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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgtgtgccacgttaccgggttctaagttttcttatgctgcatatatgttaaccttgtttttctatctttacccagCACTCCTATATTTACTGGTGAAGAAGGTGGAAGCGGTTTTGCTGCTTCCGCAGCAGCTGCCGCAGCTACTGGAGCATCTGGATTTGAATTTGGTGTGGAC

Basic information

species Zea mays
transcript GRMZM2G165926_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165926_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g13970.1 (Oryza sativa), 3'ss of exon 5
gtaattgtgtgccacgttac-cgggttctaagtt-ttcttatgctgcatatatgttaacct-tgtttttctatctttacccagCACTCCTATATTTACTGGTGAAGAAGGTGGAAGCGGTTTTGCTGCTTCCGCAGCAGCTGCCGCAGCTACTGGAGCATCTGGATTTGAATTTGGTGTGGAC
|||||  |||  ||  ||   |||| |||| ||| || || |  || || | || | ||   |   | ||  ||||| | ||| |||||||| || ||||||||||||||||||||||||||||||||||| |||||||| || ||||||||||| ||| ||||||||||||||| |||||||
gtaataatgtatcaatttgttcgggctctaggttgttgttttaatgtatttctgctgacaaattaatatccctcttttcacagTACTCCTATCTTCACTGGTGAAGAAGGTGGAAGCGGTTTTGCTGCTTCTGCAGCAGCAGCAGCAGCTACTGGTGCAGCTGGATTTGAATTTGATGTGGAC
















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|32808865|gb|CD961099.1|CD961099
EST:     ATTGTTCATATCCCTCCTGGTGAAAATGCCCTCTCTGATGTCCTCCTAAG                         CACTCCTATATTTACTGGTGAAGAAGGTGGAAGCGGTTTTGCTGCTTCCGC
genomic: ATTGTTCATATCCCTCCTGGTGAAAATGCCCTCTCTGATGTCCTCCTAAGgtaattgtgt ... ctttacccagCACTCCTATATTTACTGGTGAAGAAGGTGGAAGCGGTTTTGCTGCTTCCGC
EST: gi|84977035|gb|DW475457.1|DW475457
EST:     ATTGTTCATATCCCTCCTGGTGAAAATGCCCTCTCTGATGTCCTCCTAAG                         CACTCCTATATTTACTGGTGAAGAAGGTGGAAGCGGTTTTGCTGCTTCCGC
genomic: ATTGTTCATATCCCTCCTGGTGAAAATGCCCTCTCTGATGTCCTCCTAAGgtaattgtgt ... ctttacccagCACTCCTATATTTACTGGTGAAGAAGGTGGAAGCGGTTTTGCTGCTTCCGC
EST: gi|32838026|gb|CD977704.1|CD977704
EST:     ATTGTTCATATCCCTCCTGGTGAAAATGCCCTCTCTGATGTCCTCCTAAG                         CACTCCTATATTTACTGGTGAAGAAGGTGGAAGCGGTTTTGCTGCTTCCGC
genomic: ATTGTTCATATCCCTCCTGGTGAAAATGCCCTCTCTGATGTCCTCCTAAGgtaattgtgt ... ctttacccagCACTCCTATATTTACTGGTGAAGAAGGTGGAAGCGGTTTTGCTGCTTCCGC
EST: gi|211459834|gb|FK984334.1|FK984334
EST:     ATTGTTCATATCCCTCCTGGTGAAAATGCCCTCTCTGATGTCCTCCTAAG                         CACTCCTATATTTACTGGTGAAGAAGGTGGAAGCGGTTTTGCTGCTTCCGC
genomic: ATTGTTCATATCCCTCCTGGTGAAAATGCCCTCTCTGATGTCCTCCTAAGgtaattgtgt ... ctttacccagCACTCCTATATTTACTGGTGAAGAAGGTGGAAGCGGTTTTGCTGCTTCCGC
EST: gi|34391254|gb|CF384482.1|CF384482
EST:     ATTGTTCATATCCCTCCTGGTGAAAATGCCCTCTCTGATGTCCTCCTAAG                         CACTCCTATATTTACTGGTGAAGAAGGTGGAAGCGGTTTTGCTGCTTCCGC
genomic: ATTGTTCATATCCCTCCTGGTGAAAATGCCCTCTCTGATGTCCTCCTAAGgtaattgtgt ... ctttacccagCACTCCTATATTTACTGGTGAAGAAGGTGGAAGCGGTTTTGCTGCTTCCGC
EST: gi|148954523|gb|EC899958.2|EC899958
EST:     ATTGTTCATATCCCTCCTGGTGAAAATGCCCTCTCTGATGTCCTCCTAAG                         CACTCCTATATTTACTGGTGAAGAAGGTGGAAGCGGTTTTGCTGCTTCCGC
genomic: ATTGTTCATATCCCTCCTGGTGAAAATGCCCTCTCTGATGTCCTCCTAAGgtaattgtgt ... ctttacccagCACTCCTATATTTACTGGTGAAGAAGGTGGAAGCGGTTTTGCTGCTTCCGC
EST: gi|28987468|gb|CB351650.1|CB351650
EST:     ATTGTTCATATCCCTCCTGGTGAAAATGCCCTCTCTGATGTCCTCCTAAG                         CACTCCTATATTTACTGGTGAAG
genomic: ATTGTTCATATCCCTCCTGGTGAAAATGCCCTCTCTGATGTCCTCCTAAGgtaattgtgt ... ctttacccagCACTCCTATATTTACTGGTGAAG
EST: gi|71419001|gb|DR804614.1|DR804614
EST:     ATTGTTCATATCCCTCCTGGTGAAAATGCCCTCTCTGATGTCCTCCTAAG                         CACTCCTATATTTACTGGTGAAGAAGGTGGAAGCGGTTTTGCTGCTTCCGC
genomic: ATTGTTCATATCCCTCCTGGTGAAAATGCCCTCTCTGATGTCCTCCTAAGgtaattgtgt ... ctttacccagCACTCCTATATTTACTGGTGAAGAAGGTGGAAGCGGTTTTGCTGCTTCCGC
EST: gi|40334578|gb|CK368648.1|CK368648
EST:     ATTGTTCATATCCCTCCTGGTGAAAATGCCCTCTCTGATGTCCTCCTAAG                         CACTCCTATATTTACTGGTGAAGAAGGTGGAAAGCGGTTTTGCTGCTTCCG
genomic: ATTGTTCATATCCCTCCTGGTGAAAATGCCCTCTCTGATGTCCTCCTAAGgtaattgtgt ... ctttacccagCACTCCTATATTTACTGGTGAAGAAGGTGGAA-GCGGTTTTGCTGCTTCCG
EST: gi|32806343|gb|CD958577.1|CD958577
EST:     ATTGTTCATATCCCTCCTGGTGAAAATGCCCTCTCTGATGTCCTCCTAAG                         CACTCCTATATTTACTGGTGAAGAAGGTGGAAGCGGTTTTGCTGCTTCCGC
genomic: ATTGTTCATATCCCTCCTGGTGAAAATGCCCTCTCTGATGTCCTCCTAAGgtaattgtgt ... ctttacccagCACTCCTATATTTACTGGTGAAGAAGGTGGAAGCGGTTTTGCTGCTTCCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaagttttcttatgctgcatatatgttaaccttgtttttctatctttacccagCACTCCTATATTTACTGGTGAAGAAGGTGGAAGCGGTTTTGCTGCTTCCGCAGCAGCTGCCGCAGCTACTGGAGCATCTGGATTTGAATTTGGTGTGGAC
                         tgttaac  putative branch site (score: 2)
                               ccttgtttttctatct  CT-rich tract
                                    tttttctatcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgtgtgccacgttaccgggttctaagttttcttatgctgcatatatgttaaccttgtttttctatctttacccagCACTCCTATATTTACTGGTGAAGAAGGTGGAAGCGGTTTTGCTGCTTCCGCAGCAGCTGCCGCAGCTACTGGAGCATCTGGATTTGAATTTGGTGTGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA