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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAGgtgagatggtcccgtccttgttcgagagggaggagctggaatgcacgttcgatttgggtctgggaaatggcttctgattcctcgatctggcctgggttttgcag

Basic information

species Zea mays
transcript GRMZM2G134738_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134738_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g42650.1 (Oryza sativa), 5'ss of exon 2
AGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAGgtg-agatggtcccgtccttgttcgagaggga---------------ggagctggaatgcacgttcgatttg---ggtctgggaaatggcttc-tgattcctcgatctggcctgggttttgcag
 |||||||||||||| ||||||||||||||||||||||||||||||||| ||||| |||||||| | ||| |||||| ||||| |||||     | | || ||     |                   | | |||| |     | |  ||||   | ||||| ||  || ||| |||||   ||||||| |   ||||| ||||
GGGACAAGCCGGCGACGGTGGAGGACGTCATGCCCATCGCCACGGGGCTGGAGCGCGAGGAGCTCGCGGCGGAGCTCAAGgtggagatgcctatgccttttttttttcgtttttttttttgcttcttcgggttggagtattgctcctttttgtctgttctggaaatgggtttcgtgatttgccgatctgtctgtggtttcgcag
















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|76288217|gb|DV027785.1|DV027785
EST:     TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG                         GGGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG
genomic: TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG
EST: gi|28985245|gb|BQ538397.2|BQ538397
EST:     ATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG                         GGGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG
genomic: ATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG
EST: gi|18450528|gb|BM428806.1|BM428806
EST:     TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG                         GGGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG
genomic: TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG
EST: gi|37382992|gb|CF628470.1|CF628470
EST:     TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG                         GGGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG
genomic: TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG
EST: gi|18649503|gb|BM498322.1|BM498322
EST:     TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG                         GGGAAGAAGCGGTTCGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG
genomic: TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG
EST: gi|29130310|gb|CB381014.1|CB381014
EST:     TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG                         GGGAAGAAGCGGTTTGACATGGATTCCCCGGACGGCCCCTTCGGTACCAAG
genomic: TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG
EST: gi|18450555|gb|BM428833.1|BM428833
EST:     GCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCCAG                         GGGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAA
genomic: GCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCT-CCAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAA
EST: gi|60352341|gb|DN219314.1|DN219314
EST:     TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG                         GGGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG
genomic: TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG
EST: gi|24770192|gb|CA405321.1|CA405321
EST:     AGCTAGAGGCCGAGCTCCAG                         GGGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG
genomic: AGCTAGAGGCCGAGCTCCAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG
EST: gi|76288216|gb|DV027784.1|DV027784
EST:     CCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCCAG                         GGGAGGAAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAA
genomic: CCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAGgtgagatggt ... ggttttgcagGGGAAG-AAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAA
EST: gi|60348157|gb|DN215130.1|DN215130
EST:     TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG                         GGGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG
genomic: TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG
EST: gi|31354094|gb|CD438451.1|CD438451
EST:     TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG                         GGGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTATTTTT
genomic: TGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAGgtgagatggt ... ggttttgcagGGGAAGAAGCGGTTTGACATGGATTCCCCGGTCGGCCCCTTCGGTACCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAGgtgagatggtcccgtccttgttcgagagggaggagctggaatgcacgttcgatttgggtctgggaaatggcttctgattcctcgatctggcctgggttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT