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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATATTTGAAGAAGCTGGGTGTGACACACCAGCTAGTCCTAGTTGCGGTGCTTGTTTGGGTGGCCCGAAAGATACTTACGCACGCATGAATGAACCTAAGgcaagttccttgcttcggcccctgcatcttgtaatatactagtgtagttcaaattctacctgttacttttatccttattattatattgaaggaattgcaa...

Basic information

species Glycine max
transcript GLYMA17G37540.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G37540.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os02g03260.3 (Oryza sativa), 5'ss of exon 12
GATATTTGAAGAAGCTGGGTGTGACACACCAGCTAGTCCTAGTTGCGGTGCTTGTTTGGGTGGCCCGAAAGATACTTACGCACGCATGAATGAACCTAAGgcaagttccttgcttcggcccctgcatcttgtaatatactagtgtagttcaaattctacctgttacttttatccttattattatattgaaggaattgcaa---
||||||||| || ||||| ||||| ||||||||||| |||||||| ||||||||||||||||| ||    ||||| || || |||||||||||||||| || |||| |||  |        | | |       | ||  | || | ||   || | || |    |   |     ||||   | | ||    |||    ||   
GATATTTGAGGAGGCTGGTTGTGATACACCAGCTAGCCCTAGTTGTGGTGCTTGTTTGGGTGGTCCTCGTGATACATATGCTCGCATGAATGAACCTATGgtaagtgcctc-caaatatttcagtaaaacaggaaatgtt-gtttcgtatgaactttatcaac-atagtagaatttatagatgtcttccttgaaagataaggt

upper sequence: GLYMA17G37540.1 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM2G010044_T01 (Zea mays), 5'ss of exon 13
GATATTTGAAGAAGCTGGGTGTGACACACCAGCTAGTCCTAGTTGCGGTGCTTGTTTGGGTGGCCCGAAAGATACTTACGCACGCATGAATGAACCTAAGgcaagttccttgcttcggcccctgcatcttgtaatatactagtgtagttcaaattctacctgttactt-ttatccttattattatattgaaggaattgcaa--
||||||||| || ||||| |||||||||||||| ||||||| ||| ||||||||||||||||||||    ||||| || ||||| |||||||||||||  | ||||  |||  | |    |  | | | | || | ||  || |   |||  ||  |     | | |  ||||   |   || |  |  |   || ||||   
GATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTAATTGTGGTGCTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatctta-tgcaaatctggaaacattta-tgtataagaggcattccgatgttgttactgaatagttatgactggaatcac-taaacaaaaatgcaccc

upper sequence: GLYMA17G37540.1 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM2G133988_T01 (Zea mays), 5'ss of exon 9
GATATTTGAAGAAGCTGGGTGTGACACACCAGCTAGTCCTAGTTGCGGTGCTTGTTTGGGTGGCCCGAAAGATACTTACGCACGCATGAATGAACCTAAGgcaagttccttgcttcggcccctgcatcttgtaatatactagtgtagttcaa-attctacctgttacttttatccttattattatattgaaggaattgcaa-
| ||||||| || ||||| |||||||||||||| ||||||| ||| ||||||||||||||||||||    ||||| || ||||| |||||||||||||  | ||||  |||        |     |  ||   ||||| ||| | | | | |  || |  |||  |   ||||   |   || |      |  ||||   | 
GGTATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTAATTGTGGTGCTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatcttatgcaaatctagaaacatttatatataatag-gcattccgatgttgttactga-atagttatggctggaatcactaaacaaaaattctgaa

upper sequence: GLYMA17G37540.1 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM2G370852_T02 (Zea mays), 5'ss of exon 13
GATATTTGAAGAAGCTGGGTGTGACACACCAGCTAGTCCTAGTTGCGGTGCTTGTTTGGGTGGCCCGAAAGATACTTACGCACGCATGAATGAACCTAAGgcaagttccttgcttcggcccctgcatcttgtaatata-ctagtgtagttcaaattctacctgttacttttatccttattattatattgaaggaattgcaa---
|||||| || || ||||| ||||| |||||||| ||||||| |||||| |||||| ||||||||||    ||||| || ||||| ||||||||||||| ||   ||  ||| |      |        ||   ||| | |  |  | ||   || | |   |    ||  |   |  |||| ||| ||     |  ||| |   
GATATTCGAGGAGGCTGGTTGTGATACACCAGCAAGTCCTAATTGCGGCGCTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatcttacacacatctagaagcatttccatacaacaggcatggtggtaactgtggtt----ctagtgcacaaattagtatgttactatagatgcgatgg

upper sequence: GLYMA17G37540.1 (Glycine max), 5'ss of exon 14
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 14
GATATTTGAAGAAGCTGGGTGTGACACACCAGCTAGTCCTAGTTGCGGTGCTTGTTTGGGTGGCCCGAAAGATACTTACGCACGCATGAATGAACCTAAGgcaagttccttgcttcggcccctgcatcttgtaatatactagtgtagttcaaattctacctgttacttttatccttattattatattgaaggaattgcaa---
||| |||||||||||||| |||||||||||||| || ||||| || ||||||||  | ||||||||   ||| || ||||| ||| ||||||||||| | | | || ||    | |   |||| | | |   | ||| ||    |    | | |  |    || |   | |  |  |    | | || ||    |||  |   
GATCTTTGAAGAAGCTGGCTGTGACACACCAGCCAGCCCTAGCTGTGGTGCTTGCCTTGGTGGCCCAGCAGACACCTACGCTCGCTTGAATGAACCTCAAgtacgtaccc-attacttaccctacttatccaattat-ctgcacttcacctattcttgaaagtgagactaa--caaagacgtgttttaaaatgtttgttacag

upper sequence: GLYMA17G37540.1 (Glycine max), 5'ss of exon 14
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 5'ss of exon 14
GATATTTGAAGAAGCTGGGTGTGACACACCAGCTAGTCCTAGTTGCGGTGCTTGTTTGGGTGGCCCGAAAGATACTTACGCACGCATGAATGAACCTAAGgcaagttccttgcttcggcccctgcatcttgtaatatactagtgtagttcaaattctacctgttacttttatccttattattatattgaaggaattgcaa--
||||||||| |||||||| ||||| ||||| || |||||||  || ||||||||| ||||||| || | ||| || || |||||||||||||||||| ||||||| |  ||| ||    |   | |     | | | |  | |  |      |||| |||| | |||| |    |||||  |    ||||     |      
GATATTTGAGGAAGCTGGTTGTGATACACCTGCAAGTCCTACCTGTGGTGCTTGTATGGGTGGTCCTAGAGACACATATGCACGCATGAATGAACCTCAGgcaagata-ttgttttcctcttggtacaactttaaaaagcatttcatcaactattccacctat-acttctgcttttattcctcagatgaaacccctaactta

upper sequence: GLYMA17G37540.1 (Glycine max), 5'ss of exon 14
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 5'ss of exon 14
GATATTTGAAGAAGCTGGGTGTGACACACCAGCTAGTCCTAGTTGCGGTGCTTGTTTGGGTGGCCCGAAAGATACTTACGCACGCATGAATGAACCTAAGgcaagttccttgcttcggcccctgcatcttgtaatatactagtgtagttcaaattctacctgtt-acttttatccttattattatattgaaggaattgcaa--------
    ||||| |||||||| ||||| ||||| || ||||||||||| |||||||||||||||||||| | ||| || || ||||||||||| |||||| |||||||||  |   |||  |      | | | ||| |  | | | ||  |||| |  | | ||   ||||||    |||||        |||     |  |         
----TTTGAGGAAGCTGGTTGTGATACACCTGCAAGTCCTAGTTGTGGTGCTTGTTTGGGTGGCCCTAGAGACACATATGCACGCATGAACGAACCTCAGGCAAgttatt--attcatcttggtaaacctttaaaaggc-atttta--tcaactattccatgcccacttttgcttttattcaccagaagaaaatcatatagcctgtttg

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|193517434|gb|FK477357.1|FK477357
EST:     CTTGTTTGGGTGGCCCGAAAGATACTTACGCACGCATGAATGAACCTAAG                         GTTTGTGTTTCAACTACGAACAGGAAC
genomic: CTTGTTTGGGTGGCCCGAAAGATACTTACGCACGCATGAATGAACCTAAGgcaagttcct ... ggttgtgcagGTTTGTGTTTCAACTACGAACAGGAAC
EST: gi|11688877|gb|BF596553.1|BF596553
EST:     CTTGTTTGGGTGGCCCGAAAGATACTTACGCACGCATGAATGAACCTAAG                         GTTTGTGTTTCAACTACGAACAGGAACTTCCCGGGCCGAATGGGACACAAG
genomic: CTTGTTTGGGTGGCCCGAAAGATACTTACGCACGCATGAATGAACCTAAGgcaagttcct ... ggttgtgcagGTTTGTGTTTCAACTACGAACAGGAACTTCCCGGGCCGAATGGGACACAAG
EST: gi|208212320|gb|GE015747.1|GE015747
EST:     CTTGTTTGGGTGGCCCGAAAGATACTTACGCACGCATGAATGAACCTAAG                         GTTTGTGTTTCAACTACGAACAGGAACTTCCCGGGCCGAATGGGACACAAG
genomic: CTTGTTTGGGTGGCCCGAAAGATACTTACGCACGCATGAATGAACCTAAGgcaagttcct ... ggttgtgcagGTTTGTGTTTCAACTACGAACAGGAACTTCCCGGGCCGAATGGGACACAAG
EST: gi|254317170|gb|GR826115.1|GR826115
EST:     CTTGTTTGGGTGGCCCGAAAGATACTTACGCACGCATGAATGAACCTAAG                         GTTTGTGTGTCGACTACGAACAGGAACTTCCCGGGCCGAATGGGACACAAG
genomic: CTTGTTTGGGTGGCCCGAAAGATACTTACGCACGCATGAATGAACCTAAGgcaagttcct ... ggttgtgcagGTTTGTGTTTCAACTACGAACAGGAACTTCCCGGGCCGAATGGGACACAAG
EST: gi|120494416|gb|EH222583.1|EH222583
EST:     CTTGTTTGGGTGGCCCGAAAGATACTTACGCACGCATGAATGAACCTAAG                         GTTTGTGTTTCAACTACGAACAGGAACTTCCCGGGCCGAATGGGACACAAG
genomic: CTTGTTTGGGTGGCCCGAAAGATACTTACGCACGCATGAATGAACCTAAGgcaagttcct ... ggttgtgcagGTTTGTGTTTCAACTACGAACAGGAACTTCCCGGGCCGAATGGGACACAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATATTTGAAGAAGCTGGGTGTGACACACCAGCTAGTCCTAGTTGCGGTGCTTGTTTGGGTGGCCCGAAAGATACTTACGCACGCATGAATGAACCTAAGgcaagttccttgcttcggcccctgcatcttgtaatatactagtgtagttcaaattctacctgttacttttatccttattattatattgaaggaattgcaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccctgc