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

...gctgaattctgtacttggattcatgctcttgttcatcttggggacttagggaacctatcaggggaaagtttctcataaatttcctctgttttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATCATATCGTCCTGGGGACATTGTTAAAGCTATGGTTGTATCCTTAATTGAC

Basic information

species Zea mays
transcript GRMZM5G841900_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G841900_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g57070.2 (Oryza sativa), 3'ss of exon 3
---------------------------------------------------------------------------------gctgaattctgtacttggattc--atgctcttgttcatcttggggacttagggaacctatcaggggaaagtttctcataaatttcctctgttt---tacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATCATATCGTCCTGGGGACATTGTTAAAGCTATGGTTGTATCCTTAATTGAC
                                                                                 | |         | ||  | ||  |||||| || |   | |  |  | |     || |||||    ||||||  ||||   |   || || |    |   || ||||||||||||||||||||||||||||| ||||||||||||||||  || ||||| || ||||| || ||||| | |||  |||||||||||||||  |  
gtacgggttctgttttctttgctgatatgcttccatttaaacctttttcagggatctcttgtattgcttcgctttgagtcagttaccaaacacatttacaatccaatgctcctgcttgccatatgttccttttagac-tatcacaacaaagttcttcatggttcagctatgctcctctgtttgtagGCAGCAAGATGTTCGTGCAACTGAAATCGACAAGGTGGATATGTTTCAGTCATACCGACCTGGTGATATTGTCAGAGCCCTGGTTGTATCCTTAAGGGGA

upper sequence: GRMZM5G841900_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g57070.1 (Oryza sativa), 3'ss of exon 3
---------------------------------------------------------------------------------gctgaattctgtacttggattc--atgctcttgttcatcttggggacttagggaacctatcaggggaaagtttctcataaatttcctctgttt---tacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATCATATCGTCCTGGGGACATTGTTAAAGCTATGGTTGTATCCTTAATTGAC
                                                                                 | |         | ||  | ||  |||||| || |   | |  |  | |     || |||||    ||||||  ||||   |   || || |    |   || ||||||||||||||||||||||||||||| ||||||||||||||||  || ||||| || ||||| || ||||| | |||  |||||               
gtacgggttctgttttctttgctgatatgcttccatttaaacctttttcagggatctcttgtattgcttcgctttgagtcagttaccaaacacatttacaatccaatgctcctgcttgccatatgttccttttagac-tatcacaacaaagttcttcatggttcagctatgctcctctgtttgtagGCAGCAAGATGTTCGTGCAACTGAAATCGACAAGGTGGATATGTTTCAGTCATACCGACCTGGTGATATTGTCAGAGCCCTGGTT---------------
















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|211102908|gb|FK962289.1|FK962289
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGANATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|211118860|gb|FL110175.1|FL110175
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGT
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGT
EST: gi|32796285|gb|CD948521.1|CD948521
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|211102904|gb|FK962285.1|FK962285
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|211118861|gb|FL110176.1|FL110176
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|211118854|gb|FL110169.1|FL110169
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|76012394|gb|DT939564.1|DT939564
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|211118858|gb|FL110173.1|FL110173
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|211102910|gb|FK962291.1|FK962291
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|211118859|gb|FL110174.1|FL110174
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATSATAAG                         GCAGCAAGATGTTCGTGCAACTGAAAT
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAAT
EST: gi|211102911|gb|FK962292.1|FK962292
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|166676501|gb|EG058226.1|EG058226
EST:     AGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAAAT
genomic: AGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAA-T
EST: gi|148939988|gb|EC884719.2|EC884719
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|74244670|gb|DT652584.1|DT652584
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|50328543|gb|CO523669.1|CO523669
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|211102902|gb|FK962283.1|FK962283
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|71428020|gb|DR809070.1|DR809070
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
EST: gi|211102903|gb|FK962284.1|FK962284
EST:     ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG                         GCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC
genomic: ATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAGgtggtgcact ... ttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagggaacctatcaggggaaagtttctcataaatttcctctgttttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATCATATCGTCCTGGGGACATTGTTAAAGCTATGGTTGTATCCTTAATTGAC
                                  tttcctctgttttacc  CT-rich tract
                       tttctcataaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctgaattctgtacttggattcatgctcttgttcatcttggggacttagggaacctatcaggggaaagtttctcataaatttcctctgttttacctgcagGCAGCAAGATGTTCGTGCAACTGAAATTGACAAGGTGGATATGTACCAATCATATCGTCCTGGGGACATTGTTAAAGCTATGGTTGTATCCTTAATTGAC

gctgaat
- - - - - gtacttg
- - - - - - - - - -ttcatgc
- - - - - - - - - - - - - - - gttcatc