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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgtcaaatgatccaaaatttcttgttgacaacattgtgtccaatacctatatactatgctttttgaatttggaaacatttttacccatacttttctactgcagGGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAG

Basic information

species Zea mays
transcript GRMZM2G132712_T01
intron # 28
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G309782_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 13
-------------------------------------------------------gcatgtcaaatgatccaaaatttcttgttgacaacattgtgtccaatacctatatactatgct--ttttgaatttggaaacatttttacccatacttttctactgcagGGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAG
                                                       | | |   ||   |   |    | |      |       |     | |  ||||   |   ||  | ||||  |     ||| |  || ||||  ||  ||| | ||||||||||||||| || ||||| |||||| ||||||||||||| |||
gcatgtaaattttccctgaccattgctattgtatttacatgttactgagtatgatggacgctgaactttttgagtggtgtcccaagctgtgccattctggagagatataatttgaactgttcttgagataactcacaatactaaccatctttcgctatttcagGGAACCTCTTGTGACTAATATTATGTGGCGAAACTTGTTTGTCCAG
















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|5846745|gb|AI999828.1|AI999828
EST:     ATGAAGAGAAATCCTGTTGGTCGAAG                         GGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAG
genomic: ATGAAGAGAAATCCTGTTGGTCGAAGgcatgtcaaa ... tctactgcagGGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAG
EST: gi|5296205|gb|AI782885.1|AI782885
EST:     ATGAAGAGAAATCCTGTTGGTCGAAG                         GGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAG
genomic: ATGAAGAGAAATCCTGTTGGTCGAAGgcatgtcaaa ... tctactgcagGGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAG
EST: gi|6020890|gb|AW065818.1|AW065818
EST:     ATGAAGAGAAATCCTGTTGGTCGAAG                         GGAACCTCTTGTTACAAATATCATGAGGAGAAACTTGTTTGNTCAG
genomic: ATGAAGAGAAATCCTGTTGGTCGAAGgcatgtcaaa ... tctactgcagGGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAG
EST: gi|60340338|gb|DN207311.1|DN207311
EST:     ACCGAGCCTCCAACAGACAACCTTATGAAGAGAAATCCTGTTGGTCGAAG                         GGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAG
genomic: ACCGAGCCTCCAACAGACAACCTTATGAAGAGAAATCCTGTTGGTCGAAGgcatgtcaaa ... tctactgcagGGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAG
EST: gi|116821995|gb|EC865361.1|EC865361
EST:     ACCGAGCCTCCAACAGACAACCTTATGAAGAGAAATCCTGTTGGTCGAAG                         GGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAG
genomic: ACCGAGCCTCCAACAGACAACCTTATGAAGAGAAATCCTGTTGGTCGAAGgcatgtcaaa ... tctactgcagGGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatactatgctttttgaatttggaaacatttttacccatacttttctactgcagGGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAG
                                         cttttctact  CT-rich tract
           tttttgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgtcaaatgatccaaaatttcttgttgacaacattgtgtccaatacctatatactatgctttttgaatttggaaacatttttacccatacttttctactgcagGGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA