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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAATTCTTCAAGGAGGAATATGAGAAGGAGAAGGATCTTCTTGGGGGAGCTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACATgtattggttactttgtgtttggtctagttattttgctctatgcttgtccattgaatctgatctcttgctctcttcag

Basic information

species Zea mays
transcript GRMZM2G014116_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014116_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g63430.1 (Oryza sativa), 5'ss of exon 9
GGAATTCTTCAAGGAGGAATATGAGAAGGAGAAGGATCTTCTTGGGGGAGCTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACATgtattggttactt--------tgtgtttgg-tctagttattttgctctatgcttgtccattgaat-ctgatctcttgctctc-ttcag
||||||||| || || ||||||| ||| |||||| || |||| || ||||||||||||| ||||||| |||| ||| |||   ||||||| || |||||||||||| ||||||         || |||   | | | |   ||||| | |  |||||  |||| | |   |   ||||| |  |||||
GGAATTCTTTAAAGATGAATATGCGAATGAGAAGAATTTTCTCGGAGGAGCTTTGGGTGACAAAGCTGCAGAGGATCTGAAATTGAGGATCATTGAACATgtattgcttacttgactttatcgtatttctcttttggttccttgctttgtatttgtcagttgatttccagttctttgcttttgttcag
















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|31910182|gb|CD651296.1|CD651296
EST:     CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACAT                         AATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACATgtattggtta ... ctctcttcagAATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
EST: gi|113701567|gb|EE679071.1|EE679071
EST:     CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACAT                         AATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACATgtattggtta ... ctctcttcagAATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
EST: gi|24769954|gb|CA405083.1|CA405083
EST:     CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACAT                         AATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACATgtattggtta ... ctctcttcagAATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
EST: gi|60672488|gb|DN475194.1|DN475194
EST:     CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACAT                         AATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACATgtattggtta ... ctctcttcagAATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
EST: gi|453340|gb|T15314.1|T15314
EST:     CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACAT                         AATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACATgtattggtta ... ctctcttcagAATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
EST: gi|60343636|gb|DN210609.1|DN210609
EST:     CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACAT                         AATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACATgtattggtta ... ctctcttcagAATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
EST: gi|60341988|gb|DN208961.1|DN208961
EST:     CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACAT                         AATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACATgtattggtta ... ctctcttcagAATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
EST: gi|60344719|gb|DN211692.1|DN211692
EST:     CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACAT                         AATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACATgtattggtta ... ctctcttcagAATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
EST: gi|211150173|gb|FL276378.1|FL276378
EST:     CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACAT                         AATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACATgtattggtta ... ctctcttcagAATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
EST: gi|24766335|gb|CA401489.1|CA401489
EST:     CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACAT                         AATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACATgtattggtta ... ctctcttcagAATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
EST: gi|32907838|gb|CF012651.1|CF012651
EST:     CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACAT                         AATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACATgtattggtta ... ctctcttcagAATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
EST: gi|16379510|gb|BI992995.1|BI992995
EST:     CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACAT                         AATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACATgtattggtta ... ctctcttcagAATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
EST: gi|44681826|gb|CK786874.1|CK786874
EST:     CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGGACAT                         AATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACATgtattggtta ... ctctcttcagAATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
EST: gi|71762659|gb|DR960596.1|DR960596
EST:     CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACAT                         AATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACATgtattggtta ... ctctcttcagAATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
EST: gi|60346799|gb|DN213772.1|DN213772
EST:     CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACAT                         AATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACATgtattggtta ... ctctcttcagAATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
EST: gi|16926500|gb|BM079573.1|BM079573
EST:     CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACAT                         AATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACATgtattggtta ... ctctcttcagAATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
EST: gi|24764505|gb|CA399669.1|CA399669
EST:     CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACAT                         AATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACATgtattggtta ... ctctcttcagAATATCTTGGTTGTATCCAAGTACTATGCAAGGGTTACCCTCGAGAGGCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAATTCTTCAAGGAGGAATATGAGAAGGAGAAGGATCTTCTTGGGGGAGCTTTGGGTGCCAAAGCTTCAGAAGATTTGAGGCTGAGGATTATCGAACATgtattggttactttgtgtttggtctagttattttgctctatgcttgtccattgaatctgatctcttgctctcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT