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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgttaaactaatatccacatcatcaatatatctgtatccttctctacttcgattacttgttgaattgatgcatctctgtaccctcttgcatttgtagctaaaatgcttttactatgtataacttatgccctagtgctgtgttcttgcagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAGAAGCAACGGATGATGCACCTTGTTATGACATCAAG

Basic information

species Zea mays
transcript GRMZM2G135568_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135568_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g01740.2 (Oryza sativa), 3'ss of exon 7
---------gtatgtgttaaactaatatccacatcatcaata-tatctgtatccttctctact--tcgattacttgttgaa-ttgatgcatctctgtaccctct----------tgcatttgtagctaaaatgcttttactatgtat----aacttatgc---------cctagtgctgtgttcttgcagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAGAAGCAACGGATGATGCACCTTGTTATGACATCAAG
            ||  ||  |     ||   | | ||||||| | ||| | || ||   |  |  | | |||    || |  ||  ||| |   | | ||  ||          |   ||   ||  ||  |  ||||   | | |     ||||  | |          ||    |||| || ||| |||||||||| ||||| ||||||||||||||||| |||||||| || ||||| || || || || ||||| || ||||||||||||||
gtatagatatggtggattgtatcctcatttgcgtgatcaatagtttctttttcatttcttgattgttgtttatagatttacctttttgctttcgtatgcctcctccggggaaaataacttaagaggcaatttatttttctcaagcaccgtgaactcttacatggttatatctgcaactgtatt-ttgtagGGAGCAACTGATGAGTTTGTGTTGGATCTTGTGGAGCAATGCACATTTCAAAAACAGCGAATAATGCATCTAGTTATGACATCAAG

upper sequence: GRMZM2G135568_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT5G63640.1 (Arabidopsis thaliana), 3'ss of exon 8
gtatgtgttaaactaatatccacatcatcaatatatctgtatccttctctacttcgattacttgttgaattgatgcatctctgtaccctcttgcatttgtagctaaaatgcttttactatgtataacttatgccctagtg--ctgtgttcttgcagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAGAAGCAACGGATGATGCACCTTGTTATGACATCAAG
                               |||||   ||| | |||  |||| |  || ||       | |  ||       ||  | ||    |  |     ||   |||   ||  | || |||   |    |      | | ||| | ||||| ||||  ||||| |||    | |||||||||||||||||| ||||||||||  | ||  | |||||||| || |||||||| ||
------------------------------gtatata-atatacctcttgactttgtatagttacctccattaaacag------acattatttggctccttttctaatctcttaacctgagaatgactccagtttgatccactttttttcatccagGGGGCAAAAGATGAGTTTACTCTTGATCTTGTCGAGCAATGTTCGTTTCAGAAAGAGCGCGTAATGCACCTCGTCATGACATCGAG
















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|89249738|gb|DY621524.1|DY621524
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAGgtatgtgtta ... gttcttgcagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|37397489|gb|CF636044.1|CF636044
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAGgtatgtgtta ... gttcttgcagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|149083910|gb|EE173286.2|EE173286
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAGgtatgtgtta ... gttcttgcagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|40337041|gb|CK371111.1|CK371111
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAGgtatgtgtta ... gttcttgcagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|71757754|gb|DR955691.1|DR955691
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAGgtatgtgtta ... gttcttgcagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|101381892|gb|EB813003.1|EB813003
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAGgtatgtgtta ... gttcttgcagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|31349910|gb|CD434267.1|CD434267
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAGgtatgtgtta ... gttcttgcagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|149082655|gb|EE171861.2|EE171861
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAGgtatgtgtta ... gttcttgcagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|33103093|gb|CF063053.1|CF063053
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAG                         GGAACAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTAC
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAGgtatgtgtta ... gttcttgcagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTAC
EST: gi|88748264|gb|DY532405.1|DY532405
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAGgtatgtgtta ... gttcttgcagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
EST: gi|60339241|gb|DN206214.1|DN206214
EST:     TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAG                         GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG
genomic: TGGAAGTATTGAGGGATGTGCTTAATTCTATGGATCCTAGACACCCTGAGgtatgtgtta ... gttcttgcagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagctaaaatgcttttactatgtataacttatgccctagtgctgtgttcttgcagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAGAAGCAACGGATGATGCACCTTGTTATGACATCAAG
                     gtataac  putative branch site (score: 3)
                                            tgttctt  putative PPT
            ttttactatgtataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgttaaactaatatccacatcatcaatatatctgtatccttctctacttcgattacttgttgaattgatgcatctctgtaccctcttgcatttgtagctaaaatgcttttactatgtataacttatgccctagtgctgtgttcttgcagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAGAAGCAACGGATGATGCACCTTGTTATGACATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA