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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactccctcgcttgccagagtcaccatagcacaccaaatgagtactacgtgcttgttggcttgttgcatccatggttcttagtcacaagtcacaacatctatcatcaaaggaaaccaaattgagcaaaatttgtttgtcatatgcatgtttccggcaccgacatttaccacgccttcatcctgagcagGTTAACATGTCGCTGATAGTCCATGATAGCGATGCAAAGGCACTCGTAGAAGCCCTTCATCAGGCGTTCTTTGAAGACGATGTCCTATCACAAGTCGAAG

Basic information

species Zea mays
transcript GRMZM2G300862_T02
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G300862_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g70300.1 (Oryza sativa), 3'ss of exon 12
gtactccctcgcttgccagagtcaccatagcacaccaaatgagtactacgtgcttgttggcttgttgcatccatggttcttagtcacaagtcacaacatctatcatcaaaggaaaccaaattgagcaaaatttgtt-tgtcatatgcatgtttccggcaccgacatttaccacgccttcatcctgagcagGTTAACATGTCGCTGATAGTCCATGATAGCGATGCAAAGGCACTCGTAGAAGCCCTTCATCAGGCGTTCTTTGAAGACGATGTCCTATCACAAGTCGAAG
                                                                                                    ||       |  | ||     |   || | ||      |   ||| |||||    |   | || ||   | | |    |  | | | |||||||||||||| ||||| || ||||||||||| ||||||     | || | ||||| || ||||||||||| || |||||||||||  || ||||||| |
---------------------------------------------------------------------------------------------------gtagtccttgataagactgttct---cacacttgacaacgctgtatccatgtcctggttcctgatat---caatgttgccgccttcaacagGTTAACATGTCTCTGATTGTTCATGATAGCGAGGCAAAGCAGTGCATAAAGGCCCTCCACCAGGCGTTCTTCGAGGACGATGTCCTGACAGAAGTCGAGG
















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|149101053|gb|EE187151.2|EE187151
EST:     TGAGGAAAAGTGGGGTTAATGTTCAGATGATCTCGCAAGGAGCGTCAAAG                         GTTAACATGTCGCTGATAGTCCATGATAGCGATGCAAAGGCACTCGTAGAA
genomic: TGAGGAAAAGTGGGGTTAATGTTCAGATGATCTCGCAAGGAGCGTCAAAGgtactccctc ... tcctgagcagGTTAACATGTCGCTGATAGTCCATGATAGCGATGCAAAGGCACTCGTAGAA
EST: gi|89249156|gb|DY620942.1|DY620942
EST:     TGAGGAAAAGTGGGGTTAATGTTCAGATGATCTCGCAAGGAGCGTCAAAG                         GTTAACATGTCGCTGATAGTCCATGATAGCGATGCAAAGGCACTCGTAGAA
genomic: TGAGGAAAAGTGGGGTTAATGTTCAGATGATCTCGCAAGGAGCGTCAAAGgtactccctc ... tcctgagcagGTTAACATGTCGCTGATAGTCCATGATAGCGATGCAAAGGCACTCGTAGAA
EST: gi|4680998|gb|AI629668.1|AI629668
EST:     TGAGGAAAAGTGGGGTTAATGTTCAGATGATCTCGCAAGGAGCGTCAAAG                         GTTAACATGTCGCTGATAGTCCATGATAGCGATGCAAAGGCACTCGTAGAA
genomic: TGAGGAAAAGTGGGGTTAATGTTCAGATGATCTCGCAAGGAGCGTCAAAGgtactccctc ... tcctgagcagGTTAACATGTCGCTGATAGTCCATGATAGCGATGCAAAGGCACTCGTAGAA
EST: gi|113820685|gb|DW944259.1|DW944259
EST:     CAAGGAGCGTCAAAG                         GTTAACATGTCGCTGATAGTCCATGATAGCGATGCAAAGGCACTCGTAGAA
genomic: CAAGGAGCGTCAAAGgtactccctc ... tcctgagcagGTTAACATGTCGCTGATAGTCCATGATAGCGATGCAAAGGCACTCGTAGAA
EST: gi|50338979|gb|CO534105.1|CO534105
EST:     TGAGGAAAAGTGGGGTTAATGTTCAGATGATCTCGCAAGGAGCGTCAAAG                         GTTAACATGTCGCTGATAGTCCATGATAGCGATGCAAAGGCACTCGTAGAA
genomic: TGAGGAAAAGTGGGGTTAATGTTCAGATGATCTCGCAAGGAGCGTCAAAGgtactccctc ... tcctgagcagGTTAACATGTCGCTGATAGTCCATGATAGCGATGCAAAGGCACTCGTAGAA
EST: gi|5607844|gb|AI901511.1|AI901511
EST:     TGAGGAAAAGTGGGGTTAATGTTCAGATGATCTCGCAAGGAGCGTCAAAG                         GTTAACATGTCGCTGATAGTCCATGATAGCGATGCAAAGGCCCTCGTAGAA
genomic: TGAGGAAAAGTGGGGTTAATGTTCAGATGATCTCGCAAGGAGCGTCAAAGgtactccctc ... tcctgagcagGTTAACATGTCGCTGATAGTCCATGATAGCGATGCAAAGGCACTCGTAGAA
EST: gi|76911222|gb|DV164206.1|DV164206
EST:     TGAGGAAAAGTGGGGTTAATGTTCAGATGATCTCGCAAGGAGCGTCAAAG                         GTTAACATGTCGCTGATAGTCCATGATAGCGATGCAAAGGCACTCGTAGAA
genomic: TGAGGAAAAGTGGGGTTAATGTTCAGATGATCTCGCAAGGAGCGTCAAAGgtactccctc ... tcctgagcagGTTAACATGTCGCTGATAGTCCATGATAGCGATGCAAAGGCACTCGTAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtcatatgcatgtttccggcaccgacatttaccacgccttcatcctgagcagGTTAACATGTCGCTGATAGTCCATGATAGCGATGCAAAGGCACTCGTAGAAGCCCTTCATCAGGCGTTCTTTGAAGACGATGTCCTATCACAAGTCGAAG
                                       ccttcatcct  CT-rich tract
                           acattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactccctcgcttgccagagtcaccatagcacaccaaatgagtactacgtgcttgttggcttgttgcatccatggttcttagtcacaagtcacaacatctatcatcaaaggaaaccaaattgagcaaaatttgtttgtcatatgcatgtttccggcaccgacatttaccacgccttcatcctgagcagGTTAACATGTCGCTGATAGTCCATGATAGCGATGCAAAGGCACTCGTAGAAGCCCTTCATCAGGCGTTCTTTGAAGACGATGTCCTATCACAAGTCGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA