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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacatttgatggtgctactgatctccaagtgctgttatacttgtatgactgtaaattcttttaagtgcattacattcctattatgaatgtggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACCCAGCGTGCTGAATTTGATTATTTGCACAAAAAGCAATCTGGCGGTCAAG

Basic information

species Zea mays
transcript GRMZM2G056393_T02
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 3'ss of exon 13
-----gacatttgatggtgctactgatctccaagtgc-tgttata-cttgtatgactgtaaattcttttaagtgcattacattcctattatgaatgtggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACCCAGCGTGCTGAATTTGATTATTTGCACAAAAAGCAATCTGGCGGTCAAG
        |    ||     |  |||     |||  | | ||| | | |||||| ||    |  |||| ||    ||   | ||   || |  |||||      ||||| ||||||||||| |||||||||||||| |||||||||||||| || || |||||||||||||||||||| || ||||||||||||||||| |||||||
tcaattgaaccacatccctatgttgaaagttaagatcatcttaaatcctgtatggctactgaaactttcaa-caaatctaagtctccttctacatgtg------tagGTTGATGCAAAGGTCGGAAAACCTCGTGTGAACTTCAGGGAAACTATCACTCAGCGTGCTGAATTTGATTACTTACACAAAAAGCAATCTGGTGGTCAAG

upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA11G16460.1 (Glycine max), 3'ss of exon 13
gacatttgatggtgctactgatctccaagtgctgttatacttgta--tgactgtaaattcttttaagt--gcattacattcctattatgaatgtggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACCCAGCGTGCTGAATTTGATTATTTGCACAAAAAGCAATCTGGCGGTCAAG
|     |  |  | || |  || |  |  | || |  |  | | |  || |   |  ||   || |    |  || |||||   || ||  | |   |    |||| |||||    || ||||| || |||||||||||||| |||||  |||| || |||||||| ||||| |||||||| || ||||||  ||| || ||||
gtacccttttcatcctccacatatttattttctttcttgttcgaagctggccaaatgtttgcttcatctggagtttcattc---ttttgtctttacctgttaagGTTGATGCTTCAGTTGGAAAGCCCCGTGTTAACTTCAGAGAAACTGTTACTCAACGTGCTGATTTTGACTATTTGCATAAGAAGCAAAGTGGAGGACAAG

upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA01G14800.1 (Glycine max), 3'ss of exon 8
--gacatttgatggtgctactgatctccaagtgctgttatacttgta--tgactgtaaattcttttaagtgcattacattcctattatgaatgtggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACCCAGCGTGCTGAATTTGATTATTTGCACAAAAAGCAATCTGGCGGTCAAG
    |||||  |  | || |  || |  |  | || |  |  | | |  || |      ||  || |  || | |    | || || |   | |   |    |||| |||||    || |||||||| |||||||||||||| |||||  |||| || |||||||| ||||| |||||||| || ||||||  ||| || ||||
gtaccattt--tcatcctccacatgtttattttctttcttgttggaagctggccaatgtttgcttcatttggagtttcattctgttgtc--tttacctgttaagGTTGATGCTTCAGTTGGAAAACCCCGTGTTAACTTCAGAGAAACTGTTACTCAACGTGCTGATTTTGACTATTTGCATAAGAAGCAAAGTGGAGGACAAG

upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 13
lower sequence: AT1G45332.1 (Arabidopsis thaliana), 3'ss of exon 13
gacatttgatggtgctactgatctccaagtgct-gttatacttgtatgactgtaaattcttttaagtgcattacattcctattatgaatgtggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACCCAGCGTGCTGAATTTGATTATTTGCACAAAAAGCAATCTGGCGGTCAAG
             |   ||||  |  ||    |    ||  |  | | |    ||| |||| |       || |      ||| || |  |  | | |||||| ||||| |  || || ||||| ||||| || || ||||| || ||||||||||| ||||| ||||||||||| || || ||||||  ||| ||    |
-------------gtacctgacttttaaaccttcacaatgttcttctcaac-caaactcttat-------tttctacttaattttggaaata-tcaaatagGTTGATGCGACTGTGGGCAAACCCCGTGTCAATTTTAGGGAGACTATTACCCAGCGCGCTGAGTTTGATTATTTACATAAGAAGCAAAGTGGAGGAGCTG

upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 13
lower sequence: Vv15s0021g02450.t01 (Vitis vinifera), 3'ss of exon 13
-------------------------------------gacatttgatggtgctactgatc---tccaagtgctgttatacttgtatgactgtaaattct---tttaagtgcattacattcctattatgaatgtggttacat--agGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACCCAGCGTGCTGAATTTGATTATTTGCACAAAAAGCAATCTGGCGGTCAAG
                                     |   | |  |     | || ||    | | |||    ||     |  |  |   | |  | |    |||||| |  |   || |  |  | ||| |   |  ||  |||| |||||||  || |||| |||||||||||||||||| || ||  ||||  | ||||||||||||||||| || || || |||||| |||| || ||||
gtgcctggtctttttgtctttctttaatacagtgatgggattctagtatgattgctaattcgattctagtatgattgctaattcaaaatcttcacctgtatacttaagtactctctctttccctctttaatttacctttatgaagGTTGATGCAACTGTTGGAAGACCTCGTGTTAACTTCAGAGAGACTGTTACGAAACGTGCTGAATTTGATTACTTACATAAGAAGCAAACTGGAGGACAAG

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|91874831|gb|EB404788.1|EB404788
EST:     GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG                         GTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
genomic: GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaaac ... ggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
EST: gi|6194594|gb|AW146698.1|AW146698
EST:     GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG                         GTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
genomic: GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaaac ... ggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
EST: gi|6020648|gb|AW065681.1|AW065681
EST:     GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG                         GTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
genomic: GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaaac ... ggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
EST: gi|211410070|gb|FL355701.1|FL355701
EST:     GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG                         GTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
genomic: GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaaac ... ggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
EST: gi|211409847|gb|FL347405.1|FL347405
EST:     GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG                         GTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
genomic: GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaaac ... ggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
EST: gi|67017174|gb|CO445923.1|CO445923
EST:     GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG                         GTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
genomic: GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaaac ... ggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
EST: gi|211430479|gb|FL350077.1|FL350077
EST:     GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG                         GTGGATGCAAAGGTWGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC
genomic: GTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAGgtatggaaac ... ggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgactgtaaattcttttaagtgcattacattcctattatgaatgtggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACCCAGCGTGCTGAATTTGATTATTTGCACAAAAAGCAATCTGGCGGTCAAG
      taaattcttttaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacatttgatggtgctactgatctccaagtgctgttatacttgtatgactgtaaattcttttaagtgcattacattcctattatgaatgtggttacatagGTGGATGCAAAGGTAGGAAAACCTCGTGTTAACTTCAGGGAAACAATTACCCAGCGTGCTGAATTTGATTATTTGCACAAAAAGCAATCTGGCGGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA