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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtaaatgtttaaggatttcgtttgctttaatgtagatgctcacaaatatttaccattatgcattcgtataaattgccttttccttgttgattacctaaacttctattcagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCAGCTGATTTCAAGCTCATAGGATATGATCCTCACCAGAAGATAGAAATGAAGA

Basic information

species Glycine max
transcript GLYMA12G04480.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G04480.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 3'ss of exon 10
-----------------gtatgtgtaaat-gtttaaggatttcgtttgctttaatgtaga----tgctcacaaatatttaccattatgca---ttcgtataaattgccttttccttg-------ttgattacctaaac-ttctattcagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCAGCTGATTTCAAGCTCATAGGATATGATCCTCACCAGAAGATAGAAATGAAGA
                  ||  | ||  |  || ||     | |     |   || |  |      |||   | | |||   || || ||   | | ||| ||| |   | ||  |        || ||||  | ||   | | | ||| |||||||||| |||||   |||||| |||||||||||||| |||||| | || ||||||||  | || |||||||||||||||||||| |||||||| |
gtaagcaactcaataatttaaatttatttcattcaaaagcatggaacattcagatatgaaacagcactcctgagt-tttgtgatgattcaccttacttatcaatggtgatgtctataaatccgtttaattatatgaatactatgtgcagGTTTTGAAGATTAACCCTTTGAAGAAGGATATAGATTCTTTCGTGGCATCAGACTTCAAGCTGGTCGGTTATGATCCTCACCAGAAGATTGAAATGAAAA

upper sequence: GLYMA12G04480.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os12g26060.1 (Oryza sativa), 3'ss of exon 8
gtatgtgtaaatgtttaaggatttcgtttgctttaatg-tagatgctcacaaatatttaccattatgcattcgtataaattgccttttccttgttgattacctaaacttctattcagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCAGCTGATTTCAAGCTCATAGGATATGATCCTCACCAGAAGATAGAAATGAAGA
   |  | ||||||| |   ||||  |       |||| || ||  | |   | | |  |   |    ||| | || | |   ||  |  ||  ||| |     | |   | | ||||||||||||||||| ||   |||||||||||| |||||||||||  || | || ||||| ||  |  | |||||||||||||| ||||||||||||||||
--gtaagcaaatgttgattaatttactgcataaaaatgatatatttttattcaaagtacctgat---tatttg-attattcaactgattttttgtgagttttggatcccatctgcagATTTTGAAGATAAATCCTGTGAAGAAAGATATTGATTCTTTTGTAACATCAGACTTCAAACTGGTTCGCTATGATCCTCACCATAAGATAGAAATGAAGA

upper sequence: GLYMA12G04480.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G157586_T01 (Zea mays), 3'ss of exon 1
gtatgtgtaaatgtttaaggatttcgtttgctttaatgtagatgctcacaaatatttaccattatgcattcgtataaattgccttttccttgttgattacctaaac-ttctattcagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCAGCTGATTTCAAGCTCATAGGATATGATCCTCACCAGAAGATAGAAATGAAGA
                      |  |       ||||  |  || |   |  | | |     | | | |||    |   ||| | |||   |||   ||  |   | || |   ||||||||||||||||| ||    || || ||||||||||||||| ||||| | || ||||||||  | || |||||||| |||||||||||||| ||||| |
---------------------gtgagccactcctaatagaactgttttgatgtttctttttgtttactttctgtgaccatgcatcttctaagtt--ctatgtgggccttatgcacagATTTTGAAGATAAATCCTTCAAAAAAGGATATAGATTCTTTTATGGCATCAGACTTCAAGCTGGTTGGCTATGATCCCCACCAGAAGATAGAGATGAAAA

upper sequence: GLYMA12G04480.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G005990_T01 (Zea mays), 3'ss of exon 10
gtatgtgtaaatgtttaaggatttcgtttgctttaatgtagatgctcacaaatatttaccattatgcattcgtataaattgccttttccttgttgattacctaaac-ttctattcagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCAGCTGATTTCAAGCTCATAGGATATGATCCTCACCAGAAGATAGAAATGAAGA
                      |  |       ||||  |  || |   |  | | |     | | | |||    |   ||| | |||   |||   ||  |   | || |   ||||||||||||||||| ||    || || ||||||||||||||| ||||| | || ||||||||  | || ||||| || |||||||||||||| ||||| |
---------------------gtgagccactcctaatagaactgttttgatgtttctttttgtttactttctgtgaccatgcatcttctaagtt--ctatgtgggccttatgcacagATTTTGAAGATAAATCCTTCAAAAAAGGATATAGATTCTTTTATGGCATCAGACTTCAAGCTGGTTGGCTATGACCCCCACCAGAAGATAGAGATGAAAA

upper sequence: GLYMA12G04480.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G139880_T01 (Zea mays), 3'ss of exon 9
----------------------gtatgtgtaa---atgtttaaggatttcgtttgctttaatgtagatgctcacaaatatttaccattatgcattcgtataaattgccttttc--cttgttgattacctaaa---cttctattcagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCAGCTGATTTCAAGCTCATAGGATATGATCCTCACCAGAAGATAGAAATGAAGA
                        || || ||      | || | | ||  |  ||||| ||||   |  |      | | |     | ||  ||    |    ||||  | |  ||| |   ||   |      ||| | | ||||||||||||||||| ||   ||| || ||||||||||||||  ||||  | || ||||||||  | || |||||||||||||||||| |||| ||||| |
gtgagccaaccatttttacgaaaaatatgaaatctgcatatatgaacttgat--gctttgatgtttttttttgtgtgtgtgtgtgtgtgtgtgtttactttctgtgcccatgcatcttctaagttgtatgtgggtcttatgtgcagATTTTGAAGATAAATCCTTCGAAAAAGGATATAGATTCTTTCATGGCGTCAGACTTCAAGCTGGTTGGCTATGATCCTCACCAGAAGCTAGAGATGAAAA

upper sequence: GLYMA12G04480.1 (Glycine max), 3'ss of exon 10
lower sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatgtgtaaatgtttaaggatttcgtt--tgctttaatgtagatg----ctcacaaatattta--ccattatgcattcgtataaattgccttttccttgttgattacctaaacttctattcagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCAGCTGATTTCAAGCTCATAGGATATGATCCTCACCAGAAGATAGAAATGAAGA
||  || ||||     |     || | |  | ||| ||| | | |      | |  |||   ||  | |  |   |||| |   || |    | | ||| || ||       |  | ||  ||| ||||||||||||| ||| ||||||||||||||||||||||||| || | ||| ||  ||||||| || |||||||||||| |||| ||||| ||||| |
gtgagtataaacaaacacatgatttgctgattcttcaatcttgtttgagtttgatgaatgcataatctaccaataattctttgcaacta---tatgcttatttatctttgggatattta--cagGTTTTGAAGATAAATCCAGAGAAGAAAGATATAGATTCTTTTGTTGCGGATGACTTTGAGCTCATTGGCTATGATCCTCACAAGAAAATAGATATGAAAA

upper sequence: GLYMA12G04480.1 (Glycine max), 3'ss of exon 10
lower sequence: AT2G16370.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatgtgtaaatgtttaaggatttcgtttgctttaatgtagatgctcacaaatatttaccattatgcattcgtataaa-ttgccttttccttgttgattacc-taaactt-ctatt-cagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCAGCTGATTTCAAGCTCATAGGATATGATCCTCACCAGAAGATAGAAATGAAGA
                             |     || | |  |   |  |  ||  |  | |    ||||   ||   || || | |  |||||  |   | |   ||  ||| | ||| |  |||||||||||||  |||||||| | || ||||||||||||||  |||| ||  | |||| ||| |||||||||||| |||||||||||||||| |
-----------------------------gtaagtatatcgccgacaatgatcatcgaggaatgcatattcacctatccttaccgtgtttttgtttgtcgtcatgggctcactactgcagGTAATGAAGATAAACCCGGAGAAGAAACAAATCGATTCTTTTGTGGCTTCTGACTTTGACCTCACAGGCTATGATCCTCACAAGAAGATAGAAATGAAAA

upper sequence: GLYMA12G04480.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 9
gtatgtgtaaatgtttaaggatttcgtttgctttaatgtagatgctcacaaatatttaccattatgcattcgtataaattgccttttccttgttgattacctaaacttctattcagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCAGCTGATTTCAAGCTCATAGGATATGATCCTCACCAGAAGATAGAAATGAAGA
         || ||     | | |   ||  | | || ||     |   || || || |   ||   | |    |   |   ||| |   |  |  || |||     |   | |||||||||||||| || ||| ||||||| ||||| || || |||||||||||||||||  |||| ||||| ||| |||||||||||||||| |||||||| |
--------caaggt----agctctgcctttttcttatataccattttttaagtactttctcctagctactaccctttctgaacttctatgttgtctttgcctg----ttcctgcagATTTTGAAGATCAATCCACAGAAGAAGGATATTGAATCATTTGTGGCAGCTGATTTTGAGCTTATAGGTTATAATCCTCACCAGAAGATTGAAATGAAAA

upper sequence: GLYMA12G04480.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 11
---------------------------------------gtatgtgtaaatgtttaaggatttcgtttgctttaatgtagatgctcacaaatatttaccattatgcattcgtataaattgccttttccttgttgattacctaaacttctattcagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCAGCTGATTTCAAGCTCATAGGATATGATCCTCACCAGAAGATAGAAATGAAGA
                                        ||| |||||    |  |  ||| | ||    ||    |     |||  |    ||     || |   |   | | | |||     | | |  |  ||||    ||||  || |||||||||||||| || ||| |||||||  | || |||||||||||||||||||||||| | |||||||| ||||||||||| ||||| ||||| ||||| |
gttagtattcttgaattgattagttctattccaaattttttatttgtaaggagt--ataattcctttcttcttgtgtttttcactcttattctttcgtatttttctctctatttgagttgttccatacatcctc-ttactcgcactttaatgcagATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCTGATTTCCAACTCATAGGTTATGATCCTCATCAGAAAATAGAGATGAAAA

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|51343391|gb|CO984124.1|CO984124
EST:     ATGTGAGACCCTTGCAGGAACAGCTCCAGAACCAACCAAAACCTTTTCCA                         ATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCAGCT
genomic: ATGTGAGACCCTTGCAGGAACAGCTCCAGAACCAACCAAAACCTTTTCCAgtatgtgtaa ... ttctattcagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCAGCT
EST: gi|23050842|gb|BU577035.1|BU577035
EST:     TGTGAGACCCTTGCAGGAACAGCTCCAGAACCAACCAAAACCTTTTCCA                         ATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCAGCT
genomic: TGTGAGACCCTTGCAGGAACAGCTCCAGAACCAACCAAAACCTTTTCCAgtatgtgtaa ... ttctattcagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgcattcgtataaattgccttttccttgttgattacctaaacttctattcagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCAGCTGATTTCAAGCTCATAGGATATGATCCTCACCAGAAGATAGAAATGAAGA
                                     acctaaa  putative branch site (score: 3)
                                            cttctattc  CT-rich tract
           tataaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgtaaatgtttaaggatttcgtttgctttaatgtagatgctcacaaatatttaccattatgcattcgtataaattgccttttccttgttgattacctaaacttctattcagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCAGCTGATTTCAAGCTCATAGGATATGATCCTCACCAGAAGATAGAAATGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA