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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcaaacgttctttttattatatgccatggatggttagttggtttgctcctcttttgcaacttctggtaggaccatataatgaaattgcatttatcctagCTTTTCTATGGCAATTGATGCGGTACAACATTCTACAACTGCTGAAGAATCTTAGATTTCACTCAAATGGAAAAGAGATCACAGATAATGACATATTGGC

Basic information

species Zea mays
transcript GRMZM2G081380_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081380_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g33080.1 (Oryza sativa), 3'ss of exon 9
ttcaaacgttctttttattatatgccatggatggttagttggtttgctcctcttttgcaacttctggtaggaccatataatgaaattgca-tttat---cctagCTTTTCTATGGCAATTGATGCGGTACAACATTCTACAACTGCTGAAGAATCTTAGATTTCACTCAAATGGAAAAGAGATCACAGATAATGACATATTGGC
   |    ||||| |||   |      |   |    | |  || || || | ||    |    || |||  |     |||| | || | | |||||   || ||||||||| |||||||||||| ||||||| || || ||| || | |||||||| ||||| || |||||||| ||||||||||||||||| |||||| ||  
---agtgattcttgttaaactgctggttaactcaacaatgagtatgttc-tgttgcatagacacttgtataatttggtaatcatatggtactttatttccccagCTTTTCTGTGGCAATTGATGAGGTACAATATCCTTCAATTGTTAAAGAATCTGAGATTCCATTCAAATGGTAAAGAGATCACAGATAACGACATACTGAT

upper sequence: GRMZM2G081380_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA08G45800.1 (Glycine max), 3'ss of exon 10
---------------------------------------------------------------------ttcaaacgttctttttat-tatatgccatggatggttagttggtttgctcctcttttgcaacttctgg----taggaccatataat------gaaattgcatttatcctagCTTTTC--------TATGGCAATTGATGCGGTACAACATTCTACAACTGCTGAAGAATCTTAGATTTCACTCAAATGGAAAAGAGATCACAGATAATGACATATTGGC
                                                                     |  |  | || || || | ||  | | ||| |   ||      ||||    || |  |   ||   ||    |   ||||| ||||          |||  |||||| || || |||        | |||||||||||||| |||||||| || ||||| || ||||| || |||||||||||  |||| || || || |  |||  ||| ||  ||  
gtatgttgacctgcaaattatgtactgtaacttggtagtgaatcaattgatctattgaacatatgccaatcaattcattgttcttgtataccttctatgaaacctttcagaatttgtatttcctcagatgctagaggatgcttacaccatctaatcctaatatggttgattttatcttaactcttcagCATATTTGTGGCAATTGATGCGATACAACATCCTTCAACTTCTAAAGAACCTGAGATTTCACTCTCATGGGAAGGAAATAATTGATGCTGATATTCTGCG
















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|13178229|gb|BG349487.1|BG349487
EST:     GAATATTGCTGGAAATGATATTGTTCAAGGGAACAAAAAACTGATATTAG                         CTTTTCTATGGCAATTGATGCGGTACAACATTCTACAACTGCTGAAGAATC
genomic: GAATATTGCTGGAAATGATATTGTTCAAGGGAACAAAAAACTGATATTAGgtaagtgata ... tttatcctagCTTTTCTATGGCAATTGATGCGGTACAACATTCTACAACTGCTGAAGAATC
EST: gi|13178228|gb|BG349486.1|BG349486
EST:     GAATATTGCTGGAAATGATATTGTTCAAGGGAACAAAAAACTGATATTAG                         CTTTTCTATGGCAATTGATGCGGTACAACATTCTACAACTGCTGAAGAATC
genomic: GAATATTGCTGGAAATGATATTGTTCAAGGGAACAAAAAACTGATATTAGgtaagtgata ... tttatcctagCTTTTCTATGGCAATTGATGCGGTACAACATTCTACAACTGCTGAAGAATC
EST: gi|60340714|gb|DN207687.1|DN207687
EST:     GAATATTGCTGGAAATGATATTGTTCAAGGGAACAAAAAACTGATATTAG                         CTTTTCTATGGCAATTGATGCGGTACAACATTCTACAACTGCTGAAGAATC
genomic: GAATATTGCTGGAAATGATATTGTTCAAGGGAACAAAAAACTGATATTAGgtaagtgata ... tttatcctagCTTTTCTATGGCAATTGATGCGGTACAACATTCTACAACTGCTGAAGAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcctcttttgcaacttctggtaggaccatataatgaaattgcatttatcctagCTTTTCTATGGCAATTGATGCGGTACAACATTCTACAACTGCTGAAGAATCTTAGATTTCACTCAAATGGAAAAGAGATCACAGATAATGACATATTGGC
                                             tttatcct  CT-rich tract
                             atataatgaaattgca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcaaacgttctttttattatatgccatggatggttagttggtttgctcctcttttgcaacttctggtaggaccatataatgaaattgcatttatcctagCTTTTCTATGGCAATTGATGCGGTACAACATTCTACAACTGCTGAAGAATCTTAGATTTCACTCAAATGGAAAAGAGATCACAGATAATGACATATTGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA