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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggaatctgcttcaagacctcctgtttgcgtgccattagttaatcggggttcttatgcttttcagATGGCTGGTTTTGCACTTCACAAGAAATATGGATCGCAGTTCATGAAAATCCTATATGTGATTTCACGGTACTTTTTACCGGCTTTGAAGGAACAAGGCA

Basic information

species Zea mays
transcript GRMZM2G417217_T02
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G417217_T03 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g38250.1 (Oryza sativa), 3'ss of exon 14
gtaggaatctgcttcaagacc---------tcctgtttgcgtgccatt----------------agttaatcggggttcttatgcttttcagATGGCTGGTTTTGCACTTCACAAGAAATATGGATCGCAGTTCATGAAAATCCTATATGTGATTTCACGGTACTTTTTACCGGCTTTGAAGGAACAAGGCA
|||  ||| ||||||||||||         |||| |  | |||   ||                ||  ||   || ||||  | || ||||| | |||||||||||||||||||||||||| ||||| |||||||||||| | ||| |||| || |  |||| ||| ||||| |||||||||||||||||| 
gtaaaaatatgcttcaagacccccatcccctcctatgcgtgtgtgcttgtagcaggtttgttgtagccaacttggattctgtttctgttcagGTTGCTGGTTTTGCACTTCACAAGAAATACGGATCACAGTTCATGAAACTTCTAGATGTAATATTGCGGTGCTTCTTACCCGCTTTGAAGGAACAAGGCT
















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|31355428|gb|CD439785.1|CD439785
EST:     CTCTTCCAGCTACTACAGCCACTGCTTGTGCCCTTCACGCCTTCCTCAAG                         ATGGCTGGTTTTGCACTTCACAAGAAATATGGATCGCAGTTCATGAAAATC
genomic: CTCTTCCAGCTACTACAGCCACTGCTTGTGCCCTTCACGCCTTCCTCAAGgtaggaatct ... tgcttttcagATGGCTGGTTTTGCACTTCACAAGAAATATGGATCGCAGTTCATGAAAATC
EST: gi|67016820|gb|CO445569.1|CO445569
EST:     AGCCACTGTTTGTGCCCTTCACGCCTTCCTCAAG                         A-GGCTGGTTTTGCACTTCACAAGAAATATGGATCGCAGTTCATGAAAATC
genomic: AGCCACTGCTTGTGCCCTTCACGCCTTCCTCAAGgtaggaatct ... tgcttttcagATGGCTGGTTTTGCACTTCACAAGAAATATGGATCGCAGTTCATGAAAATC
EST: gi|24769979|gb|CA405108.1|CA405108
EST:     CTCTTCCAGCTACTACAGCCACTGCTTGTGCCCTTCACGCCTTCCTCAAG                         ATGGCTGGTTTTGCACTTCACAAGAAATATGGATCGCAGTTCATGAAAATC
genomic: CTCTTCCAGCTACTACAGCCACTGCTTGTGCCCTTCACGCCTTCCTCAAGgtaggaatct ... tgcttttcagATGGCTGGTTTTGCACTTCACAAGAAATATGGATCGCAGTTCATGAAAATC
EST: gi|149076572|gb|EE165207.2|EE165207
EST:     CTCTTCCAGCTACTACAGCCACTGCTTGTGCCCTTCACGCCTTCCTCAAG                         ATGGCTGGTTTTGCACTTCACAAGAAATATGGATCGCAGTTCATGAAAATC
genomic: CTCTTCCAGCTACTACAGCCACTGCTTGTGCCCTTCACGCCTTCCTCAAGgtaggaatct ... tgcttttcagATGGCTGGTTTTGCACTTCACAAGAAATATGGATCGCAGTTCATGAAAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaagacctcctgtttgcgtgccattagttaatcggggttcttatgcttttcagATGGCTGGTTTTGCACTTCACAAGAAATATGGATCGCAGTTCATGAAAATCCTATATGTGATTTCACGGTACTTTTTACCGGCTTTGAAGGAACAAGGCA
                           agttaat  putative branch site (score: 4)
                                       ttcttatgcttttc  putative PPT
                        attagttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggaatctgcttcaagacctcctgtttgcgtgccattagttaatcggggttcttatgcttttcagATGGCTGGTTTTGCACTTCACAAGAAATATGGATCGCAGTTCATGAAAATCCTATATGTGATTTCACGGTACTTTTTACCGGCTTTGAAGGAACAAGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA