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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catttagtttttaataggattatttccccctttttttaatgagtgctacattaagtttgttcccttttgtctgtttttgttttgcttcttgaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGCTATAGGATTGCATATAGGTCTATGGAACGTTCTCTCACTGATGAGGAAA

Basic information

species Glycine max
transcript GLYMA02G10060.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 8
catttagtttttaataggattatttccccctttttttaatgagtgctacatta-agtttgttcccttttgtctgtttttgttttgct------tcttgaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGCTATAGGATTGCATATAGGTCTATGGAACGTTCTCTCACTGATGAGGAAA
      ||   |||     |   |    | ||      |||| || |||| |  | ||| ||    |     |  |||| |   |||      |  |    ||||||||  || |||| ||||| ||||||||||||||||||||||| ||||| ||||| ||||| || |||||||| ||||||||||| || || |||||||| |
------gtgcctaactttgtgcgtctaacattaccagtatga-tgatacactggaatttattgtgctcgtcataattttatcaggctaaagtgttgttcgtttgcagGTAAAACTAATTGACAATTTCACCAACAAGAAAGGAATGACGAGCCATTGCTACAGGATAGCCTATAGGTCAATGGAACGTTCACTTACCGATGAGGAGA

upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 8
catttagttttta-ataggattatttccccctttttttaatgagtgctacattaagtttgttcccttttgtctgtttttgttttgcttcttgaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGCTATAGGATTGCATATAGGTCTATGGAACGTTCTCTCACTGATGAGGAAA
    |||||| |  ||   ||       |  |  |||       |  |  | |      | |       || |||||  |  |  ||| ||    ||||||||  || | || || || ||||||||||||||||| ||||| || || ||||| || || ||||||||||| ||||||||||| ||||| || ||||| |
agcctagtttgtgcatccaatctaaaatctgtagtttggtcatataatggaatttaaaagctattcagagtatgtttgagactgacttttttgt-ttgcagGTAAAACTTATTGATAATTTCACCAACAAGAAAGGCATGACAAGTCATTGCTACAGAATAGCATATAGGTCAATGGAACGTTCGCTCACAGACGAGGAGA

upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv19s0027g01480.t01 (Vitis vinifera), 3'ss of exon 3
catttagtttttaataggattatttccccctttttttaatgagtgctacattaagtttgttccct--tttgtctgtttttgttttgcttcttgaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGCTATAGGATTGCATATAGGTCTATGGAACGTTCTCTCACTGATGAGGAAA
  || |     |      | ||  ||||  ||||  || ||  ||  |    |  |   |||     |||       | |    | | | ||  | || ||||||||||| || ||||| |||||||||||||||||||||||||| || || ||| |||| |||||  |||| ||||| ||||| || || |||||||| |
--ttgaaacagtggccataataagtccctattttcctagtgcctgaaagtgaagctccattctgaagttttctgaactataagatacatttttgacttccagGTGCAATTGATCGACAATTTCACCAACAAGAAAGGAATGACCAGTCAATGTTATCGGATAGCATACCGGTCCATGGAGCGTTCACTTACAGATGAGGAGA

upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv19s0027g01200.t01 (Vitis vinifera), 3'ss of exon 8
catttagtttttaataggattatttccccctttttttaatgagtgctacattaagtttgttccct--tttgtctgtttttgttttgcttcttgaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGCTATAGGATTGCATATAGGTCTATGGAACGTTCTCTCACTGATGAGGAAA
   |||     |      | ||  ||||  ||||  || ||  ||  |    |  |   |||     |||       | |    | | | ||  | || ||||||||||| || ||||| ||||||||||| |||||||||||||| || || ||| |||| |||||  |||| ||||| ||||| || || |||||||| |
--gttaaacagtggccataataagtccctattttcctagtgcctgaaagtgaagctccattctgaagttttctaaactataagatacatttttgacttccagGTGCAATTGATCGACAATTTCACCAACAACAAAGGAATGACCAGTCAATGTTATCGGATAGCATACCGGTCCATGGAGCGTTCACTTACAGATGAGGAGA

upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv11s0103g00120.t01 (Vitis vinifera), 3'ss of exon 8
--catttagtttt--taataggattatttccccctttttttaatgagtgctacattaagtttgttcccttttgtctgtttttgttttgcttcttgaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGCTATAGGATTGCATATAGGTCTATGGAACGTTCTCTCACTGATGAGGAAA
   |   ||||    |||| |      |||| ||   |       ||||   | | |   ||||    |||| |    | ||   |   || ||||  |  ||||||||||| || ||||| |||||||||||||||||||||||||| || || ||| |||| |||||  |||| ||||| ||||| || || |||||||| |
gtgaaacagttgccataatggtccctgttcctcccagtgcctgaaagtggagcttca---ttgtgaagttttctaaactattagatatatttttgac-tgccagGTGCAATTGATTGACAATTTCACCAACAAGAAAGGAATGACCAGTCAATGTTATCGGATAGCATACCGGTCCATGGAGCGTTCACTTACAGATGAGGAGA

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|208206292|gb|GE004183.1|GE004183
EST:     GATCTTGTAGAGGAG                         GTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
genomic: GATCTTGTAGAGGAGgtatatcttt ... gaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
EST: gi|208338432|gb|GE135646.1|GE135646
EST:     GCCGGGGATCTTGTAGAGGAG                         GTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
genomic: GCCGGGGATCTTGTAGAGGAGgtatatcttt ... gaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
EST: gi|14196099|gb|BE657918.2|BE657918
EST:     ACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAGAGGAG                         GTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
genomic: ACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAGAGGAGgtatatcttt ... gaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
EST: gi|8669342|gb|BE190449.1|BE190449
EST:     ACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAGAGGAG                         GTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
genomic: ACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAGAGGAGgtatatcttt ... gaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
EST: gi|193406503|gb|FK371808.1|FK371808
EST:     GCCGGGGATCTTGTAGAGGAG                         GTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
genomic: GCCGGGGATCTTGTAGAGGAGgtatatcttt ... gaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
EST: gi|208310649|gb|GE106009.1|GE106009
EST:     GCCGGGGATCTTGTAGAGGAG                         GTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
genomic: GCCGGGGATCTTGTAGAGGAGgtatatcttt ... gaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
EST: gi|207771423|gb|GD745306.1|GD745306
EST:     GATCTTGTCGAGGAG                         GTGCAATTAATAGACAATTTCACCAACAAGAAAGGAATGACCAGCCACTGC
genomic: GATCTTGTAGAGGAGgtatatcttt ... gaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
EST: gi|207823121|gb|GD797002.1|GD797002
EST:     GCCGGGGATCTTGTAGAGGAG                         GTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
genomic: GCCGGGGATCTTGTAGAGGAGgtatatcttt ... gaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
EST: gi|207754805|gb|GD730338.1|GD730338
EST:     GCCGGGGATCTTGTAGAGGAG                         GTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCGGCCACTGC
genomic: GCCGGGGATCTTGTAGAGGAGgtatatcttt ... gaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
EST: gi|298182211|gb|HO026386.1|HO026386
EST:     ACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAGAGGAG                         GTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
genomic: ACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAGAGGAGgtatatcttt ... gaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
EST: gi|31310201|gb|CD395404.1|CD395404
EST:     ACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAGAGGAG                         GTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
genomic: ACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAGAGGAGgtatatcttt ... gaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
EST: gi|11689832|gb|BF597508.1|BF597508
EST:     ACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAGAGGAG                         GTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
genomic: ACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAGAGGAGgtatatcttt ... gaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
EST: gi|208327704|gb|GE124592.1|GE124592
EST:     GCCGGGGATCTTGTTAGAGGAG                         GTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTG
genomic: GCCGGGGATCTTG-TAGAGGAGgtatatcttt ... gaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTG
EST: gi|19053701|gb|BM732368.1|BM732368
EST:     ACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTCGAGGAG                         GTGCAATTAATAGACAATTTCACCAACAAGAAAGGAATGACCAGCCACTGC
genomic: ACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAGAGGAGgtatatcttt ... gaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
EST: gi|193670284|gb|FK613234.1|FK613234
EST:     GCCGGGGATCTTGTAGAGGAG                         GTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
genomic: GCCGGGGATCTTGTAGAGGAGgtatatcttt ... gaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
EST: gi|193653407|gb|FK595219.1|FK595219
EST:     GCCGGGGATCTTGTAGAGGAG                         GTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
genomic: GCCGGGGATCTTGTAGAGGAGgtatatcttt ... gaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
EST: gi|16341914|gb|BI967509.1|BI967509
EST:     ACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAGAGGAG                         GTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
genomic: ACAATCTGTGTGAAGTTGTTAGAGGAATAGCCGGGGATCTTGTAGAGGAGgtatatcttt ... gaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
EST: gi|207786084|gb|GD756195.1|GD756195
EST:     GGGGATCTTGTAGAGGAG                         GTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
genomic: GGGGATCTTGTAGAGGAGgtatatcttt ... gaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
EST: gi|208106121|gb|GD908324.1|GD908324
EST:     GATCTTGTAGAGGAG                         GTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
genomic: GATCTTGTAGAGGAGgtatatcttt ... gaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
EST: gi|208338162|gb|GE133934.1|GE133934
EST:     GCCGGGGATCTTGTAGAGGAG                         GTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
genomic: GCCGGGGATCTTGTAGAGGAGgtatatcttt ... gaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
EST: gi|193622449|gb|FK570091.1|FK570091
EST:     GATCTTGTAGAGGAG                         GTGCAATTAATAGACAGCTTCACCAACAAGAAAGGAATGACCAGCCACCGC
genomic: GATCTTGTAGAGGAGgtatatcttt ... gaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
EST: gi|193583291|gb|FK540185.1|FK540185
EST:     CTTGTAGAGGAG                         GTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
genomic: CTTGTAGAGGAGgtatatcttt ... gaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
EST: gi|193719750|gb|FK650946.1|FK650946
EST:     GCCGGGGATCTTGTAGAGGAG                         GTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC
genomic: GCCGGGGATCTTGTAGAGGAGgtatatcttt ... gaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacattaagtttgttcccttttgtctgtttttgttttgcttcttgaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGCTATAGGATTGCATATAGGTCTATGGAACGTTCTCTCACTGATGAGGAAA
                                       cttcttg  CT-rich tract
                            tttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catttagtttttaataggattatttccccctttttttaatgagtgctacattaagtttgttcccttttgtctgtttttgttttgcttcttgaaattgcagGTGCAATTAATAGACAACTTCACCAACAAGAAAGGAATGACCAGCCACTGCTATAGGATTGCATATAGGTCTATGGAACGTTCTCTCACTGATGAGGAAA

- - - - - - - - - - - -ttccccc
- - - - - - - - - - - - - - - - - - - - - -tgctaca