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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattataccaagttccttttacattttctttcttgcttgatgccaatgaacttgaaaaggctacttactgcccttcaaaatttacgttgcccaaatgcagAATTTATGGAGTGCATGACGAAGCGAAGGATAAAGCTTTCGAGTTGGAGTTGAGCTGGATCTGCGATGAATCGAACCACCAGCATCAGAAG

Basic information

species Zea mays
transcript GRMZM2G008623_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008623_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g59600.1 (Oryza sativa), 3'ss of exon 9
--tattataccaagttccttttacattttctttcttgcttgatgccaatgaacttgaaaaggctacttactgcccttcaaaatttacgttgcccaaatgcagAATTTATGGAGTGCATGACGAAGCGAAGGATAAAGCTTTCGAGTTGGAGTTGAGCTGGATCTGCGATGAATCGAACCACCAGCATCAGAAG
  | || |  | | |    |||| |  | |||| |||  | | || | |   ||   |||    |   | | | |       | ||  |||  |   ||||| ||||||||||| ||||| ||||| ||||| |||||||| |||||||| || |||||||| || |||||||| || | |||||||||||||
tgttttttctctaataatatttagaaatccttt-ttgaataaagctacttgtctgacaaaaaaaaaacagttctcactttcttataatttgttctg-tgcagCATTTATGGAGTACATGATGAAGCTAAGGACAAAGCTTTTGAGTTGGAATTAAGCTGGATATGTGATGAATCAAATCGCCAGCATCAGAAG
















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|91049728|gb|EB160146.1|EB160146
EST:     AAACTTTCAGAGCTTACGTGCCGGGAAGGCATTGTTGAAGTTGCAAAGAT                         AATTTATGGAGTGCATGACGAAGCGAAAGGATAA-GCTTTCGAGTTGGAGT
genomic: AAACTTTCAGAGCTTACGTGCCGGGAAGGCATTGTTGAAGTTGCAAAGATgtatgtctaa ... ccaaatgcagAATTTATGGAGTGCATGACGAAGCGAA-GGATAAAGCTTTCGAGTTGGAGT
EST: gi|22491453|gb|BU051376.1|BU051376
EST:     AAACTTTCAGAGCTTACGTTCCGGGAAGGCATTGTTGAAGTTGCAAAGAT                         AATTTATGGAGTGCATGACGAAGCGAAGGATAAAGCTTTCGAGTTGGAGTT
genomic: AAACTTTCAGAGCTTACGTGCCGGGAAGGCATTGTTGAAGTTGCAAAGATgtatgtctaa ... ccaaatgcagAATTTATGGAGTGCATGACGAAGCGAAGGATAAAGCTTTCGAGTTGGAGTT
EST: gi|78106192|gb|DV524610.1|DV524610
EST:     AAACTTTCAGAGCTTACGTGCCGGGAAGGCATTGTTGAAGTTGCAAAGAT                         AATTTATGGAGTGCATGACGAAGCGAAGGATAAAGCTTTCGAGTTGGAGTT
genomic: AAACTTTCAGAGCTTACGTGCCGGGAAGGCATTGTTGAAGTTGCAAAGATgtatgtctaa ... ccaaatgcagAATTTATGGAGTGCATGACGAAGCGAAGGATAAAGCTTTCGAGTTGGAGTT
EST: gi|6342734|gb|AW165558.1|AW165558
EST:     AAACTTTCAGAGCTTACGTGCCGGGAAGGCATTGTTGAAGTTGCAAAGAT                         AATTTATGGAGTGCATGACGAAGCGAAGGATAAAGCTTTCGAGTTGGAGTT
genomic: AAACTTTCAGAGCTTACGTGCCGGGAAGGCATTGTTGAAGTTGCAAAGATgtatgtctaa ... ccaaatgcagAATTTATGGAGTGCATGACGAAGCGAAGGATAAAGCTTTCGAGTTGGAGTT
EST: gi|93284361|gb|EB676625.1|EB676625
EST:     AAACTTTCAGAGCTTACGTGCCGGGAAGGCATTGTTGAAGTTGCAAAGAT                         AATTTATGGAGTGCATGACGAAGCGAAGGATAAAGCTTTCGAGTTGGAGTT
genomic: AAACTTTCAGAGCTTACGTGCCGGGAAGGCATTGTTGAAGTTGCAAAGATgtatgtctaa ... ccaaatgcagAATTTATGGAGTGCATGACGAAGCGAAGGATAAAGCTTTCGAGTTGGAGTT
EST: gi|78106193|gb|DV524611.1|DV524611
EST:     AAACTTTCAGAGCTTACGTGCCGGGAAGGCATTGTTGAAGTTGCAAAGAT                         AATTTATGGAGTGCATGACGAAGCGAAGGGATAA-GCTTTCGAGTTGGAGT
genomic: AAACTTTCAGAGCTTACGTGCCGGGAAGGCATTGTTGAAGTTGCAAAGATgtatgtctaa ... ccaaatgcagAATTTATGGAGTGCATGACGAAGCGAAGG-ATAAAGCTTTCGAGTTGGAGT
EST: gi|71431491|gb|DR812541.1|DR812541
EST:     AAACTTTCAGAGCTTACGTGCCGGGAAGGCATTGTTGAAGTTGCAAAGAT                         ATTTTATGGAGTGCATGACGAAGCGAAGGATAAAGC
genomic: AAACTTTCAGAGCTTACGTGCCGGGAAGGCATTGTTGAAGTTGCAAAGATgtatgtctaa ... ccaaatgcagAATTTATGGAGTGCATGACGAAGCGAAGGATAAAGC
EST: gi|148931430|gb|EC874390.2|EC874390
EST:     AACTTTCAGAGCTTACGTGCCCGGGA-GGCATTGTTGAAGTTGCAAAGAT                         AATTTATGGAGTGCATGA
genomic: AACTTTCAGAGCTTACGTGCC-GGGAAGGCATTGTTGAAGTTGCAAAGATgtatgtctaa ... ccaaatgcagAATTTATGGAGTGCATGA
EST: gi|148981882|gb|EE027956.2|EE027956
EST:     AAACTTTCAGAGCTTACGTGCCGGGAAGGCATTGTTGAAGTTGCAAAGAT                         AATTTATGGAGTGCATGACGAAGCGGAGGATAAAGCTTTCGAGTTGGAGTT
genomic: AAACTTTCAGAGCTTACGTGCCGGGAAGGCATTGTTGAAGTTGCAAAGATgtatgtctaa ... ccaaatgcagAATTTATGGAGTGCATGACGAAGCGAAGGATAAAGCTTTCGAGTTGGAGTT
EST: gi|148949932|gb|EC895439.2|EC895439
EST:     AAACTTTCAGAGCTTACGTGCCGGGAAGGCATTGTTGAAGTTGCAAAGAT                         AATTTATGGAGTGCATGACGAACCGAAGGATAAAGCTTTCGAGTTGGAGTT
genomic: AAACTTTCAGAGCTTACGTGCCGGGAAGGCATTGTTGAAGTTGCAAAGATgtatgtctaa ... ccaaatgcagAATTTATGGAGTGCATGACGAAGCGAAGGATAAAGCTTTCGAGTTGGAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaacttgaaaaggctacttactgcccttcaaaatttacgttgcccaaatgcagAATTTATGGAGTGCATGACGAAGCGAAGGATAAAGCTTTCGAGTTGGAGTTGAGCTGGATCTGCGATGAATCGAACCACCAGCATCAGAAG
                tacttac  putative branch site (score: 1)
                            ttcaaaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattataccaagttccttttacattttctttcttgcttgatgccaatgaacttgaaaaggctacttactgcccttcaaaatttacgttgcccaaatgcagAATTTATGGAGTGCATGACGAAGCGAAGGATAAAGCTTTCGAGTTGGAGTTGAGCTGGATCTGCGATGAATCGAACCACCAGCATCAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA