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

gtctctctctttaaaatgcttcattcgtcactgcttatggtgcattgttgactaacagaatgtttcctacctctagGGTTACAAAGAAAAGCTTGTTGATATCAGGGAAGAGATTATGCGCAAGCGCAGAGCTGGGAAACTTCCTGGAGATACTGCATCTGTGCTGAAAGCTTGGT

Basic information

species Zea mays
transcript GRMZM2G370332_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G370332_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g08544.2 (Oryza sativa), 3'ss of exon 3
-----gtctctctctttaaaatgcttcattcgtcactgcttatggtgcattgttgactaacagaatgtttcctacctctagGGTTACAAAGAAAAGCTTGTTGATATCAGGGAAGAGATTATGCGCAAGCGCAGAGCTGGGAAACTTCCTGGAGATACTGCATCTGTGCTGAAAGCTTGGT
      | |    |||| ||||||||||| | |||  |    | ||||||| ||    |||  ||  | |||| ||| ||||| ||||||||||||||||| ||||| |||||||||||  | |||||||| |||||||| ||||||||||| |||||||||||| | || ||||||||||
gtagccttttgtcctttgaaatgcttcatccatcatcg----tagtgcattatttgtgaaccaaa-atgtcctgcctgtagGGGTACAAAGAAAAGCTTGTGGATATTAGGGAAGAGATCCTTCGCAAGCGGAGAGCTGGTAAACTTCCTGGTGATACTGCATCTATACTAAAAGCTTGGT
















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|71330383|gb|DR801947.1|DR801947
EST:     GATCCTTAGTTGAGCGTGTACGGCAGGAGCTAAAGAACGAGCTTAAGCAG                         GGTTACAAAGAAAAGCTTGTTGATATCAGGGAAGAGATTATGCGCAAGCGC
genomic: GATCCTTAGTTGAGCGTGTACGGCAGGAGCTAAAGAACGAGCTTAAGCAGgtctctctct ... ctacctctagGGTTACAAAGAAAAGCTTGTTGATATCAGGGAAGAGATTATGCGCAAGCGC
EST: gi|32868323|gb|CF008005.1|CF008005
EST:     GTACGGCAGGAGCTAAAGAGCGAGCTTAAGCAG                         GGTTACAAAGAAAAGCTTGTTGATATCAGGGAAGAGATTATGCGCAAGCGC
genomic: GTACGGCAGGAGCTAAAGAACGAGCTTAAGCAGgtctctctct ... ctacctctagGGTTACAAAGAAAAGCTTGTTGATATCAGGGAAGAGATTATGCGCAAGCGC
EST: gi|71330382|gb|DR801946.1|DR801946
EST:     GATCCTTAGTTGAGCGTGTACGGCAGGAGCTAAAGAACGAGCTTAAGCAG                         GGTTACAAAGAAAAGCTTGTTGATATCAGGGAAGAGATTATGCGCAAGCGC
genomic: GATCCTTAGTTGAGCGTGTACGGCAGGAGCTAAAGAACGAGCTTAAGCAGgtctctctct ... ctacctctagGGTTACAAAGAAAAGCTTGTTGATATCAGGGAAGAGATTATGCGCAAGCGC
EST: gi|60397901|gb|DN230717.1|DN230717
EST:     CGAGCTTAAGCAG                         GGTTACAAAGAAAAGCTTGTTGATATCAGGGAAGAGATTATGCGCAAGCGC
genomic: CGAGCTTAAGCAGgtctctctct ... ctacctctagGGTTACAAAGAAAAGCTTGTTGATATCAGGGAAGAGATTATGCGCAAGCGC
EST: gi|93280940|gb|EB673204.1|EB673204
EST:     GATCCTTAGTTGAGCGTGTACGGCAGGAGCTAAAGAACGAGCTTAAGCAG                         GGTTACAAAGAAAAGCTTGTTGATATCAGGGAAGAGATTATGCGCAAGCGC
genomic: GATCCTTAGTTGAGCGTGTACGGCAGGAGCTAAAGAACGAGCTTAAGCAGgtctctctct ... ctacctctagGGTTACAAAGAAAAGCTTGTTGATATCAGGGAAGAGATTATGCGCAAGCGC
EST: gi|31611855|gb|CD568477.1|CD568477
EST:     GATCCTTAGTTGAGCGTGTACGGCAGGAGCTAAAGAACGAGCTTAAGCAG                         GGTTACAAAGAAAAGCTTGTTGATATCAGGGAAGAGATTATGCGCAAGCGC
genomic: GATCCTTAGTTGAGCGTGTACGGCAGGAGCTAAAGAACGAGCTTAAGCAGgtctctctct ... ctacctctagGGTTACAAAGAAAAGCTTGTTGATATCAGGGAAGAGATTATGCGCAAGCGC
EST: gi|32868033|gb|CF007715.1|CF007715
EST:     GTACGGCAGGAGCTAAAGAACGAGCTTAAGCAG                         GGTTACAAAGAAAAGCTTGTTGATATCAGGGAAGAGATTATGCGCAAGCGC
genomic: GTACGGCAGGAGCTAAAGAACGAGCTTAAGCAGgtctctctct ... ctacctctagGGTTACAAAGAAAAGCTTGTTGATATCAGGGAAGAGATTATGCGCAAGCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattcgtcactgcttatggtgcattgttgactaacagaatgtttcctacctctagGGTTACAAAGAAAAGCTTGTTGATATCAGGGAAGAGATTATGCGCAAGCGCAGAGCTGGGAAACTTCCTGGAGATACTGCATCTGTGCTGAAAGCTTGGT
                            gactaac  putative branch site (score: 1)
                                       tgtttcctacctct  putative PPT
                                     aatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctctctctttaaaatgcttcattcgtcactgcttatggtgcattgttgactaacagaatgtttcctacctctagGGTTACAAAGAAAAGCTTGTTGATATCAGGGAAGAGATTATGCGCAAGCGCAGAGCTGGGAAACTTCCTGGAGATACTGCATCTGTGCTGAAAGCTTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT