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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgttctgatcccatttcctgtcattgtctgtttaattcctattagatacttatgcgtgtcctgttcttgccctcagGAGATTCAAGAGCTATTTAGTTTGCCACAACAAGGATTTGATGTTTCCCTCACACATAAGCAGTTGCAAGAAGAGCATGGTCAACAAGTTGTTCT

Basic information

species Zea mays
transcript GRMZM2G138125_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138125_T02 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os04g59624.3 (Oryza sativa), 3'ss of exon 14
gtacttgttctgatcccatttcctgtcattgtctgtttaattcctattagatactt------atgcgtgtcctgttcttgccctcagGAGATTCAAGAGCTATTTAGTTTGCCACAACAAGGATTTGATGTTTCCCTCACACATAAGCAGTTGCAAGAAGAGCATGGTCAACAAGTTGTTCT
||||||  | |||| |  || | ||| ||||| |  |   | | |||| |||| ||      |||  | |  |||   | |  |||||| ||||||||||| || ||| ||||  | ||||| ||||||||||| || ||||| ||||| ||||||||||||||||| |||||| ||||  |
gtacttagtgtgatacggtt-cttgttattgttttctctgt-catattggataatttataatatggctattttgtgtgtacattcagGATATTCAAGAGCTTTTCAGTCTGCCTGAGCAAGGTTTTGATGTTTCGCTGACACAAAAGCAATTGCAAGAAGAGCATGGACAACAACTTGTGAT
















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|5525254|gb|AI861093.1|AI861093
EST:     GTTACTTCAGCAAGAGT                         GAGATTCAAGAGCTATTTAGTTTGCCACAACAAGGATTTGATGTTTCCCTC
genomic: GTTACTTCAGCAAGAGTgtacttgttc ... ttgccctcagGAGATTCAAGAGCTATTTAGTTTGCCACAACAAGGATTTGATGTTTCCCTC
EST: gi|32943511|gb|CF048330.1|CF048330
EST:     TCAGGACAGCTACGGAGCAAAAAGAGCAAACACGTTACTTCAGCAAGAGT                         GAGATTCAAGAGCTATTTAGTTTGCCACAACAAGGATTTGATGTTTCCCTC
genomic: TCAGGACAGCTACGGAGCAAAAAGAGCAAACACGTTACTTCAGCAAGAGTgtacttgttc ... ttgccctcagGAGATTCAAGAGCTATTTAGTTTGCCACAACAAGGATTTGATGTTTCCCTC
EST: gi|67034321|gb|CO462871.1|CO462871
EST:     TCAGGACAGCTACGGAGCAAAAAGAGCAAACACGTTACTTCAGCAAGAGT                         GAGATTCAAGAGCTATTTAGTTTGCCACAACAAGGATTTGATGTTTCCCTC
genomic: TCAGGACAGCTACGGAGCAAAAAGAGCAAACACGTTACTTCAGCAAGAGTgtacttgttc ... ttgccctcagGAGATTCAAGAGCTATTTAGTTTGCCACAACAAGGATTTGATGTTTCCCTC
EST: gi|71419756|gb|DR804887.1|DR804887
EST:     TCAGGACAGCTACGGAGCAAAAAGAGCAAACACGTTACTTCAGCAAGAGT                         GAGATTCAAGAGCTATTTAGTTTGCCACAACAAGGATTTGATGTTTCCCTC
genomic: TCAGGACAGCTACGGAGCAAAAAGAGCAAACACGTTACTTCAGCAAGAGTgtacttgttc ... ttgccctcagGAGATTCAAGAGCTATTTAGTTTGCCACAACAAGGATTTGATGTTTCCCTC
EST: gi|71419751|gb|DR804886.1|DR804886
EST:     GACAGTTACGGAGCAAAAAGAGCAAACACGTTACTTCAGCAAGAGT                         GAGATTCAAGAGCTATTTAGTTTGCCACAACAAGGATTTGATGTTTCCCTC
genomic: GACAGCTACGGAGCAAAAAGAGCAAACACGTTACTTCAGCAAGAGTgtacttgttc ... ttgccctcagGAGATTCAAGAGCTATTTAGTTTGCCACAACAAGGATTTGATGTTTCCCTC
EST: gi|31909601|gb|CD651000.1|CD651000
EST:     CAGCTACGGAGCAAAAAGAGCAAACCCGTTACTTCAGCAAGAGT                         GAGATTCAAGAGCTATTTAGTTTGCCACAACAAGGATTTGATGTTTCCCTC
genomic: CAGCTACGGAGCAAAAAGAGCAAACACGTTACTTCAGCAAGAGTgtacttgttc ... ttgccctcagGAGATTCAAGAGCTATTTAGTTTGCCACAACAAGGATTTGATGTTTCCCTC
EST: gi|60355698|gb|DN222671.1|DN222671
EST:     TCCGGACAGCTACGGAGCAAAAAGAGCAAACACGTTACTTCAGCAAGAGT                         GAGATTCAAGAGCTATTTAGTTTGCCACAACAAGGATTTGATGTTTCCCTC
genomic: TCAGGACAGCTACGGAGCAAAAAGAGCAAACACGTTACTTCAGCAAGAGTgtacttgttc ... ttgccctcagGAGATTCAAGAGCTATTTAGTTTGCCACAACAAGGATTTGATGTTTCCCTC
EST: gi|78022845|gb|DV491232.1|DV491232
EST:     TCAGGACAGCTACGGAGCAAAAAGAGCAAACACGTTACTTCAGCAAGAGT                         GAGATTCAAGAGCTATTTAGTTTGCCACAACAAGGATTTGATGTTTCCCTC
genomic: TCAGGACAGCTACGGAGCAAAAAGAGCAAACACGTTACTTCAGCAAGAGTgtacttgttc ... ttgccctcagGAGATTCAAGAGCTATTTAGTTTGCCACAACAAGGATTTGATGTTTCCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgtctgtttaattcctattagatacttatgcgtgtcctgttcttgccctcagGAGATTCAAGAGCTATTTAGTTTGCCACAACAAGGATTTGATGTTTCCCTCACACATAAGCAGTTGCAAGAAGAGCATGGTCAACAAGTTGTTCT
        gtttaat  putative branch site (score: 4)
                                     tcctgttcttgccctc  putative PPT
         tttaattcctatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttgttctgatcccatttcctgtcattgtctgtttaattcctattagatacttatgcgtgtcctgttcttgccctcagGAGATTCAAGAGCTATTTAGTTTGCCACAACAAGGATTTGATGTTTCCCTCACACATAAGCAGTTGCAAGAAGAGCATGGTCAACAAGTTGTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA