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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACCGGAAAGCACAACTTGCTCTTCAGAAAGGTGAAGAAGATCTTGCTCGTGAAGCACTTAAGAGGCGTAAATCTTATGCGgtacattctcattttgttgaatgattttgtgctaatatttgttttgaatttctatgttaggttttaaaaagggctgctaatttgtggagtgtaaatgagt...

Basic information

species Glycine max
transcript GLYMA12G05330.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G05330.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os01g67000.1 (Oryza sativa), 5'ss of exon 5
GTACCGGAAAGCACAACTTGCTCTTCAGAAAGGTGAAGAAGATCTTGCTCGTGAAGCACTTAAGAGGCGTAAATCTTATGCGgtacattctcattttgttgaatgattttgtgctaatatttgttttgaatttctatgttaggttttaaaaagggctgctaatttgtggagtgtaaatgagt
||| ||||  || ||||||||||||||||| ||||| || ||||||||||||||||| |||||| |||||||||| ||||| |||  |          |  || | | | |  | || || ||     |   | |    ||  |     |   |  |   ||||| |      |   || | 
GTATCGGAGGGCTCAACTTGCTCTTCAGAAGGGTGATGAGGATCTTGCTCGTGAAGCCCTTAAGCGGCGTAAATCATATGCTgtaggtatcatgcaaatctaaagttctggatcaaagatctgcccatatcatattgagtaactacacgattagttttaaaatttcttactctttcgtgtgc

upper sequence: GLYMA12G05330.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G017077_T01 (Zea mays), 5'ss of exon 5
GTACCGGAAAGCACAACTTGCTCTTCAGAAAGGTGAAGAAGATCTTGCTCGTGAAGCACTTAAGAGGCGTAAATCTTATGCGgtacattctcattttgttgaatgattt--tgtgctaatatttg---ttttgaatttctatgttaggttttaaaaagggctgctaatttgtggagtgtaaatgagt--------------------------------------------------
||| ||||  || |||||||||||||| || ||||| || ||||||||||||||||| |||||| |||||||||| ||||| |||  |   | |  || ||  |  |    ||||||  | || |      | |     |   || |  |  ||     | | |  || | ||     |   ||| |                                                  
GTATCGGAGGGCTCAACTTGCTCTTCAAAAGGGTGACGAGGATCTTGCTCGTGAAGCCCTTAAGCGGCGTAAATCATATGCTgtatgtgtccttgatgatgtgtagtacaatgtgcttgttttaggatcccttaccacattgattggaatagaatgtatgttacatatctatgtgacatgt-tgaatcaacatatcgaagtcctaatatagacttactatttgtgtggtttgtttag

upper sequence: GLYMA12G05330.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G024607_T01 (Zea mays), 5'ss of exon 5
GTACCGGAAAGCACAACTTGCTCTTCAGAAAGGTGAAGAAGATCTTGCTCGTGAAGCACTTAAGAGGCGTAAATCTTATGCGgtacattctcattttgttgaatgattttgtgctaatatttgttttgaatttctatgttaggtt---ttaaaaagggctgctaatttgtggagtgta-aatgagt-----------------------------------------------------------------
||| || |  || |||||||||||||| || ||||| || ||||||||||| ||||| |||||| |||||||||| ||||| |||  |     |  || ||  |  |    ||    |  |||||||   |||   |   |  ||   |  || ||   |  |  |   |    | |   |   ||                                                                 
GTATCGAAGGGCTCAACTTGCTCTTCAAAAGGGTGACGAGGATCTTGCTCGCGAAGCCCTTAAGCGGCGTAAATCATATGCTgtatgtgtcattgatgatgtgtagtacaatg----tgcttgttttaggttttcttaccacattgattcgaatagaatttatgttacattatctatgcgacatgttttttttcaacagtctatgctgttgaatcaacatatcaaattgtattgcgtgattgtttgcttag

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|151411201|gb|EV281012.1|EV281012
EST:     GTGAAGAAGATCTTGCTCGTGAAGCACTTAAGAGGCGTAAATCTTATGCG                         GATAATGCCAGTTCTTTGAAGGCTCAACTTGATCAACAAAAGACTGTTGTT
genomic: GTGAAGAAGATCTTGCTCGTGAAGCACTTAAGAGGCGTAAATCTTATGCGgtacattctc ... tatgttgcagGATAATGCCAGTTCTTTGAAGGCTCAACTTGATCAACAAAAGACTGTTGTT
EST: gi|5509270|gb|AI855828.1|AI855828
EST:     TAAATCTTATGCG                         GATAATGCCAGTTCTTTGAAGGCTCAACTTGATCAACAAAAGACTGTTGTT
genomic: TAAATCTTATGCGgtacattctc ... tatgttgcagGATAATGCCAGTTCTTTGAAGGCTCAACTTGATCAACAAAAGACTGTTGTT
EST: gi|10235157|gb|BE804045.1|BE804045
EST:     GTGAAGAAGATCTTGCTCGTGAAGCACTTAAGATGCGTAAATCTTATGCG                         GATAATGCCAGCTCTGTGAACGCTCATCTTGATCAACAAA-GACTGTTGGT
genomic: GTGAAGAAGATCTTGCTCGTGAAGCACTTAAGAGGCGTAAATCTTATGCGgtacattctc ... tatgttgcagGATAATGCCAGTTCTTTGAAGGCTCAACTTGATCAACAAAAGACTGTTGTT
EST: gi|7283859|gb|AW596461.1|AW596461
EST:     GTGAAGAAGATCTTGCTCGTGAAGCACTTAAGAGGCGTAAATCTTATGCG                         GATAATGCCAGTTCTTTGAAGGCTCAACTTGATCAACAAAAGACTGTTGTT
genomic: GTGAAGAAGATCTTGCTCGTGAAGCACTTAAGAGGCGTAAATCTTATGCGgtacattctc ... tatgttgcagGATAATGCCAGTTCTTTGAAGGCTCAACTTGATCAACAAAAGACTGTTGTT
EST: gi|192300720|gb|FG989677.1|FG989677
EST:     GTGAAGAAGATCTTGCTCGTGAAGCACTTAAGAGGCGTAAATCTTATGCG                         GATAATGCCAGTTCTTTGAAGGCTCAACTTGATCAACAAAAGACTGTCGTT
genomic: GTGAAGAAGATCTTGCTCGTGAAGCACTTAAGAGGCGTAAATCTTATGCGgtacattctc ... tatgttgcagGATAATGCCAGTTCTTTGAAGGCTCAACTTGATCAACAAAAGACTGTTGTT
EST: gi|19053083|gb|BM731750.1|BM731750
EST:     GTGAAGAAGATCTTGCTCGTGAAGCACTTAAGAGGCGTAAATCTTATGCG                         GATAATGCCAGTTCTTTGAAGGCTCAACTTGATCAACAAAAGACTGTTGTT
genomic: GTGAAGAAGATCTTGCTCGTGAAGCACTTAAGAGGCGTAAATCTTATGCGgtacattctc ... tatgttgcagGATAATGCCAGTTCTTTGAAGGCTCAACTTGATCAACAAAAGACTGTTGTT
EST: gi|120533309|gb|EH261442.1|EH261442
EST:     GTGAAGAAGATCTTGCTCGTGAAGCACTTAAGAGGCGTAAATCTTATGCG                         GATAATGCCAGTTCTTTGAAGGCTCAACTTGATCAACAAAAGACTGTTGTT
genomic: GTGAAGAAGATCTTGCTCGTGAAGCACTTAAGAGGCGTAAATCTTATGCGgtacattctc ... tatgttgcagGATAATGCCAGTTCTTTGAAGGCTCAACTTGATCAACAAAAGACTGTTGTT
EST: gi|298167301|gb|HO010740.1|HO010740
EST:     GTGAAGAAGATCTTGCTCGTGAAGCACTTAAGAGGCGTAAATCTTATGCG                         GATAATGCCAGTTCTTTG
genomic: GTGAAGAAGATCTTGCTCGTGAAGCACTTAAGAGGCGTAAATCTTATGCGgtacattctc ... tatgttgcagGATAATGCCAGTTCTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACCGGAAAGCACAACTTGCTCTTCAGAAAGGTGAAGAAGATCTTGCTCGTGAAGCACTTAAGAGGCGTAAATCTTATGCGgtacattctcattttgttgaatgattttgtgctaatatttgttttgaatttctatgttaggttttaaaaagggctgctaatttgtggagtgtaaatgagt

- - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG