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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctcaagttatctttattcaagtattgaacatctgaacagaaaccactgtttttttgttttagttgtgtgctgagattttaaactttccttcttttcagTTTTCTGCTGGTGGGATTGTCAAAATACCGAAGTTTGAGATGATGATGTCTAAAAGTGAAGCAAACAACAAGCCTGTTCTAGCTGCAGATGATGTTTACA

Basic information

species Zea mays
transcript GRMZM2G444692_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G444692_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g26140.2 (Oryza sativa), 3'ss of exon 6
ttctcaagttatct---ttattcaa---gtattgaacatctgaacagaaaccactgtttttttgttttagttgtgtgctgagattttaaactttccttcttttcagTTTTCTGCTGGTGGGATTGTCAAAATACCGAAGTTTGAGATGATGATGTCTAAAAGTGAAGCAAACAACAAGCCTGTTCTAGCTGCAGATGATGTTTACA
     |   |||||    || ||||    |||| |||||   |||| | |  | ||||||| | ||| |||||  |||| | ||||||  ||||   |  | |||||||||||||||||||||||||||| | || |||||||||||||  ||| |||||||||||||||||||||| |||||||||||||| ||||||||| | |
aaacaagactatctgttctaatcaatatttatttaacattcaaacaaagaaaa-tgtttttgtattt-agttgcctgctaa-attttactcttt---ttctgtcagTTTTCTGCTGGTGGGATTGTCAAATTGCCTAAGTTTGAGATGACAATGACTAAAAGTGAAGCAAACAACAAACCTGTTCTAGCTGCTGATGATGTTCATA
















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|22546357|gb|BU098668.1|BU098668
EST:     TGATTCTACTTGCTTCTGGAATGCAATGCACGATGTTTACTGGCTATCAG                         TTTTCTGCTGGNGGGATTGTCAAAATACCGAAGTTTGAGATGATGATGTCT
genomic: TGATTCTACTTGCTTCTGGAATGCAATGCACGATGTTTACTGGCTATCAGgtaatgtcac ... ttcttttcagTTTTCTGCTGGTGGGATTGTCAAAATACCGAAGTTTGAGATGATGATGTCT
EST: gi|22472312|gb|BU036792.1|BU036792
EST:     TGATTCTACTTGCTTCTGGAATGCAATGCACGATGTTTACTGGCTATCAG                         TTTTCTGCTGGTGGGATTGTCAAAATACCGAAGTTTGAGATGATGATGTCT
genomic: TGATTCTACTTGCTTCTGGAATGCAATGCACGATGTTTACTGGCTATCAGgtaatgtcac ... ttcttttcagTTTTCTGCTGGTGGGATTGTCAAAATACCGAAGTTTGAGATGATGATGTCT
EST: gi|211115210|gb|FL153544.1|FL153544
EST:     TGATTCTACTTGCTTCTGGAATGCAATGCACGATGTTTACTGGCTATCAG                         TTTTCTGCTGGTGGGATTGTCAAAATACCGAAGTT
genomic: TGATTCTACTTGCTTCTGGAATGCAATGCACGATGTTTACTGGCTATCAGgtaatgtcac ... ttcttttcagTTTTCTGCTGGTGGGATTGTCAAAATACCGAAGTT
EST: gi|211115211|gb|FL153545.1|FL153545
EST:     TGATTCTACTTGCTTCTGGAATGCAATGCACGATGTTTACTGGCTATCAG                         TTTTCTGCTGGTGGGATTGTCAAAATACCGAAGTTTGAGATGATGATGTC
genomic: TGATTCTACTTGCTTCTGGAATGCAATGCACGATGTTTACTGGCTATCAGgtaatgtcac ... ttcttttcagTTTTCTGCTGGTGGGATTGTCAAAATACCGAAGTTTGAGATGATGATGTC
EST: gi|26558469|gb|CA830704.1|CA830704
EST:     TGATTCTACTTGCTTCTGGAATGCAATGCACGATGTTTACTGGCTATCAG                         TTTTCTGCTGGTGGGATCTGTCCAAATACCGAAGCTTGAGATGATGATGTC
genomic: TGATTCTACTTGCTTCTGGAATGCAATGCACGATGTTTACTGGCTATCAGgtaatgtcac ... ttcttttcagTTTTCTGCTGGTGGGAT-TGTCAAAATACCGAAGTTTGAGATGATGATGTC
EST: gi|87155752|gb|DY400541.1|DY400541
EST:     TGATTCTACTTGCTTCTGGAATGCAATGCACGATGTTTACTGGCTATCAG                         TTTTCTGCTGGTGGGATTGTCAAAATACCGAAGTTTGAGATGATGATGTCT
genomic: TGATTCTACTTGCTTCTGGAATGCAATGCACGATGTTTACTGGCTATCAGgtaatgtcac ... ttcttttcagTTTTCTGCTGGTGGGATTGTCAAAATACCGAAGTTTGAGATGATGATGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactgtttttttgttttagttgtgtgctgagattttaaactttccttcttttcagTTTTCTGCTGGTGGGATTGTCAAAATACCGAAGTTTGAGATGATGATGTCTAAAAGTGAAGCAAACAACAAGCCTGTTCTAGCTGCAGATGATGTTTACA
                                ttttaaactttccttc  CT-rich tract
     tttttttgttttagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctcaagttatctttattcaagtattgaacatctgaacagaaaccactgtttttttgttttagttgtgtgctgagattttaaactttccttcttttcagTTTTCTGCTGGTGGGATTGTCAAAATACCGAAGTTTGAGATGATGATGTCTAAAAGTGAAGCAAACAACAAGCCTGTTCTAGCTGCAGATGATGTTTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - -ctgaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgctga