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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacacatgctacacaattttacttccttactcttgatcaagacacccccaaaacattgtatttgtagcttatatgacagagcctgtttgctctaatgcagCTAGTTGCGATGATGTCGACGCCTTCAGCTACGGTTTTTGTCAGGCGCAGTTTTTCCTACTTGATGAATGGGCAAGCAGAGCTCGCTCTACGGGACGCAA

Basic information

species Zea mays
transcript GRMZM2G054634_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054634_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os10g42110.1 (Oryza sativa), 3'ss of exon 9
--aacacatgctacacaattttacttccttactcttgatcaagacacccccaaaacattgtatttgtagcttatatgacagagcctgtttgctctaatgcagCTAGTTGCGATGATGTCGACGCCTTCAGCTACGGTTTTTGTCAGGCGCAGTTTTTCCTACTTGATGAATGGGCAAGCAGAGCTCGCTCTACGGGACGCAA
  |  |   ||   |     |   |   | |||  |    |     |      || ||  | |       |  ||||||| |||   |||||  | |||||||| ||||  ||||||||   ||||||||| || ||||||| | || | ||||| ||||| ||||||||||||||  ||||||| ||||| ||||||||||
ccactagtagccttatgtggtccttatgtgacttatatatagtgagcgttatgaatatcttctgcccta-tggtatgaca-agctcatttgccatgatgcagCTTGTTGGAATGATGTCAGTGCCTTCAGCCACAGTTTTTGCCCGGAGAAGTTTCTCCTATTTGATGAATGGGCAGTCAGAGCTTGCTCTCCGGGACGCAA
















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|60397751|gb|DN230567.1|DN230567
EST:     TTGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTACTCCAAG                         CTAGTTGCGATGATGTCGACGCCTTCAGCTACGGTTTTTGTCAGGCGCAGT
genomic: TTGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTACTCCAAGgtatcaacat ... tctaatgcagCTAGTTGCGATGATGTCGACGCCTTCAGCTACGGTTTTTGTCAGGCGCAGT
EST: gi|60357873|gb|DN224846.1|DN224846
EST:     TTTTAAGACTGCAATTGACTACTACTCCAAG                         CTAGTTGCGATGATGTCGACGCCTTCAGCTACGGTTTTTGTCAGGCGCAGT
genomic: TTTTAAGACTGCAATTGACTACTACTCCAAGgtatcaacat ... tctaatgcagCTAGTTGCGATGATGTCGACGCCTTCAGCTACGGTTTTTGTCAGGCGCAGT
EST: gi|32943562|gb|CF048381.1|CF048381
EST:     TGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTACTCCCAAG                         CTAGTTGCGATTGATGTCGACGCCTTCAGCTACGGTTTTTGTCAGGCGCA
genomic: TGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTACT-CCAAGgtatcaacat ... tctaatgcagCTAGTTGCGA-TGATGTCGACGCCTTCAGCTACGGTTTTTGTCAGGCGCA
EST: gi|89249972|gb|DY621758.1|DY621758
EST:     TTGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTACTCCAAG                         CTAGTTGCGATGATGTGGACGCCTTCAGCTACGGTTTTTGTCAGGCGCAGT
genomic: TTGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTACTCCAAGgtatcaacat ... tctaatgcagCTAGTTGCGATGATGTCGACGCCTTCAGCTACGGTTTTTGTCAGGCGCAGT
EST: gi|211405598|gb|FL390185.1|FL390185
EST:     TTGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTACTCCAAG                         CTAGTTGCGATGATGTCGACGCCTTCAGCTACGGTTTTTGTCAGGCGCAGT
genomic: TTGCATTTAGAGACAAGGATTTTAAGACTGCAATTGACTACTACTCCAAGgtatcaacat ... tctaatgcagCTAGTTGCGATGATGTCGACGCCTTCAGCTACGGTTTTTGTCAGGCGCAGT
EST: gi|113704357|gb|EE681861.1|EE681861
EST:     GGATTTTAAGACTGCAATTGACTACTACTCCAAG                         CTAGTTGCGATGATGTCGACGCCTTCAGCTACAGTTTTTGTCAGGCGCAGT
genomic: GGATTTTAAGACTGCAATTGACTACTACTCCAAGgtatcaacat ... tctaatgcagCTAGTTGCGATGATGTCGACGCCTTCAGCTACGGTTTTTGTCAGGCGCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccccaaaacattgtatttgtagcttatatgacagagcctgtttgctctaatgcagCTAGTTGCGATGATGTCGACGCCTTCAGCTACGGTTTTTGTCAGGCGCAGTTTTTCCTACTTGATGAATGGGCAAGCAGAGCTCGCTCTACGGGACGCAA
                                            ctctaat  putative branch site (score: 3)
                                        tttgctct  CT-rich tract
         attgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacacatgctacacaattttacttccttactcttgatcaagacacccccaaaacattgtatttgtagcttatatgacagagcctgtttgctctaatgcagCTAGTTGCGATGATGTCGACGCCTTCAGCTACGGTTTTTGTCAGGCGCAGTTTTTCCTACTTGATGAATGGGCAAGCAGAGCTCGCTCTACGGGACGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
aacacat
- - - -gctacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgc