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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagacaaacaaggggacaatcttactttattttatagttctgtttacttcatttattctggatctgacttttcacttctctttgtcaatag

Basic information

species Zea mays
transcript GRMZM2G056393_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056393_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 5'ss of exon 10
GATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagacaaacaagggg-acaatcttactttatttta----tagttctgtttacttcatt--tattctggatctgacttttcacttctctttgtcaatag---------------------------------------
||||||||||||||| ||||||| |||||||||||||| ||||||||||||||||| |||||||        |   | | | |    |  |   ||||  |    ||  |||||  |||  | |   ||      |  || |||    |    |||    ||                                         
GATATTCAAGAAGCACATGCTGGTCAAATTGTTGCTGTCTTTGGTGTTGATTGTGCGTCAGgtaaatttttgagtgaagtgtagggccacaggctattcaagaagtacctctgtccactatactaccatgtgctcttcgattttctgttgacattttcggatttgttctgtgttggtctgattatttgttctcgcatcaatag

upper sequence: GRMZM2G056393_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA11G16460.1 (Glycine max), 5'ss of exon 10
GATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagacaaacaaggggacaatcttactttattttatagttctgtttacttcatttattctggatctgactt---ttcacttctctttgtcaatag---
|| |||||||| ||  ||||||| ||||| |||||||| |||||||| || ||||||||||||                |   || | ||     ||||  | || | | |   || | | ||  | || |   ||   |       | |||| ||| |    
GACATTCAAGAGGCTCATGCTGGGCAAATAGTTGCTGTATTTGGTGTCGACTGTGCATCAGgt-tattcttttgtctttgcttaaacctatgcattttttgaattttatattgctcctgtgttg-gaatttattttgggtgggtaggtgtttgccaagaatct

upper sequence: GRMZM2G056393_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA01G14800.1 (Glycine max), 5'ss of exon 5
GATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagacaaacaaggggacaatcttactttattttatagttctgtttacttcatttattctggatctgactt---ttcacttctctttgtcaatag---
|| |||||||| ||  ||||||| ||||| |||||||| |||||||| || ||||||||||||                     | | ||     ||||  | ||   | |   || | |||| |  || |   ||   |       | |||| ||| |    
GACATTCAAGAGGCTCATGCTGGGCAAATAGTTGCTGTATTTGGTGTCGAATGTGCATCAGgt-tattcttttgtcttttcttgaacctatgcattttttgaatttgatattgctcctgtattgta-atttattttgggtgggtaggtgtttgccaagaatct

upper sequence: GRMZM2G056393_T02 (Zea mays), 5'ss of exon 10
lower sequence: AT2G45030.1 (Arabidopsis thaliana), 5'ss of exon 10
GATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagacaaacaaggggacaatcttactttattttatagttctgtttacttcatttattctgga--tctgacttttcacttctctttg--tcaatag-----------
||||||||||| ||| | ||||| |||||||| ||||| |||||| |||| ||||||||||||||  ||  ||| |      |   |||  |  |  |||        ||| ||||  |     || |  |||||  ||    || |  |||  |||||             
GATATTCAAGAGGCACACGCTGGACAAATTGTAGCTGTGTTTGGTATTGAGTGTGCATCAGgtac--agtaaaatattcttccgtacttgttcgaactta--acataatttgcttctctggggatgaaattctgatattgtgtttgttgttgggtcaattttcctaaatcag

upper sequence: GRMZM2G056393_T02 (Zea mays), 5'ss of exon 10
lower sequence: AT1G45332.1 (Arabidopsis thaliana), 5'ss of exon 10
GATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagacaaacaaggggacaatcttactttattttatagttctgtttacttcatttattctgga--tctgacttttcacttctctttg--tcaatag-----------
||||||||||| ||| ||||||| ||||| || ||||| |||||| |||| ||||||||||||||  ||  ||| |          |||  ||     | ||      ||| ||||  |     || |  |||||  ||    ||||  |||  ||| |             
GATATTCAAGAGGCACATGCTGGACAAATCGTAGCTGTGTTTGGTATTGAGTGTGCATCAGgtac--agtaaaatattcttgtgtacttggttcgaact-taacataatttgcttctctagggatgaaagtctgatattgtgtttcttgttgggtcacttttcctaaatcag

upper sequence: GRMZM2G056393_T02 (Zea mays), 5'ss of exon 10
lower sequence: Vv15s0021g02450.t01 (Vitis vinifera), 5'ss of exon 10
GATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgt---acgcagacaa-acaaggggacaatcttactttattttatagttctgt-ttacttcatttattctggatctgacttttcacttctctttgtcaatag--
|| |||||||| ||  ||||||| ||||| |||||||| || |||||||||||||| ||||||   ||  |  ||   ||      |||||  || | |   | |  |||| | ||  ||    || |||  |    |  ||| |||   |   | |   |   
GACATTCAAGAGGCCCATGCTGGGCAAATAGTTGCTGTCTTCGGTGTTGATTGTGCTTCAGgtttgacttacccactgcatacatgcaatcaaacatgagaatttgtttctatgttgttttccgtagtcttaa---aaaatttgactggaccagggcggaatca

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|32930091|gb|CF034903.1|CF034903
EST:     AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAG                         GCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
genomic: AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagac ... ttgtcaatagGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
EST: gi|67019503|gb|CO448252.1|CO448252
EST:     GCATATGCTGGGCCAAAT-GTTGCTGTTTTTGGTGGTGATTGTGCATCAG                         GCGATACATTTACGGATGGGACAGTGAAATATACTATGACTTCAATGAATG
genomic: GCATATGCTGG-CCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagac ... ttgtcaatagGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
EST: gi|91874831|gb|EB404788.1|EB404788
EST:     AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAG                         GCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
genomic: AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagac ... ttgtcaatagGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
EST: gi|211410070|gb|FL355701.1|FL355701
EST:     AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAG                         GCGATACATTTACGGATGGAACAGTGAAATATACTATGACTT-AATGAATG
genomic: AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagac ... ttgtcaatagGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
EST: gi|118406757|gb|EH038205.1|EH038205
EST:     AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAG                         GCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
genomic: AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagac ... ttgtcaatagGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
EST: gi|211409847|gb|FL347405.1|FL347405
EST:     AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAG                         GCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
genomic: AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagac ... ttgtcaatagGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
EST: gi|67017174|gb|CO445923.1|CO445923
EST:     AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAG                         GCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
genomic: AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagac ... ttgtcaatagGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
EST: gi|211430479|gb|FL350077.1|FL350077
EST:     AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAG                         GCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG
genomic: AGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagac ... ttgtcaatagGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAGgtacgcagacaaacaaggggacaatcttactttattttatagttctgtttacttcatttattctggatctgacttttcacttctctttgtcaatag

- - - - - - - - ATGCTG
- - - - - - - - - - - - - - - -  GCTGTT