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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcgagcttaactgacccagagcgcaaggcgtttctgtaccatttagcatgctgctttgcttaactatttcactatgacagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGCAGTCTTGCGTCCATGCCTGACATTGCGTTCACCATTGGAGGCAAGAAGT

Basic information

species Zea mays
transcript GRMZM2G065757_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065757_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os05g49200.2 (Oryza sativa), 3'ss of exon 10
gcgagcttaactgacccagagcgcaaggcgtttctgtaccatttagcatg----ctgctttgcttaactatt-tcactatgacagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGCAGTCTTGCGTCCATGCCTGACATTGCGTTCACCATTGGAGGCAAGAAGT
| |||||||  | || |       | |||  ||  ||||   |  | ||      | | |||||||||| || ||| | | |||||| || ||    || || ||||| |||||||||||| | |||||||||||||| ||||| ||||||||||| ||| | ||||||||||||||||| ||||
gtgagcttagttaactcctgctctagggccatt--gtactggtagggatagattttccgttgcttaactgttatcaattttacagCTCTGTGACAAGCTCCCAAGTCCAATGGGAGAATCATCTGTGGACTGTGGCAGCCTTGCATCCATGCCTGAGATTTCATTCACCATTGGAGGCAAAAAGT
















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|213184093|gb|FM191578.1|FM191578
EST:     AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAG                         CTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
genomic: AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... actatgacagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
EST: gi|67017226|gb|CO445975.1|CO445975
EST:     AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAG                         CTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
genomic: AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... actatgacagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
EST: gi|33096169|gb|CF056163.1|CF056163
EST:     AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAG                         CTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
genomic: AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... actatgacagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
EST: gi|211092713|gb|FK945553.1|FK945553
EST:     AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAG                         CTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCTGTGGACTGTGGC
genomic: AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... actatgacagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
EST: gi|31354952|gb|CD439309.1|CD439309
EST:     AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAG                         CTTTGCGAGCGTCTTCCGAGTCCAATGGGAGAATCAGCCGTGGACTGTGGC
genomic: AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... actatgacagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
EST: gi|32918238|gb|CF023050.1|CF023050
EST:     AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAG                         CTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
genomic: AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... actatgacagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
EST: gi|16919046|gb|BM074015.1|BM074015
EST:     AAGACACAGGAGCTCATCCTGAACTACATTAATCAG                         CTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
genomic: AAGACACAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... actatgacagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
EST: gi|211361839|gb|FL432808.1|FL432808
EST:     GAGCTCATCCTGAACTACATTAATCAG                         CTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCTGTGGACTGTGGC
genomic: GAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... actatgacagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
EST: gi|21621076|gb|BQ619082.1|BQ619082
EST:     AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAG                         CTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
genomic: AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... actatgacagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
EST: gi|116816042|gb|EC858742.1|EC858742
EST:     AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAG                         CTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
genomic: AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... actatgacagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
EST: gi|33096356|gb|CF056350.1|CF056350
EST:     AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAG                         CTNTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
genomic: AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... actatgacagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC
EST: gi|60337171|gb|DN204144.1|DN204144
EST:     AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAG                         CTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCTGTGGACTGTGGC
genomic: AACTTGCCCAGAACAAGACACAGGAGCTCATCCTGAACTACATTAATCAGgcgagcttaa ... actatgacagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggcgtttctgtaccatttagcatgctgctttgcttaactatttcactatgacagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGCAGTCTTGCGTCCATGCCTGACATTGCGTTCACCATTGGAGGCAAGAAGT
                                gcttaac  putative branch site (score: 3)
                                         tttcact  putative PPT
                                  ttaactattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcgagcttaactgacccagagcgcaaggcgtttctgtaccatttagcatgctgctttgcttaactatttcactatgacagCTTTGCGAGCGTCTTCCGAGTCCGATGGGAGAATCAGCCGTGGACTGTGGCAGTCTTGCGTCCATGCCTGACATTGCGTTCACCATTGGAGGCAAGAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT