL103370
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|211339987|gb|FL103357.1|FL103357
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCNAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|211339985|gb|FL103355.1|FL103355
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAWGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|78074190|gb|DV502624.1|DV502624
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|211337598|gb|FL103350.1|FL103350
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|211339993|gb|FL103363.1|FL103363
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|32909541|gb|CF014353.1|CF014353
EST:     ATGCAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GTACTAGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|148958294|gb|EC904514.2|EC904514
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|78117499|gb|DV535886.1|DV535886
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|211337592|gb|FL103344.1|FL103344
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|211342378|gb|FL103371.1|FL103371
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|211339992|gb|FL103362.1|FL103362
EST:     ATGCAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTAGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|211337591|gb|FL103343.1|FL103343
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|211339989|gb|FL103359.1|FL103359
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|211337597|gb|FL103349.1|FL103349
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGT
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGT
EST: gi|211339997|gb|FL103367.1|FL103367
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGT
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGT
EST: gi|71772229|gb|DR970166.1|DR970166
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|71435377|gb|DR816427.1|DR816427
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAT                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
EST: gi|211025378|gb|FL421223.1|FL421223
EST:     ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGAA                         GCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG
genomic: ATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATG

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: 314

AGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 74

AGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 80

AGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

AGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacct ... tttcatctagGCACTGGTGGGAGAAGCTGCAAACAATCTTCAGGAGTACTTCAGAACAATGTACAAGAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCCAAAGAGAAGTTTCAGCAGCTGCAGAAGGTTATATCCATTCTTGGAGATGTAGAGAAAAGAGCTTTATATGATGAGACTGGCATCACTGATGATGATgtgtgcacctcatttatagcactccaattctacctttcagattcaagcaatatttttatgaatcttcctttttcatctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT