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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAGCCGTCCAGGATGGGATACAACCGCCACAGGCGTGGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTGgtaattggttctgtttcaactctaaattatattttacctcgtggtaattggatttttgccactcataatgttgtcttcttgttataattaacactgtgtc...

Basic information

species Zea mays
transcript GRMZM2G114758_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114758_T05 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g09920.1 (Oryza sativa), 5'ss of exon 1
---------GGAAGCCGTCCAGGATGGGATACAACCGCCACAGGCGTGGCCGGGGATCATCCTCA---TCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTGgtaattg----gttctgtttcaactctaa-attatattttacctcgtggtaattggatttttgccactcataatgttgtcttcttgttataattaacactgtgtc
          |  |   | |  |||||||||||||||    || || ||||| ||||| |||||    ||||| ||||||||||||||||| |||||| ||||||||||     |  |  |||    ||||       ||| |   ||     ||    |   |  ||  |   |  | | ||      || | |||    ||||   
TGCCGTCGCCGGCGAGCTTCGCGATGGGATACAACCGG---AGACGCGGCCGTGGATCCTCCTCCTCCTCGTCGTCGCGCCGCACCAAGCAGGAAGCCGCGTGgtaattatagcgcgcgatttgctatctaccgccgaattatgtttccgtccaa---aaccctctccctttggagggctttcaaagatttttgattcctgctgtt--
















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|50330066|gb|CO525192.1|CO525192
EST:     CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTG                         TGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAGAAG
genomic: CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTGgtaattggtt ... ttggtttcagTGATGATGATGGCCTTGGGACATCACTTCCAAGGC---AAGAAG
EST: gi|88758037|gb|DY542178.1|DY542178
EST:     CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTG                         TGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAGAAG
genomic: CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTGgtaattggtt ... ttggtttcagTGATGATGATGGCCTTGGGACATCACTTCCAAGGC---AAGAAG
EST: gi|213167931|gb|FM194811.1|FM194811
EST:     CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTG                         TGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAG
genomic: CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTGgtaattggtt ... ttggtttcagTGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAG
EST: gi|20301530|gb|BQ164473.1|BQ164473
EST:     CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTC--G                         TG-TGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAGAAG
genomic: CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTGgtaattggtt ... ttggtttcagTGATGATGATGGCCTTGGGACATCACTTCCAAGGC---AAGAAG
EST: gi|4753352|gb|AI657257.1|AI657257
EST:     CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTG                         TGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAGAAG
genomic: CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTGgtaattggtt ... ttggtttcagTGATGATGATGGCCTTGGGACATCACTTCCAAGGC---AAGAAG
EST: gi|31356143|gb|CD440500.1|CD440500
EST:     CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTG                         TGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAG
genomic: CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTGgtaattggtt ... ttggtttcagTGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAG
EST: gi|74244151|gb|DT652065.1|DT652065
EST:     CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTG                         TGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAGAAG
genomic: CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTGgtaattggtt ... ttggtttcagTGATGATGATGGCCTTGGGACATCACTTCCAAGGC---AAGAAG
EST: gi|211261561|gb|FL168251.1|FL168251
EST:     CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTG                         TGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAG
genomic: CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTGgtaattggtt ... ttggtttcagTGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAG
EST: gi|76016358|gb|DT943528.1|DT943528
EST:     CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTG                         TGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAG
genomic: CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTGgtaattggtt ... ttggtttcagTGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAG
EST: gi|20506938|gb|BQ279408.1|BQ279408
EST:     CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTC--G                         TG-TGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAGAAG
genomic: CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTGgtaattggtt ... ttggtttcagTGATGATGATGGCCTTGGGACATCACTTCCAAGGC---AAGAAG
EST: gi|91055730|gb|EB166148.1|EB166148
EST:     CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTG                         TGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAG
genomic: CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTGgtaattggtt ... ttggtttcagTGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAG
EST: gi|26456351|gb|CA827934.1|CA827934
EST:     CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTC--G                         TG-TGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAGAAG
genomic: CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTGgtaattggtt ... ttggtttcagTGATGATGATGGCCTTGGGACATCACTTCCAAGGC---AAGAAG
EST: gi|78118561|gb|DV536945.1|DV536945
EST:     CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTG                         TGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAGAAG
genomic: CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTGgtaattggtt ... ttggtttcagTGATGATGATGGCCTTGGGACATCACTTCCAAGGC---AAGAAG
EST: gi|76937011|gb|DV175004.1|DV175004
EST:     CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTG                         TGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAG
genomic: CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTGgtaattggtt ... ttggtttcagTGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAG
EST: gi|91048770|gb|EB159188.1|EB159188
EST:     CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTG                         TGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAGAAG
genomic: CGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTGgtaattggtt ... ttggtttcagTGATGATGATGGCCTTGGGACATCACTTCCAAGGC---AAGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAGCCGTCCAGGATGGGATACAACCGCCACAGGCGTGGCCGGGGATCATCCTCATCGTCTTCGCGCCGCACCAAGCAAGAAGCCTCGTGgtaattggttctgtttcaactctaaattatattttacctcgtggtaattggatttttgccactcataatgttgtcttcttgttataattaacactgtgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC