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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtaattttatatcttattactactccatgtagtgttgtactccatccaaattagatgtcactgcatccagGTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCT

Basic information

species Zea mays
transcript GRMZM2G042027_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042027_T05 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g29860.1 (Oryza sativa), 3'ss of exon 6
-------------gtctgtaattttatatcttattactactccatgtagtgttgtactccatccaaattagatgtcactgcatccagGTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCT
              |||| | | ||  |  || ||  |  |  || || ||||||  | ||   ||| | |||  || | | | ||||| ||||||||||| |||||||| |||||||||| |||||||||||||||||||||||||||||||| |||||||||||| | ||| || ||||||
gtcagtttttctattctgaactctttcacatttttcttgatgaatttaatgttgttttacactgaaaattgattgcattcctttcagGTTGTCAAACAAAGAATGCAAACAGGTCAATTCAGGTCTGCACCTGATGCTGTTCGTCTCATTGTTGGTAAAGAAGGATTCAGAGGTCTTTACGCT

upper sequence: GRMZM2G042027_T05 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G36580.3 (Glycine max), 3'ss of exon 7
gtctgtaattttatatcttattactactccatgtagt--gttgtactccatccaaattagatgtcactgcatccagGTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCT
||   ||  ||||  |||| ||  | |   || |  |  | | |  |  |     | || ||     |   || |||| || || ||||||||||| | ||| ||||| || || || || |||||||| ||||| ||||||||||| || || |||||||| || |  || 
gtaattagctttacttctt-ttgttgccaaatattttctgctttcttgaacttggaatatattcatgtctttctagGTTGTTAAGCAAAGGATGCAGATTGGGCAATTTAAATCAGCCCCAGATGCTGTCCGTCTTATTGTTGCTAATGAGGGTTTTAAAGGTCTTTTTGCG
















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|211371111|gb|FL037583.1|FL037583
EST:     CAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACAGAG                         GTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCT
genomic: CAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACAGAGgtctgtaatt ... ctgcatccagGTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCT
EST: gi|50325364|gb|CO520490.1|CO520490
EST:     CAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACAGAG                         GTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCT
genomic: CAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACAGAGgtctgtaatt ... ctgcatccagGTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCT
EST: gi|71436673|gb|DR817723.1|DR817723
EST:     CAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACAGAG                         GTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCT
genomic: CAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACAGAGgtctgtaatt ... ctgcatccagGTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCT
EST: gi|71302083|gb|DR787129.1|DR787129
EST:     CAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACAGAG                         GTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCT
genomic: CAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACAGAGgtctgtaatt ... ctgcatccagGTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCT
EST: gi|76011416|gb|DT938586.1|DT938586
EST:     CAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACAGAG                         GTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCT
genomic: CAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACAGAGgtctgtaatt ... ctgcatccagGTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCT
EST: gi|211226520|gb|FL435621.1|FL435621
EST:     GCTTCCCTCGTCCGTGTCCCTACAGAG                         GTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCT
genomic: GCTTCCCTCGTCCGTGTCCCTACAGAGgtctgtaatt ... ctgcatccagGTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCT
EST: gi|91054196|gb|EB164614.1|EB164614
EST:     CAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACAGAG                         GTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCT
genomic: CAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACAGAGgtctgtaatt ... ctgcatccagGTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCT
EST: gi|78083391|gb|DV511784.1|DV511784
EST:     CAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACAGAG                         GTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCT
genomic: CAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACAGAGgtctgtaatt ... ctgcatccagGTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCT
EST: gi|60342707|gb|DN209680.1|DN209680
EST:     CAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACAGAG                         GTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCT
genomic: CAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACAGAGgtctgtaatt ... ctgcatccagGTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCT
EST: gi|67018887|gb|CO447636.1|CO447636
EST:     CAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACAGAG                         GTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCT
genomic: CAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACAGAGgtctgtaatt ... ctgcatccagGTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attactactccatgtagtgttgtactccatccaaattagatgtcactgcatccagGTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCT
                                aaattagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtaattttatatcttattactactccatgtagtgttgtactccatccaaattagatgtcactgcatccagGTGGTCAAACAAAGGATGCAAACTGGTCAATTCAAGTCTGCACCTGATGCTGTTCGTCTCATTGTTGCTAAAGAAGGATTTAAAGGACTGTACGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG