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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGCTTAAGGATGGACTTTGGGATGTATACAATGACTGTGCCATGGGAATGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAGgtctctcactgtcttctgttataattttattcctatgtttgtcaaaacataggtggtagtttccagtagttggttaatattggcaattattcttttgaga...

Basic information

species Zea mays
transcript GRMZM2G085474_T04
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085474_T04 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 6
CATGCTTAAGGATGGACTTTGGGATGTATACAATGACTGTGCCATGGGAATGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAGgtctctcactgtcttctgttataatttta--ttcctatgtt-tgtcaaaacataggtggtagtttccagtagttggttaatattggcaattattcttttgaga
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CATGCTTAAAGATGGCCTTTGGGATGTATACGGTGATTTTGCCATGGGAAATTGTGCTGAGCTTTGTGCTGACAATCATGCTCTGACAAGGGAAGACCAGgtattttttta-ctagtactataaataggagtaactaccttctgttgtaatattattcttacacttgtctacctgactcaaaaaaccaaa-actatcttagt-
















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|71765528|gb|DR963465.1|DR963465
EST:     TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAG                         GATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAGgtctctcact ... ttgttcatagGATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|78114650|gb|DV533038.1|DV533038
EST:     TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAG                         GATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGA
genomic: TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAGgtctctcact ... ttgttcatagGATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGA
EST: gi|149076180|gb|EE164774.2|EE164774
EST:     TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAG                         GATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAGgtctctcact ... ttgttcatagGATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|211292809|gb|FL187023.1|FL187023
EST:     TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAG                         GATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAGgtctctcact ... ttgttcatagGATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|149008746|gb|EE040943.2|EE040943
EST:     TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGA-GACCAG                         GATGCTTTTGC
genomic: TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAGgtctctcact ... ttgttcatagGATGCTTTTGC
EST: gi|148964641|gb|EC905928.2|EC905928
EST:     TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAG                         GATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAGgtctctcact ... ttgttcatagGATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|149050402|gb|EE155650.2|EE155650
EST:     TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAG                         GATGCTTTTGCTATCCAAAAGCA-CCAGCGTGGAATTGCTGCTCGTGACAG
genomic: TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAGgtctctcact ... ttgttcatagGATGCTTTTGCTATCCAAA-GCAACCAGCGTGGAATTGCTGCTCGTGACAG
EST: gi|211385847|gb|FL095517.1|FL095517
EST:     GTGTGCCGAACTTTGTGCTGACNATCATGCCCTCACAAGAGAAGACCCAG                         -ATGCTTTTGCTATCCAAAGCAACCAGCGTGGGAATTGCTGCTCGTGACA
genomic: GTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACC-AGgtctctcact ... ttgttcatagGATGCTTTTGCTATCCAAAGCAACCAGCGTGG-AATTGCTGCTCGTGACA
EST: gi|71769365|gb|DR967302.1|DR967302
EST:     TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAG                         GATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAGgtctctcact ... ttgttcatagGATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|32863231|gb|CF002913.1|CF002913
EST:     TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAG                         GATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGA
genomic: TGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAGgtctctcact ... ttgttcatagGATGCTTTTGCTATCCAAAGCAACCAGCGTGGAATTGCTGCTCGTGA

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGCTTAAGGATGGACTTTGGGATGTATACAATGACTGTGCCATGGGAATGTGTGCCGAACTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAGgtctctcactgtcttctgttataattttattcctatgtttgtcaaaacataggtggtagtttccagtagttggttaatattggcaattattcttttgaga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaacata