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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattgctgaaatctgtgtctgcctgccgccttgttccttccccggttcttccgattcgttttctttttcctgagacgtcacgtgtttgcttctggtgttgtagCAGCGAGCGGGGGCAAGTCGATGGTGAAGTACGAGGGCGGCTACACCGTGGAGACGGTCTTCGACGGCAGCAAGCTGGGGATCGAGCCCTACTCCGTGGA

Basic information

species Zea mays
transcript GRMZM2G075260_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075260_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g49770.1 (Oryza sativa), 3'ss of exon 2
gtgattgctgaaatctgtgtc-tgcctgccgccttgttccttccccggttcttccgattcgttttctttttcctgagacgtcacgtgtttgcttctggtgttgtagCAGCGAGCGGGGGCAAGTCGATGGTGAAGTACGAGGGCGGCTACACCGTGGAGACGGTCTTCGACGGCAGCAAGCTGGGGATCGAGCCCTACTCCGTGGA---
|||||||||| ||||| | || |||  |  || ||  |||  ||| ||            |||||  || |    ||   |     | |  ||  | | | || |||||  ||||| || |||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||||||||| | |||||   
gtgattgctggaatctttctcgtgctcgtggcgtttctcc--ccctgg------------gttttggttgtttgaagcaatttttcgctctctgattgcgatggagcagGAAGCGGAGGGAAGTCGATGGTGAAGTACGAGGGCGGGTACACCGTGGAGACGGTCTTCGACGGGAGCAAGCTGGGGATCGAGCCCTACGCGGTGGAGGT
















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|78081385|gb|DV509797.1|DV509797
EST:     TTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAG                         C-G--AGCGGGGGCAAGTCGATGGTGAAGTACGAGGGCGGCTACACCGTGG
genomic: TTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAGgtgattgctg ... ggtgttgtagCAGCGAGCGGGGGCAAGTCGATGGTGAAGTACGAGGGCGGCTACACCGTGG
EST: gi|71436276|gb|DR817326.1|DR817326
EST:     TTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAG                         C-G--AGCGGGGGCAAGTCGATGGTGAAGTACGAGGGCGGCTACACCGTGG
genomic: TTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAGgtgattgctg ... ggtgttgtagCAGCGAGCGGGGGCAAGTCGATGGTGAAGTACGAGGGCGGCTACACCGTGG
EST: gi|91048035|gb|EB158453.1|EB158453
EST:     TTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAG                         C-G--AGCGGGGGCAAGTCGATGGTGAAGTACGAGGGCGGCTACACCGTGG
genomic: TTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAGgtgattgctg ... ggtgttgtagCAGCGAGCGGGGGCAAGTCGATGGTGAAGTACGAGGGCGGCTACACCGTGG
EST: gi|211042150|gb|FL156952.1|FL156952
EST:     TTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAG                         C-G--AGCGGGGGCAAGTCGATGGTGAAGTACGAGGGCGGCTACACCGTGG
genomic: TTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAGgtgattgctg ... ggtgttgtagCAGCGAGCGGGGGCAAGTCGATGGTGAAGTACGAGGGCGGCTACACCGTGG
EST: gi|50334127|gb|CO529253.1|CO529253
EST:     TTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGAT--                         -AGCGAGCGGGGGCAAGTCGATGGTGAAGTACGAGGGCGGCTACACCGTGG
genomic: TTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAGgtgattgctg ... ggtgttgtagCAGCGAGCGGGGGCAAGTCGATGGTGAAGTACGAGGGCGGCTACACCGTGG
EST: gi|71327834|gb|DR800547.1|DR800547
EST:     TTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAG                         C-G--AGCGGGGGCAAGTCGATGGTGAAGTACGAGGGCGGCTACACCGTGG
genomic: TTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAGgtgattgctg ... ggtgttgtagCAGCGAGCGGGGGCAAGTCGATGGTGAAGTACGAGGGCGGCTACACCGTGG
EST: gi|31357778|gb|CD442135.1|CD442135
EST:     TTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGAT--                         -AGCGAGCGGGGGCAAGTCGATGGTGAAGTACGAGGGCGGCTACACCGTGG
genomic: TTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAGgtgattgctg ... ggtgttgtagCAGCGAGCGGGGGCAAGTCGATGGTGAAGTACGAGGGCGGCTACACCGTGG
EST: gi|211499168|gb|FL156948.1|FL156948
EST:     TTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAG                         C-G--AGCGGGGGCAAGTCGATGGTGAAGTACGAGGGCGGCTACACCGTGG
genomic: TTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAGgtgattgctg ... ggtgttgtagCAGCGAGCGGGGGCAAGTCGATGGTGAAGTACGAGGGCGGCTACACCGTGG
EST: gi|148939778|gb|EC884477.2|EC884477
EST:     TTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAG                         CAGCGAGCGGGGGCAAGTCGATGGTGAAGTACGAGGGCGGCTACACCGTGG
genomic: TTCGGCGGTGGTGAAGCGGCTGTGGTCGCTCAAATCCACCACCAAGATAGgtgattgctg ... ggtgttgtagCAGCGAGCGGGGGCAAGTCGATGGTGAAGTACGAGGGCGGCTACACCGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccgattcgttttctttttcctgagacgtcacgtgtttgcttctggtgttgtagCAGCGAGCGGGGGCAAGTCGATGGTGAAGTACGAGGGCGGCTACACCGTGGAGACGGTCTTCGACGGCAGCAAGCTGGGGATCGAGCCCTACTCCGTGGA
          ttttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattgctgaaatctgtgtctgcctgccgccttgttccttccccggttcttccgattcgttttctttttcctgagacgtcacgtgtttgcttctggtgttgtagCAGCGAGCGGGGGCAAGTCGATGGTGAAGTACGAGGGCGGCTACACCGTGGAGACGGTCTTCGACGGCAGCAAGCTGGGGATCGAGCCCTACTCCGTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG