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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcatttttagtacctgacattgatattacacctgaactcttaactagatgttgttaaggtcacacacacacctgctcgaataaatagctgtcttgtttttataattcatgctatgaacatatatgtgtttttagcccattagcttttaacagatagctggttgacaatttttctacattttcagATCGTGATTGCCTTCAGCATTGTAGATCGCATGAAGAAGATGTTTTATTCTGAGCAAGCGGCTAATTCTAG

Basic information

species Zea mays
transcript GRMZM2G102196_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102196_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os01g06270.1 (Oryza sativa), 3'ss of exon 14
gttcatttttagtacctgacattgatattacacctgaactcttaactagatgttgttaaggtcacacacacacctgctcgaataaatagctgtcttgtttttataattcatgctatgaacatatatgtgtttttagcccatta------gcttttaa--cagatagct------ggttgacaatttttctacatttt-cagATCGTGATTGCCTTCAGCATTGTAGATCGCATGAAGAAGATGTTTTATTCTGAGCAAGCGGCTAATTCTAG
                                                                                                     || |||||||   ||||||   ||||| ||||||||| |||       ||||  ||   |||||  |       | ||||||| | || | ||||| ||||| || |||||||| |||||    |||| |||||||||| | ||||||||||| |||| || |||||||||
----------------------------------------------------------------------------------------------------gtacaattcatatcatgaactggtatgt-tttttagcctattccgcattgcttacaaattagatattttcagtgagctgacaatatgtcaatatttttcagATTGTAATTGCCTTTAGCATCACTGATCACATGAAGAAGCTCTTTTATTCTGAACAAGGGGTTAATTCTAG
















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|61119836|gb|DN560797.1|DN560797
EST:     CAAGTCCACAAAAGTCCCTTGAGGAGGAATATTTGGAAACTGAAAAGAAG                         ATCGTGATTGCCTTCAGCATTGTAGATCGCATGAAGAAGATGTTTTATTCT
genomic: CAAGTCCACAAAAGTCCCTTGAGGAGGAATATTTGGAAACTGAAAAGAAGgttcattttt ... acattttcagATCGTGATTGCCTTCAGCATTGTAGATCGCATGAAGAAGATGTTTTATTCT
EST: gi|60354570|gb|DN221543.1|DN221543
EST:     CAAGTCCACAAAAGTCCCTTGAGGAGGAATATTTGGAAACTGAAAAGAAG                         ATCGTGATTGCCTTCAGCATTGTAGATCGCATGAAGAAGATGTTTTATTCT
genomic: CAAGTCCACAAAAGTCCCTTGAGGAGGAATATTTGGAAACTGAAAAGAAGgttcattttt ... acattttcagATCGTGATTGCCTTCAGCATTGTAGATCGCATGAAGAAGATGTTTTATTCT
EST: gi|4621437|gb|AI612270.1|AI612270
EST:     CAAGTCCACAAAAGTCCCTTGAGGAGGAATATTTGGAAACTGAAAAGAAG                         ATCGTGATTGCCTTCAGCATTGTAGATCGCATGAAGAAGATGTTTTATTCT
genomic: CAAGTCCACAAAAGTCCCTTGAGGAGGAATATTTGGAAACTGAAAAGAAGgttcattttt ... acattttcagATCGTGATTGCCTTCAGCATTGTAGATCGCATGAAGAAGATGTTTTATTCT
EST: gi|60339229|gb|DN206202.1|DN206202
EST:     CAAGTCCACAAAAGTCCCTTGAGGAGGAATATTTGGAAACTGAAAAGAAG                         ATCGTGATTGCCTTCAGCATTGTAGATCGCATGAAGAAGATGTTTTATTCT
genomic: CAAGTCCACAAAAGTCCCTTGAGGAGGAATATTTGGAAACTGAAAAGAAGgttcattttt ... acattttcagATCGTGATTGCCTTCAGCATTGTAGATCGCATGAAGAAGATGTTTTATTCT
EST: gi|31352028|gb|CD436385.1|CD436385
EST:     CAAGTCCACAAAAGTCCCTTGAGGAGGAATATTTGGAAACTGAAAAGAAG                         ATCGTGACTGCCTTCAGCATTGTAGATCGCATGAAGAAGATGTTTTATTCT
genomic: CAAGTCCACAAAAGTCCCTTGAGGAGGAATATTTGGAAACTGAAAAGAAGgttcattttt ... acattttcagATCGTGATTGCCTTCAGCATTGTAGATCGCATGAAGAAGATGTTTTATTCT
EST: gi|60340698|gb|DN207671.1|DN207671
EST:     CAAGTCCACAAAAGTCCCTTGAGGAGGAATATTTGGAAACTGAAAAGAAG                         ATCGTGATTGCCTTCAGCATTGTAGATCGCATGAAGAAGATGTTTTATTCT
genomic: CAAGTCCACAAAAGTCCCTTGAGGAGGAATATTTGGAAACTGAAAAGAAGgttcattttt ... acattttcagATCGTGATTGCCTTCAGCATTGTAGATCGCATGAAGAAGATGTTTTATTCT
EST: gi|60337011|gb|DN203984.1|DN203984
EST:     CAAGTCCACAAAAGTCCCTTGAGGAGGAATATTTGGAAACTGAAAAGAAG                         ATCGTGATTGCCTTCAGCATTGTAGATCGCATGAAGAAGATGTTTTATTCT
genomic: CAAGTCCACAAAAGTCCCTTGAGGAGGAATATTTGGAAACTGAAAAGAAGgttcattttt ... acattttcagATCGTGATTGCCTTCAGCATTGTAGATCGCATGAAGAAGATGTTTTATTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagcccattagcttttaacagatagctggttgacaatttttctacattttcagATCGTGATTGCCTTCAGCATTGTAGATCGCATGAAGAAGATGTTTTATTCTGAGCAAGCGGCTAATTCTAG
                                      tttttctacattttc  CT-rich tract
                                    aatttttctacatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcatttttagtacctgacattgatattacacctgaactcttaactagatgttgttaaggtcacacacacacctgctcgaataaatagctgtcttgtttttataattcatgctatgaacatatatgtgtttttagcccattagcttttaacagatagctggttgacaatttttctacattttcagATCGTGATTGCCTTCAGCATTGTAGATCGCATGAAGAAGATGTTTTATTCTGAGCAAGCGGCTAATTCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG