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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAGgtgcacctctgatcagatgtggcaagggaattcacgcttgttgtcttactctcttaactgactctgttcatatatatggcatttgcag

Basic information

species Zea mays
transcript GRMZM2G027851_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027851_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 8
GCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAGgtgcacctctgatcagatgtggcaagggaattcacgcttg---ttgtcttactctcttaactgactctgttcatatatatggcatttgcag
|||||| ||||||||||||||||| ||||||||||||||||||||||| || || |||||||| ||||||  |||||| |  ||||  | |    ||||  |   |    |  | |||   | | |  | |     ||  | | | ||  ||| ||||
GCATTCTACTGACCGTGAGGTTGCCCTTATGATGCTCATGGCTTACCTTTCATATATGCTGGCTGAGgtgtgcctctgctttgatgcagtatcaaaatttgcatatagtttcattttatagtttgattttatctactttgtttgtttgatattggcag

upper sequence: GRMZM2G027851_T03 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA19G42900.1 (Glycine max), 5'ss of exon 8
GCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAGgtgcacctctga-----tcagatgtg----gcaagggaa-----ttcacgcttgttgtct-tactctctt---aactgactctgttcatatatatggcatttgcag
||| || || || ||||||||||| ||||||||||| ||||| ||||| |||||||| ||||| || ||     |   |     |||||  |     | |  | |      ||   |||   | ||| |  | ||||   ||  |  |||| | |||| ||     | |||||
GCACTCTACAGATCGTGAGGTTGCTCTTATGATGCTAATGGCATACCTTTCCTACATTCTGGCTGAAgtaagttttaaagaacttcagaaatattttgtagagtatgtctttttgagctctatatctattttttcttgtgaaagggttctgat-atatctacaagttctgcag

upper sequence: GRMZM2G027851_T03 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA10G30020.1 (Glycine max), 5'ss of exon 9
GCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAGgtgcacctctgatcagatgtggcaagggaattcacgcttgttgtc----ttactctcttaactgactctgttcatatatatggcatttgcag
||| || || || ||||||||||| ||||||||| | ||||| ||||| ||||||||||| || || ||  |  | | |  |  | | | || |   || | |  || ||||    ||  ||  | |  |||  ||| |  ||| ||   |  ||||||
GCACTCTACAGATCGTGAGGTTGCTCTTATGATGTTAATGGCATACCTGTCCTACATGCTTGCTGAAgta-agttgtaaagaattttagtaatg--ttttatggatgctgtcaacatttgtcgttgacatgatgctgat-gtatctacatctgttgcag

upper sequence: GRMZM2G027851_T03 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA03G40290.1 (Glycine max), 5'ss of exon 8
GCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAGgtgcacctctga-----tcagatgtg----gcaagggaattcacgcttgttgtcttactctcttaactgactctgttcatatatatggcatttgcag-------------------
||| || || || ||||||||||| ||||||||||| ||||| ||||| |||||||| ||||| || ||     |   |     |||||  ||    | |  | |  ||    |||   |||   ||| ||   ||     || |||  ||    ||||  | |                   
GCACTCTACAGATCGTGAGGTTGCTCTTATGATGCTAATGGCATACCTTTCCTACATTCTGGCTGAAgtaagttttaaagaacttcagaaatgttctgtacagtatgtcttttttgagctctatatctattttttgttgtggtacattcattaatcattaacgggttctgatatattctgcag

upper sequence: GRMZM2G027851_T03 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA20G37370.1 (Glycine max), 5'ss of exon 9
GCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAGgtgcacctctgatcagatgtggcaagggaattcacgcttgttgtcttactctc--ttaactgactctgttcatatatatggcatttgcag
||| || || || || |||||||| ||||||||| | ||||| ||||||||||||||||| || || ||  |  | | |  |  | | | || |   || | |  || ||    | |     |||||  |  ||| |  ||| ||   | | |||||
GCACTCTACAGATCGCGAGGTTGCTCTTATGATGTTAATGGCATACCTCTCCTACATGCTTGCTGAAgta-agttttaaagaattttagtaatg--ttttatggatgctgcaacatttgtcattaacatatgctgat-gtatctacatcttctgcag

upper sequence: GRMZM2G027851_T03 (Zea mays), 5'ss of exon 6
lower sequence: Vv14s0030g00710.t01 (Vitis vinifera), 5'ss of exon 8
GCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAGgtgcacctctgatcagatg--tggcaagggaattcacgcttgttgtcttactctcttaactgactctgttcatatata-tggcatttgcag------------------------------------------------
||| || ||||| || |||||||| ||||||||||| ||||| ||||| |||||||| || || || ||     |    | |  |   |||  |      |  | | ||||||||       || | ||  ||| || | ||  |   | |  |  |                                                 
GCACTCTACTGATCGGGAGGTTGCCCTTATGATGCTTATGGCATACCTTTCCTACATACTTGCTGAAgtaagatttcttttaacttcttgggcacttccctggcccctgttgtctattggcattgagtg-ttctatttagattcaacagtagatatatcaatcatttaaagtctttccattgttagtaactttggttgtcctgcag

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|71437105|gb|DR818155.1|DR818155
EST:     AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG                         CTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
genomic: AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAGgtgcacctct ... gcatttgcagCTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
EST: gi|78093452|gb|DV521826.1|DV521826
EST:     AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG                         CTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
genomic: AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAGgtgcacctct ... gcatttgcagCTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
EST: gi|71761590|gb|DR959527.1|DR959527
EST:     AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG                         CTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
genomic: AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAGgtgcacctct ... gcatttgcagCTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
EST: gi|71446906|gb|DR827956.1|DR827956
EST:     AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG                         CTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
genomic: AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAGgtgcacctct ... gcatttgcagCTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
EST: gi|71758416|gb|DR956353.1|DR956353
EST:     AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG                         CTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
genomic: AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAGgtgcacctct ... gcatttgcagCTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
EST: gi|78074782|gb|DV503216.1|DV503216
EST:     AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG                         CTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
genomic: AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAGgtgcacctct ... gcatttgcagCTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
EST: gi|78080130|gb|DV508542.1|DV508542
EST:     AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG                         CTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
genomic: AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAGgtgcacctct ... gcatttgcagCTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
EST: gi|211100374|gb|FL186479.1|FL186479
EST:     AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG                         CTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
genomic: AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAGgtgcacctct ... gcatttgcagCTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
EST: gi|76013009|gb|DT940179.1|DT940179
EST:     AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG                         CTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
genomic: AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAGgtgcacctct ... gcatttgcagCTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
EST: gi|74239374|gb|DT647288.1|DT647288
EST:     AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG                         CTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
genomic: AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAGgtgcacctct ... gcatttgcagCTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
EST: gi|71427238|gb|DR808288.1|DR808288
EST:     TGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG                         CTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
genomic: TGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAGgtgcacctct ... gcatttgcagCTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
EST: gi|78093453|gb|DV521827.1|DV521827
EST:     AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG                         CTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCNGCATCGTGATG
genomic: AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAGgtgcacctct ... gcatttgcagCTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
EST: gi|78115472|gb|DV533860.1|DV533860
EST:     ATGGCTTACCTCTCCTACCATGCTGGCCGAG                         CTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
genomic: ATGGCTTACCTCTCCTA-CATGCTGGCCGAGgtgcacctct ... gcatttgcagCTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
EST: gi|76936699|gb|DV174843.1|DV174843
EST:     AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAG                         CTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
genomic: AGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAGgtgcacctct ... gcatttgcagCTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
EST: gi|78080129|gb|DV508541.1|DV508541
EST:     CATGGCTTACCTCTCCTACATGCTGGCCGAG                         CTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG
genomic: CATGGCTTACCTCTCCTACATGCTGGCCGAGgtgcacctct ... gcatttgcagCTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATTCCACTGACCGTGAGGTTGCGCTTATGATGCTCATGGCTTACCTCTCCTACATGCTGGCCGAGgtgcacctctgatcagatgtggcaagggaattcacgcttgttgtcttactctcttaactgactctgttcatatatatggcatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG