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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccctgtcagaataaatcagcgtgtcctcaggtctttattactatctgactatttgagccttggaacagaaggtttacatacgcaagctcttgtgatttagATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTTTACGGATGGGGATGGAACAAG

Basic information

species Zea mays
transcript GRMZM2G003565_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003565_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g35570.3 (Oryza sativa), 3'ss of exon 5
---------------------------------ccctgtcagaataaatcagc-gtgtcctcaggtctttattactatctgactat--ttgagccttggaa---cagaaggtttacatacgcaa-gctcttgtgatttagATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTTTACGGATGGGGATGGAACAAG
                                 |  ||    | |   |   | || ||||| | |  || | | ||| |   |    ||    |||||||   || | |  |||  |||  |    |||  | |||||||||||||| || ||||||||||| ||||| ||||||||||| ||||||||||| || ||||| |||||||||
gtacactcgctagcactaacaatattctgggaactatgctgaagttcttggcctgtttcctctgatgattgtcagtatatatttgcccttttctcttggaatttcacacgtcttatttacaaagtattctactaatttagATTTCAGGTGGATGGAGGCATACAATGGCGCTTACATCAGATGGAAAGCTTTATGGTTGGGGGTGGAACAAG
















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|211087172|gb|FL255715.1|FL255715
EST:     ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAG                         ATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTT
genomic: ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAGgtaaatatac ... tgtgatttagATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTT
EST: gi|194716840|gb|FK933999.1|FK933999
EST:     ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAG                         ATTTCAGGCGGCTGGAGGCACACGATGGCACTTACATCAGAGGGAGAGCTT
genomic: ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAGgtaaatatac ... tgtgatttagATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTT
EST: gi|50331209|gb|CO526335.1|CO526335
EST:     ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAG                         ATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATC
genomic: ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAGgtaaatatac ... tgtgatttagATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATC
EST: gi|76919945|gb|DV167932.1|DV167932
EST:     ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAG                         ATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGGAAGCTT
genomic: ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAGgtaaatatac ... tgtgatttagATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTT
EST: gi|211471127|gb|FL255671.1|FL255671
EST:     ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAG                         ATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTT
genomic: ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAGgtaaatatac ... tgtgatttagATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTT
EST: gi|211476174|gb|FL255694.1|FL255694
EST:     ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAG                         ATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTT
genomic: ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAGgtaaatatac ... tgtgatttagATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTT
EST: gi|211471121|gb|FL255665.1|FL255665
EST:     ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAG                         ATTTCAGGCGGCTGGAGGCATACGATGGCAC
genomic: ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAGgtaaatatac ... tgtgatttagATTTCAGGCGGCTGGAGGCATACGATGGCAC
EST: gi|29130842|gb|CB381546.1|CB381546
EST:     ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAG                         ATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTT
genomic: ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAGgtaaatatac ... tgtgatttagATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTT
EST: gi|71771589|gb|DR969526.1|DR969526
EST:     ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAG                         ATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGGAAGCTT
genomic: ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAGgtaaatatac ... tgtgatttagATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTT
EST: gi|76283808|gb|DV023376.1|DV023376
EST:     ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAG                         ATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTT
genomic: ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAGgtaaatatac ... tgtgatttagATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgactatttgagccttggaacagaaggtttacatacgcaagctcttgtgatttagATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTTTACGGATGGGGATGGAACAAG
 atctgac  putative branch site (score: 3)
                                         ctcttgt  putative PPT
                           tttacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccctgtcagaataaatcagcgtgtcctcaggtctttattactatctgactatttgagccttggaacagaaggtttacatacgcaagctcttgtgatttagATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTTTACGGATGGGGATGGAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA