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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctctacataatgctcaatattattgtatctactttacttgtcaatagttgactgaagtaaaactctcgtatgatctttttcatcagATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAG

Basic information

species Zea mays
transcript GRMZM2G015730_T03
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015730_T03 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g17930.1 (Oryza sativa), 3'ss of exon 9
--------------gtatgctctacataatgctcaatattattgtat-ctactttacttgtcaatagttgactgaagtaaaac---tctcgtatgatcttttt-catcagATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAG
                    |  |  | | || |||| | ||| | | ||   |||        | ||  || ||| |||||    | |   ||||||||||| ||||||||| |   | | |||||  |||| |||||||| ||||||||  ||||| | ||||||||||| |||||| ||||||| |||||| | ||||| |||
gtacgagtgatcatactcatttgagttcacgcacaatgtcattctgttcttagttatcaaatgtttgtccacagaaataaaaaaaatattccatgatctttttgcatcagATGGTGAAGCTTATAAAGGATCTAAAGAAGGATAATGAATTCATGAAGAGTAAATGTGAGAATTCAGATGTTGCTCTAGTGAAGTTGATTGAGGAG
















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|60350738|gb|DN217711.1|DN217711
EST:     TGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAA                         ATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGA
genomic: TGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAAgtatgctcta ... ttttcatcagATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGA
EST: gi|211265994|gb|FL478571.1|FL478571
EST:     TGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAA                         ATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGA
genomic: TGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAAgtatgctcta ... ttttcatcagATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGA
EST: gi|24766462|gb|CA401615.1|CA401615
EST:     TGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAA                         ATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGA
genomic: TGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAAgtatgctcta ... ttttcatcagATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGA
EST: gi|67019010|gb|CO447759.1|CO447759
EST:     TGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAA                         ATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGA
genomic: TGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAAgtatgctcta ... ttttcatcagATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGA
EST: gi|40337560|gb|CK371630.1|CK371630
EST:     TGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAA                         ATGATTTTGGTGAT
genomic: TGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAAgtatgctcta ... ttttcatcagATGATTTTGGTGAT
EST: gi|31354045|gb|CD438402.1|CD438402
EST:     TGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAA                         ATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGA
genomic: TGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAAgtatgctcta ... ttttcatcagATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGA
EST: gi|74244820|gb|DT652734.1|DT652734
EST:     TGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAA                         ATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTTTGAAGGGA
genomic: TGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAAgtatgctcta ... ttttcatcagATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGA
EST: gi|24769021|gb|CA404150.1|CA404150
EST:     TGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAA                         ATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGA
genomic: TGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAAgtatgctcta ... ttttcatcagATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGA
EST: gi|148952378|gb|EC898193.2|EC898193
EST:     TGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAA                         ATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGA
genomic: TGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAAgtatgctcta ... ttttcatcagATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGA
EST: gi|37400434|gb|CF637568.1|CF637568
EST:     TGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAA                         ATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGA
genomic: TGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAAgtatgctcta ... ttttcatcagATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGA
EST: gi|60339601|gb|DN206574.1|DN206574
EST:     TGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAA                         ATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGA
genomic: TGTCAAAAAGCAATGAAGTCTTTGAAACTTACAAGCAGGAGATGGAAAAAgtatgctcta ... ttttcatcagATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttacttgtcaatagttgactgaagtaaaactctcgtatgatctttttcatcagATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAG
              agttgac  putative branch site (score: 4)
                                          tctttttcatc  putative PPT
                       aagtaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctctacataatgctcaatattattgtatctactttacttgtcaatagttgactgaagtaaaactctcgtatgatctttttcatcagATGATTTTGGTGATAAAAAATCTTAAGAAGGACAATGAATTTCTGAAGGGAAAATGTGAGAACTCAGATATTGCTCTTGTGAAGCTCATTGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA