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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATCAAAGAGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCTgtaagtttgcactgcactctagaattgaggacatgtactttcatattccattacaatgtttctgtcattctttagtactgtttctcagtcctcactatcc...

Basic information

species Zea mays
transcript GRMZM2G013750_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013750_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g63430.2 (Oryza sativa), 5'ss of exon 4
TGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATCAAAGAGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCTgtaagtttgcactgcactctaga-attgaggacatgtactttcatatt--ccattacaatgtttctgtcattctttagtactgtttctcagtcctcactatcc-
||| ||||||||||||||||||||||||||||| |||||||| |||||||||||||||||| ||||||| |||||||||||||| ||||||||||||||||||||||    ||||||| ||   || |   |||  ||| |  |   |  |||  | | ||||    ||     |   || ||| |  ||    |||   ||  
TGTGGAGATAGAGAGAGCAAGATTGATCAAAAGACTTGCAAAAATCAAAGAGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAGTTGCTgtaagttcaagctgcactataatcatggcacacagttacatctactataaccaccatagtgttgtcttcgcatctacataatgtctaacaagt-tcatcctcag
















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|32931087|gb|CF035899.1|CF035899
EST:     AGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCT                         GTCGAAACATTTGGCTCCATGGCAAAGACGGAC
genomic: AGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCTgtaagtttgc ... tatttatcagGTCGAAACATTTGGCTCCATGGCAAAGACGGAG
EST: gi|13316089|gb|BG410536.1|BG410536
EST:     AGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCT                         GTCGAAACATTTGGCTCCATGGCAAAGACGGAG
genomic: AGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCTgtaagtttgc ... tatttatcagGTCGAAACATTTGGCTCCATGGCAAAGACGGAG
EST: gi|32846815|gb|CD986496.1|CD986496
EST:     AGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCT                         GTCGAAACATTTGGCTCCATGGCAAAGACGGAC
genomic: AGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCTgtaagtttgc ... tatttatcagGTCGAAACATTTGGCTCCATGGCAAAGACGGAG
EST: gi|31909275|gb|CD650837.1|CD650837
EST:     AGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCT                         GTCGAAACATTTGGCTCCATGGCAAAGACGGAG
genomic: AGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCTgtaagtttgc ... tatttatcagGTCGAAACATTTGGCTCCATGGCAAAGACGGAG
EST: gi|13316088|gb|BG410535.1|BG410535
EST:     AGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCT                         GTCGAAACATTTGGCTCCATGGCAAAGACGGAG
genomic: AGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCTgtaagtttgc ... tatttatcagGTCGAAACATTTGGCTCCATGGCAAAGACGGAG
EST: gi|4753426|gb|AI657336.1|AI657336
EST:     AGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCT                         GTCGAAACATTTGGCTCCATGGCAAAGACGGAG
genomic: AGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCTgtaagtttgc ... tatttatcagGTCGAAACATTTGGCTCCATGGCAAAGACGGAG
EST: gi|9952312|gb|BE638895.1|BE638895
EST:     AGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCT                         GTCGAAACATTTGGCTCCATGGCAAAGACGGAG
genomic: AGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCTgtaagtttgc ... tatttatcagGTCGAAACATTTGGCTCCATGGCAAAGACGGAG
EST: gi|148974705|gb|EE025514.2|EE025514
EST:     AGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCT                         GTCGAAACATTTGGCTCCCTGGCAAAGACGGAG
genomic: AGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCTgtaagtttgc ... tatttatcagGTCGAAACATTTGGCTCCATGGCAAAGACGGAG
EST: gi|211448768|gb|FL325252.1|FL325252
EST:     AGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCT                         GTCGAAACATTTGGCTCCATGGCAAAGACGGAG
genomic: AGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCTgtaagtttgc ... tatttatcagGTCGAAACATTTGGCTCCATGGCAAAGACGGAG
EST: gi|20803197|gb|BQ294247.1|BQ294247
EST:     AGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCT                         GTCGAAACATTTGGCTCCATGGCAAAGA
genomic: AGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCTgtaagtttgc ... tatttatcagGTCGAAACATTTGGCTCCATGGCAAAGA
EST: gi|32943967|gb|CF048786.1|CF048786
EST:     AGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCT                         GTCGAAACATTTGGCTCCATGGCAAAGACGGAC
genomic: AGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCTgtaagtttgc ... tatttatcagGTCGAAACATTTGGCTCCATGGCAAAGACGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGAGATAGAGAGAGCAAGATTGATCAAAAGGCTTGCAAATATCAAAGAGGAGCAGGGAAAGATTGACGAGGCTGCTGATTTGATGCAAGAAGTTGCTgtaagtttgcactgcactctagaattgaggacatgtactttcatattccattacaatgtttctgtcattctttagtactgtttctcagtcctcactatcc

- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT