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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGGCGGCAAGGGCGACCGCGAGCAGCGGATCTACCTCTGGTTCGACCCCACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcacccgcatcatatatccatcgcattgcttttgcgtccgtcacacacacatcatcactctgcatctgcaatgcaatgcaatccccccgctgctcc...

Basic information

species Zea mays
transcript GRMZM2G004699_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004699_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g33270.1 (Oryza sativa), 5'ss of exon 2
CCGGCGGCAAGGGCGACCGCGAGCAGCGGATCTACCTCTGGTTCGACCCCACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagc-acccgcatcatatatccatcgcattgcttttgcgtccgtcacacacacatcatcactctgcatctgcaatgcaatgcaatccc--cccgctgctcc
||||||| ||||| ||||| |||||| ||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| || |    |  |  ||   || | |      ||| | | | |   || | | ||||    |         ||    | | || | |   |  |  ||  
CCGGCGGGAAGGGGGACCGGGAGCAGAGGATCTACCTCTGGTTCGACCCCACCAAGGACTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtacgctaattacccctcattaacacccccacttatttacttgcattgtactccc-tcattttccgaagaaaataaaaataaggaagcacaatctacaact--

upper sequence: GRMZM2G004699_T03 (Zea mays), 5'ss of exon 2
lower sequence: EFJ15023 (Selaginella moellendorffii), 5'ss of exon 2
CCGGCGGCAAGGGCGACCGCGAGCAGCGGATCTACCTCTGGTTCGACCCCACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcacccgcatcatatatccatcgcattgcttttgcgtccgtcacacacacatcatcactctgcatctgcaatgcaatgcaatccccccgctgctcc
||   |||   ||  |||| ||||||||   |||||||||||||||||||||  |||| | |||| |||| |||||||||||||||    |   ||||  |||||               |   | ||      ||| ||    || | || ||    |   | ||   |  ||                          
CCAATGGCGTTGGAAACCGGGAGCAGCGACACTACCTCTGGTTCGACCCCACTCAGGACTTCCACACCTATTCCGTCCTCTGGAACAAGCAGCAGATCATgtaag---------------ttttttgcgaaaacttttcgataatcgctcaaac--tgtggttttggtccctcag-------------------------

upper sequence: GRMZM2G004699_T03 (Zea mays), 5'ss of exon 2
lower sequence: EFJ25994 (Selaginella moellendorffii), 5'ss of exon 2
CCGGCGGCAAGGGCGACCGCGAGCAGCGGATCTACCTCTGGTTCGACCCCACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcacccgcatcatatatccatcgcattgcttttgcgtccgtcacacacacatcatcactctgcatctgcaatgcaatgcaatccccccgctgctcc
||   |||   ||  |||| ||||||||   |||||||||||||||||||||  |||| | ||||  |||||||||||||||||||    |   ||||  |||               | |   | ||      ||| ||    || | || ||    |   | ||   |  ||                          
CCAATGGCGTTGGAAACCGGGAGCAGCGACACTACCTCTGGTTCGACCCCACTCAGGACTTCCACAGCTACTCCGTCCTCTGGAACAAGCAGCAGATCATgta---------------tgttttttgcgaacacttttcgataatcgctcaaac--tgtggttttggtccctcag-------------------------

upper sequence: GRMZM2G004699_T03 (Zea mays), 5'ss of exon 2
lower sequence: EFJ14395 (Selaginella moellendorffii), 5'ss of exon 2
CCGGCGGCAAGGGCGACCGCGAGCAGCGGATCTACCTCTGGTTCGACCCCACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcacccgcatcatatatccatcgcattgcttttgcgtccgtcacacacacatcatcactctgcatctgcaatgcaatgcaatccccccgctgctcc
||   |||   ||  |||| ||||||||   |||||||||||||||||||||  |||| | ||||  ||||||| |||||||||||    |   ||||  |||||     ||    |||| | |    || | |  |  |               | ||| ||| |                                  
CCAATGGCGTTGGAAACCGGGAGCAGCGACACTACCTCTGGTTCGACCCCACTCAGGACTTCCACAGCTACTCCTTCCTCTGGAACAAGCAGCAGATCATgtaagt--tagccctctatagctactcgatcgatcat-tgctgaaactgtggttttgatccctcag----------------------------------

upper sequence: GRMZM2G004699_T03 (Zea mays), 5'ss of exon 2
lower sequence: EFJ26221 (Selaginella moellendorffii), 5'ss of exon 2
CCGGCGGCAAGGGCGACCGCGAGCAGCGGATCTACCTCTGGTTCGACCCCACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcacccgcatcatatatccatcgcattgcttttgcgtccgtcacacacacatcatcactctgcatctgcaatgcaatgcaatccccccgctgctcc
||   |||   ||  |||| ||||||||   |||||||||||||||||||||  |||| | ||||  |||||||||||||||||||    |   ||||  |||||               |   | ||      ||| ||    || | || ||    |   | ||   |  ||                          
CCAATGGCGTTGGAAACCGGGAGCAGCGACACTACCTCTGGTTCGACCCCACTCAGGACTTCCACAGCTACTCCGTCCTCTGGAACACGCAGCAGATCATgtaag---------------ttttttgcgaacacttttcgataatcgctcaaac--tgtggttttggtccctcag-------------------------

upper sequence: GRMZM2G004699_T03 (Zea mays), 5'ss of exon 2
lower sequence: EFJ25990 (Selaginella moellendorffii), 5'ss of exon 2
CCGGCGGCAAGGGCGACCGCGAGCAGCGGATCTACCTCTGGTTCGACCCCACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcacccgcatcatatatccatcgcattgcttttgcgtccgtcac-acacacatcatcactctgcatctgcaatgcaatgcaatccccccgctgctcc
||   |||   ||  |||| ||||||||   |||||||||||||||||||||  |||| | ||||  ||||||| |||||||||||    |   ||||  |||||     ||     ||| |||     ||   |     ||  |||   |  |     |   | ||   |  ||                          
CCAATGGCGTTGGAAACCGGGAGCAGCGACACTACCTCTGGTTCGACCCCACTCAGGACTTCCACAGCTACTCCTTCCTCTGGAACAAGCAGCAGATCATgtaagtg--agccctccatagccactagtttatatcga--tcgatcattgctgaagctgtggttttggtccctcag-------------------------

upper sequence: GRMZM2G004699_T03 (Zea mays), 5'ss of exon 2
lower sequence: EFJ14399 (Selaginella moellendorffii), 5'ss of exon 2
CCGGCGGCAAGGGCGACCGCGAGCAGCGGATCTACCTCTGGTTCGACCCCACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcacccgcatcatatatccatcgcattgcttttgcgtccgtcacacacacatcatcactctgcatctgcaatgcaatgcaatccccccgctgctcc
||   |||   ||  |||| ||||||||   |||||||||||||||||||||  |||| | ||||  |||||||||||||||||||    |   ||||  |||||          | |  ||      || |||    |    ||      | |                                              
CCAATGGCGTTGGAAACCGGGAGCAGCGACACTACCTCTGGTTCGACCCCACTCAGGACTTCCACAGCTACTCCGTCCTCTGGAACAAGCAGCAGATCATgtaagttttttgcgaacacttctcgataatcgctcaaactgtggttttggtcccccag------------------------------------------

upper sequence: GRMZM2G004699_T03 (Zea mays), 5'ss of exon 2
lower sequence: EFJ14520 (Selaginella moellendorffii), 5'ss of exon 2
CCGGCGGCAAGGGCGACCGCGAGCAGCGGATCTACCTCTGGTTCGACCCCACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcacccgcatcatatatccatcgcattgcttttgcgtccgtcacacacacatcatcactctgcatctgcaatgcaatgcaatccccccgctgctcc
||   |||   ||  |||| ||||||||   |||||||||||||||||||||  |||| | ||||  |||||||||||||||||||    |   ||||  |||||        | | |  |       || |||    |    ||      | |                                              
CCAATGGCGTTGGAAACCGGGAGCAGCGACACTACCTCTGGTTCGACCCCACTCAGGACTTCCACAGCTACTCCGTCCTCTGGAACAAGCAGCAGATCATgtaagttttttgctaacacttttcgataatcgctcaaactgtggttttggtcccccag------------------------------------------

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|33467747|gb|CF244796.1|CF244796
EST:     ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGC                         GTTCTTCGTGGACGACGTGCCGATCCGG
genomic: ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcaccc ... gctccgccagGTTCTTCGTGGACGACGTGCCGATCCGG
EST: gi|9255437|gb|BE345905.1|BE345905
EST:     ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGC                         GTTCTTCGTGGACGACGTGCCGATCCGG
genomic: ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcaccc ... gctccgccagGTTCTTCGTGGACGACGTGCCGATCCGG
EST: gi|22546122|gb|BU098443.1|BU098443
EST:     ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGC                         GTTCTTCGTGGACGACGTGCCGATCCGGGGGTTCAAGAACACGAGCGCCGA
genomic: ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcaccc ... gctccgccagGTTCTTCGTGGACGACGTGCCGATCCGGGTGTTCAAGAACACGAGCGCCGA
EST: gi|22819448|gb|BU499538.1|BU499538
EST:     ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGC                         GTTCTTCGTGGACGACGTGCCGATCCGGGTGTTCAAGAACACGAGCGCCGA
genomic: ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcaccc ... gctccgccagGTTCTTCGTGGACGACGTGCCGATCCGGGTGTTCAAGAACACGAGCGCCGA
EST: gi|89761345|gb|DY689393.1|DY689393
EST:     ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGC                         GTTCTTCGTGGACGACGTGCCGATCCGGGTGTTCAAGAACACGAGCGCCGA
genomic: ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcaccc ... gctccgccagGTTCTTCGTGGACGACGTGCCGATCCGGGTGTTCAAGAACACGAGCGCCGA
EST: gi|29130857|gb|CB381561.1|CB381561
EST:     ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGC                         GTTCTTCGTGGACGACGTGCCGATCCGGGTGTTCAAGAACACGAGC
genomic: ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcaccc ... gctccgccagGTTCTTCGTGGACGACGTGCCGATCCGGGTGTTCAAGAACACGAGC
EST: gi|23357642|gb|BU645291.1|BU645291
EST:     ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGC                         GTTCTTCGTGGACGACGT
genomic: ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcaccc ... gctccgccagGTTCTTCGTGGACGACGT
EST: gi|50326237|gb|CO521363.1|CO521363
EST:     ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGC                         GTTCTTCGTGGACGACGTGCCGATCCGGGTGT
genomic: ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcaccc ... gctccgccagGTTCTTCGTGGACGACGTGCCGATCCGGGTGT
EST: gi|211298984|gb|FL169196.1|FL169196
EST:     ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGC                         GTTCTTCGTGGACGACGTGCCGATCCGGGTGTTCAAGAACACGAGC
genomic: ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcaccc ... gctccgccagGTTCTTCGTGGACGACGTGCCGATCCGGGTGTTCAAGAACACGAGC
EST: gi|26456139|gb|CA827722.1|CA827722
EST:     ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGC                         GTTCTTCGTGGACGACGTGCCGATCCGGGTGTTCAAGAACACGAGCGCCGA
genomic: ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcaccc ... gctccgccagGTTCTTCGTGGACGACGTGCCGATCCGGGTGTTCAAGAACACGAGCGCCGA
EST: gi|60343742|gb|DN210715.1|DN210715
EST:     ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGC                         GTTCTTCGTGGACGACGTGCCGATCCGGGTGTTCAAGAACACGAGCGCCG
genomic: ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcaccc ... gctccgccagGTTCTTCGTGGACGACGTGCCGATCCGGGTGTTCAAGAACACGAGCGCCG
EST: gi|211298980|gb|FL169192.1|FL169192
EST:     ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGTACCTCTACATGATCGC                         GTTCTTCGTGGACGACGTGCCGGATCCCGGTGGTCAAGAACACGAGCGCCG
genomic: ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcaccc ... gctccgccagGTTCTTCGTGGACGACGTGCCG-ATCCGGGTGTTCAAGAACACGAGCGCCG
EST: gi|22546396|gb|BU098707.1|BU098707
EST:     ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGC                         GTTCTTCGTGGACGACGTGCCGATCCGGGTGTTCAAGAACACGAGCGCCGA
genomic: ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcaccc ... gctccgccagGTTCTTCGTGGACGACGTGCCGATCCGGGTGTTCAAGAACACGAGCGCCGA
EST: gi|76018116|gb|DT945286.1|DT945286
EST:     ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGC                         GTTCTTCGTGGACGACGTGCCGATCCGGGTGTTCAAGAACACGAGCGCCGA
genomic: ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcaccc ... gctccgccagGTTCTTCGTGGACGACGTGCCGATCCGGGTGTTCAAGAACACGAGCGCCGA
EST: gi|50329318|gb|CO524444.1|CO524444
EST:     ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGC                         GTTCTTCGTGGACGACGTGCCGATCCGGGTGTTCAAGAACACGAGCGCCGA
genomic: ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcaccc ... gctccgccagGTTCTTCGTGGACGACGTGCCGATCCGGGTGTTCAAGAACACGAGCGCCGA
EST: gi|148960072|gb|EE153316.2|EE153316
EST:     ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGC                         GTTCTTCGTGGACGACGTGCCGATCCGGGTGTTTCA-GAACACGAGCGCCG
genomic: ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcaccc ... gctccgccagGTTCTTCGTGGACGACGTGCCGATCCGGGTGTT-CAAGAACACGAGCGCCG
EST: gi|211296836|gb|FL169175.1|FL169175
EST:     ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGC                         GTTCTTCGTGGACGACG
genomic: ACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcaccc ... gctccgccagGTTCTTCGTGGACGACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGGCGGCAAGGGCGACCGCGAGCAGCGGATCTACCTCTGGTTCGACCCCACCAAGGAGTACCACTCCTACTCCGTCCTCTGGAACCTCTACATGATCGCgtaagcacccgcatcatatatccatcgcattgcttttgcgtccgtcacacacacatcatcactctgcatctgcaatgcaatgcaatccccccgctgctcc

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG